Biology subjects

Chang, S.

Publications and source records attributed to Chang, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Multiplatform molecular profiling and functional genomic screens identify prognostic signatures and mechanisms underlying MEK inhibitor response in somatic NF1 mutant glioblastoma

NF1 is recurrently mutated in glioblastoma yet the molecular landscape and efficacy of targeted therapies remain unclear. Here, we combine bulk and single cell genomics of human somatic NF1 mutant, IDH-wildtype glioblastomas with functional genomic analysis of cell lines and mouse intracranial tumor models to identify molecular subgroups within NF1 mutant glioblastomas and mechanisms underlying MEK inhibitor response. Targeted DNA sequencing showed homozygous deletion of the cell cycle regulator CDKN2A/B is a poor prognostic marker in somatic NF1 mutant, but not NF1 wildtype, tumors. DNA methylation array profiling revealed three epigenetic groups highlighted by distinct clinical features, co-mutation patterns, and reference methylation classifier identities. Genome-wide CRISPRi screens in glioblastoma cells revealed cell cycle regulators are conserved mediators of cell growth while response to the MEK inhibitor selumetinib converges on Ras/RAF/MEK pathway activation. Repression of the RAF regulator SHOC2 sensitizes glioblastomas to selumetinib in vitro and in vivo in mouse intracranial glioblastoma models. Single cell RNA-sequencing of mouse intracranial glioblastomas treated with the MEK inhibitor selumetinib reveals distinct responses between mesenchymal-like (MES-like) and non MES-like subpopulations suggesting non-MES like cells are intrinsically resistant to MEK inhibition. Finally, single nuclear RNA-sequencing (snRNA-seq) of human NF1 mutant, CDKN2A/B deleted glioblastomas reveals MES-like tumor cells are associated with selumetinib sensitivity signatures while non MES-like cells exhibit increased cell cycle progression and lack selumetinib sensitivity, further supporting the notion that MEK inhibition specifically targets MES-like tumor cell subpopulations. Taken together, our data underscores the heterogeneity between and within somatic NF1 mutant glioblastomas and delineates mechanisms of MEK inhibitor response across distinct tumor subpopulations, guiding the development of future therapeutic strategies that may synergize with MEK inhibition for NF1 mutant tumors. The tumor suppressor NF1 is mutated in 15% of glioblastomas,1-3 the most common malignant brain tumor with poor outcomes and few effective treatments.4 NF1 is a GTPase activating protein (GAP) that negatively regulates Ras, and thus, NF1 loss leads to induction of Ras/RAF/MEK/ERK signaling, driving tumorigenesis and comprising a targetable molecular cascade.5,6 Genomic analysis of glioblastoma demonstrates NF1 mutation is associated with a mesenchymal-like (MES-like) transcriptomic tumor cell subpopulation and altered tumor microenvironment.7,8 More broadly, DNA methylation analysis reveals multiple epigenetic subgroups with overlapping relationships to transcriptomic subtype and DNA alterations, underscoring the complex relationship between genetic drivers and molecular signatures.9 While the updated 2021 Central Nervous System WHO tumor classification incorporates an ever increasing amount of molecular criteria for diffuse astrocytic tumors,10 the existence and clinical significance of molecular subgroups within somatic NF1 mutant, IDH-wildtype glioblastomas based on genetic co-mutations, epigenetic profile, or transcriptomic signatures remain unclear. Preclinical data support the utility of MEK inhibition in NF1 mutant gliomas,11,12 and the MEK inhibitor selumetinib is FDA approved for tumors arising in patients with syndromic neurofibromatosis type 1 (NF-1) harboring a germline NF1 mutation.13,14 In NF-1 associated gliomas, MEK inhibition demonstrates efficacy in a limited case series,15 and combined BRAF/MEK inhibition shows efficacy in BRAF p.V600E mutant gliomas,16 further supporting the translational potential of Ras/Raf/MEK/ERK blockade within genetically defined glioma subtypes. Nevertheless, treatment resistance to molecular monotherapy remains a challenge,17-20 and the mechanisms underlying MEK inhibitor resistance in NF1 mutant glioma are unknown. Here, we integrate targeted DNA sequencing, DNA methylation profiling, and single nuclear RNA-sequencing (snRNA-seq) of human patient somatic NF1 mutant, IDH-wildtype glioblastomas with single cell RNA-sequencing (scRNA-seq), genome-wide clustered regularly interspaced short palindromic repeats interference (CRISPRi) screens, and pharmacologic studies in cell lines and mouse intracranial glioblastoma models to define molecular subgroups and functional mediators of MEK inhibitor response. Targeted DNA sequencing of NF1 mutant, IDH-wildtype glioblastomas (n=186 tumors) revealed CDKN2A/B deletion was associated with poor outcomes in NF1 mutant, but not NF1 wildtype, glioblastomas. DNA methylation profiling (n=129 tumors) demonstrated three epigenetic subgroups with distinct clinical features, co- mutation patterns across cell cycle genes, and reference methylation classifier identities. Genome-wide CRISPRi screens in mouse SB28 and human GBM43 glioblastoma cells identified a conserved cell cycle gene network mediating cell growth, consistent with the clinical importance of additional hits affecting the cell cycle in human somatic NF1 mutant glioblastomas. Moreover, genome-wide mediators of selumetinib response converged upon two Ras pathway effectors mediating selumetinib sensitivity: BRAF and SHOC2. SHOC2 repression in glioblastoma cells significantly improved selumetinib response both in vitro and in intracranial allografts in vivo. Single cell RNA-sequencing (scRNA-seq) of mouse intracranial glioblastomas treated with the MEK inhibitor selumetinib revealed MES-like tumor cells correlated with CDKN2A retention and the CRISPRi screen selumetinib sensitivity signature, with selumetinib resistant cells displaying Ras pathway induction. In contrast, non-MES like tumor cells were CDKN2A deficient and lacked expression of the CRISPRi screen selumetinib sensitivity signature, with selumetinib resistant cells inducing a glial de-differentiation program. Finally, snRNA-seq of NF1 mutant, CDKN2A/B deleted, IDH-wildtype glioblastomas (n=9) showed non MES-like tumor cells exhibit increased cell cycle progression and were not associated with the CRISPRi screen selumetinib sensitivity signature. MES-like tumor cells within newly diagnosed, but not recurrent, tumors retained expression of the CRISPRi screen selumetinib sensitivity signature, suggesting resistance can arise both between and within specific transcriptomic glioblastoma cell tumor cell subpopulations. Taken together, our data identifies clinically important subgroups of NF1 mutant, IDH-wildtype glioblastomas and supports a model in which heterogeneity between tumors and within tumor cell subpopulations underlies MEK inhibitor response, supporting the need for additional synergistic therapeutic approaches beyond maximal Ras pathway blockade for NF1 mutant glioblastomas.

genomics↗

bioRxiv2024

Food and water uptake are regulated by distinct central amygdala circuits revealed using intersectional genetics

The central amygdala (CeA) plays a crucial role in defensive and appetitive behaviours. It contains genetically defined GABAergic neuron subpopulations distributed over three anatomical subregions, capsular (CeC), lateral (CeL), and medial (CeM). The roles that these molecularly- and anatomically-defined CeA neurons play in appetitive behavior remain unclear. Using intersectional genetics, we found that neurons driving food or water consumption are confined to the CeM. Separate CeM subpopulations exist for water only versus water or food consumption. In vivo calcium imaging revealed that CeMHtr2a neurons promoting feeding are responsive towards appetitive cues with little regard for their physical attributes. CeMSst neurons involved in drinking are sensitive to the physical properties of salient stimuli. Both CeM subtypes receive inhibitory input from CeL and send projections to the parabrachial nucleus to promote appetitive behavior. These results suggest that distinct CeM microcircuits evaluate liquid and solid appetitive stimuli to drive the appropriate behavioral responses.

neuroscience↗

bioRxiv2024

Cell-Graph Compass: Modeling Single Cells with Graph Structure Foundation Model

Inspired by the advancements in pre-trained Large Language Models, there has been a surge of studies in the Life Sciences focusing on constructing foundation models with large scale single-cell RNA-seq data. These studies typically involve pre-training a transformer model on large-scale single-cell sequencing data, followed by fine-tuning for a variety of downstream tasks, achieving notable performance. However, these models all share a common short-coming: to utilize the transformer architecture, originally designed for textual data, they artificially impose a sequential structure on genes within cells, simplifying the complex interactions between genes. Furthermore, they focus solely on transcriptomic data, neglecting other relevant biological information. To address these issues, here we introduce Cell-Graph Compass (CGC), the first foundational model that leverages graph structures to model single cells and describes cells from multiple perspectives, including transcriptional profiles, gene text summaries, transcription factor regulatory networks, gene co-expression patterns, and gene positional relationships. By incorporating self-attention mechanisms, we pretrained the model on 50 million human single-cell sequencing data, resulting in a robust digital representation of cells. Extensive downstream experiments demonstrate that our approach can capture meaningful biological knowledge and achieve superior results in various problem scenarios, achieving the state-of-the-art (SOTA).

bioinformatics↗

bioRxiv2024

A bipartite interaction with the processivity clamp potentiates Pol IV-mediated TLS

Processivity clamps mediate polymerase switching for translesion synthesis (TLS). All three E. coli TLS polymerases interact with the {beta}2 processivity clamp through a conserved clamp-binding motif (CBM), which is indispensable for TLS. Notably, Pol IV also makes a unique secondary contact with the clamp through non-CBM residues. However, the role of this "rim contact" in Pol IV-mediated TLS remains poorly understood. Here we show that the rim contact is critical for TLS past strong replication blocks. In in vitro reconstituted Pol IV-mediated TLS, ablating the rim contact compromises TLS past 3-methyl dA, a strong block, while barely affecting TLS past N2-furfuryl dG, a weak block. Similar observations are also made in E. coli cells bearing a single copy of these lesions in the genome. Within lesion-stalled replication forks, the rim interaction and ssDNA binding protein cooperatively poise Pol IV to better compete with Pol III for binding to a cleft through its CBM. We propose that this bipartite clamp interaction enables Pol IV to rapidly resolve lesion-stalled replication through TLS at the fork, which reduces damage induced mutagenesis.

biochemistry↗

bioRxiv2024

An unbiased method to partition diverse neuronal responses into functional ensembles reveals interpretable population dynamics during innate social behavior

In neuroscience, understanding how single-neuron firing contributes to distributed neural ensembles is crucial. Traditional methods of analysis have been limited to descriptions of whole population activity, or, when analyzing individual neurons, criteria for response categorization varied significantly across experiments. Current methods lack scalability for large datasets, fail to capture temporal changes and rely on parametric assumptions. Theres a need for a robust, scalable, and non-parametric functional clustering approach to capture interpretable dynamics. To address this challenge, we developed a model-based, statistical framework for unsupervised clustering of multiple time series datasets that exhibit nonlinear dynamics into an a-priori-unknown number of parameterized ensembles called Functional Encoding Units (FEUs). FEU outperforms existing techniques in accuracy and benchmark scores. Here, we apply this FEU formalism to single-unit recordings collected during social behaviors in rodents and primates and demonstrate its hypothesis-generating and testing capacities. This novel pipeline serves as an analytic bridge, translating neural ensemble codes across model systems.

neuroscience↗

bioRxiv2024

Molecular and neural mechanisms of behavioural integration in the extended-amygdala

Integration of diverse stimuli is crucial for organisms to adapt and communicate effectively, enabling overall homeostasis and survival. Studies have been performed on identifying specific neuronal encoding of individual behaviours, but how neurons integrate diverse behaviours across contexts remains elusive. Here we use Ca2+ imaging in freely moving mice to identify neural ensembles in the extended amygdala encoding behaviours across six distinct contexts. We found extensive flexibility in these ensemble encodings that may act as reserves for behavioural integration, with those encoding aversive stimuli showing greater specificity. Finally, we identified differential gene expression profiles between ensembles that are enriched in associations with human psychiatric and neurodegenerative disorders. Overall, our results demonstrate the molecular mechanisms behind behavioural integration, and their potential implications in health and disease.

neuroscience↗

bioRxiv2024

Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans

TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on chromosome 17. We find that most humans vary along two TBC1D3 clusters where human haplotypes are highly variable in copy number, differing by as many as 20 copies, and structure (structural heterozygosity 90%). We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Lastly, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL. These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.

genetics↗

bioRxiv2024

Activation of locus coeruleus noradrenergic neuronsrapidly drives homeostatic sleep pressure

Homeostatic sleep regulation is essential for optimizing the amount and timing of sleep, but the underlying mechanism remains unclear. Optogenetic activation of locus coeruleus noradrenergic neurons immediately increased sleep propensity following transient wakefulness. Fiber photometry showed that repeated optogenetic or sensory stimulation caused rapid declines of locus coeruleus calcium activity and noradrenaline release. This suggests that functional fatigue of noradrenergic neurons, which reduces their wake-promoting capacity, contributes to sleep pressure.

neuroscience↗

bioRxiv2024

The Origins of ATP Dependence in Biological Nitrogen Fixation

Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg2+, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the key N2-reducing enzyme nitrogenase. We show that the ancestor has a strict requirement for ATP and its hydrolysis is coupled to electron transfer for N2 reduction. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme, and underscore how biomolecular constraints can entirely decouple cofactor selection from environmental availability.

evolutionary biology↗

bioRxiv2024

Architecture of intact mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis

The multi-enzyme pyruvate dehydrogenase complex (PDC) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A and is essential for cellular energy metabolism. Although individual components have been characterized, the structure of intact PDC remains unclear, hampering our understanding of its composition and multi-step catalytic reactions. Here, we report the in-situ architecture of intact PDC within mammalian mitochondria by cryo-electron tomography. The organization of peripheral E1 and E3 multimers varies substantially among PDCs. We discovered 1-46 E1 heterotetramers surrounding each PDC core, and up to 12 E3 dimers locating primarily along the pentagonal openings. Furthermore, we observed dynamic interactions of the substrate translocating lipoyl domains (LDs) with both E1 and E2, implicating the mechanism of substrate channeling. Our findings reveal the intrinsic dynamics of PDC peripheral compositions, suggesting an additional model in which the number of assembled E1 heterotetramer, E3 dimer, and functional LDs of PDC may be regulated to further control its catalytic activity.

cell biology↗

bioRxiv2023

Tumor-selective effects of active RAS inhibition in pancreatic ductal adenocarcinoma

Broad-spectrum RAS inhibition holds the potential to benefit roughly a quarter of human cancer patients whose tumors are driven by RAS mutations. However, the impact of inhibiting RAS functions in normal tissues is not known. RMC-7977 is a highly selective inhibitor of the active (GTP-bound) forms of KRAS, HRAS, and NRAS, with affinity for both mutant and wild type (WT) variants. As >90% of human pancreatic ductal adenocarcinoma (PDAC) cases are driven by activating mutations in KRAS, we assessed the therapeutic potential of RMC-7977 in a comprehensive range of PDAC models, including human and murine cell lines, human patient-derived organoids, human PDAC explants, subcutaneous and orthotopic cell-line or patient derived xenografts, syngeneic allografts, and genetically engineered mouse models. We observed broad and pronounced anti-tumor activity across these models following direct RAS inhibition at doses and concentrations that were well-tolerated in vivo. Pharmacological analyses revealed divergent responses to RMC-7977 in tumor versus normal tissues. Treated tumors exhibited waves of apoptosis along with sustained proliferative arrest whereas normal tissues underwent only transient decreases in proliferation, with no evidence of apoptosis. Together, these data establish a strong preclinical rationale for the use of broad-spectrum RAS inhibition in the setting of PDAC.

cancer biology↗

bioRxiv2023

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8

The RGD (Arg-Gly-Asp)-binding integrins v{beta}6 and v{beta}8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between the two closely related integrin proteins and other RGD integrins, stabilize specific conformational states, and have sufficient stability enabling tissue restricted administration could have considerable therapeutic utility. Existing small molecules and antibody inhibitors do not have all of these properties, and hence there is a need for new approaches. Here we describe a method for computationally designing hyperstable RGD-containing miniproteins that are highly selective for a single RGD integrin heterodimer and conformational state, and use this strategy to design inhibitors of v{beta}6 and v{beta}8 with high selectivity. The v{beta}6 and v{beta}8 inhibitors have picomolar affinities for their targets, and >1000-fold selectivity over other RGD integrins. CryoEM structures are within 0.6-0.7[A] root-mean-square deviation (RMSD) to the computational design models; the designed v{beta}6 inhibitor and native ligand stabilize the open conformation in contrast to the therapeutic anti-v{beta}6 antibody BG00011 that stabilizes the bent-closed conformation and caused on-target toxicity in patients with lung fibrosis, and the v{beta}8 inhibitor maintains the constitutively fixed extended-closed v{beta}8 conformation. In a mouse model of bleomycin-induced lung fibrosis, the v{beta}6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics when delivered via oropharyngeal administration mimicking inhalation, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.

biochemistry↗

bioRxiv2023

Multi-Scale Label-free Human Brain Imaging with Integrated Serial Sectioning Polarization Sensitive Optical Coherence Tomography and Two-Photon Microscopy

The study of neurodegenerative processes in the human brain requires a comprehensive understanding of cytoarchitectonic, myeloarchitectonic, and vascular structures. Recent computational advances have enabled volumetric reconstruction of the human brain using thousands of stained slices, however, tissue distortions and loss resulting from standard histological processing have hindered deformation-free reconstruction of the human brain. The development of a multi-scale and volumetric human brain imaging technique that can measure intact brain structure would be a major technical advance. Here, we describe the development of integrated serial sectioning Polarization Sensitive Optical Coherence Tomography (PSOCT) and Two Photon Microscopy (2PM) to provide label-free multi-contrast imaging, including scattering, birefringence and autofluorescence of human brain tissue. We demonstrate that high-throughput reconstruction of 4x4x2cm3 sample blocks and simple registration of PSOCT and 2PM images enable comprehensive analysis of myelin content, vascular structure, and cellular information. We show that 2 m in-plane resolution 2PM images provide microscopic validation and enrichment of the cellular information provided by the PSOCT optical property maps on the same sample, revealing the sophisticated capillary networks and lipofuscin filled cell bodies across the cortical layers. Our method is applicable to the study of a variety of pathological processes, including demyelination, cell loss, and microvascular changes in neurodegenerative diseases such as Alzheimers disease (AD) and Chronic Traumatic Encephalopathy (CTE).

neuroscience↗

bioRxiv2023

A parabrachial-hypothalamic parallel circuit governs cold defense in mice

Thermal homeostasis is vital for mammals and is controlled by brain neurocircuits. Remarkable advances have been made in understanding how neurocircuits centered in the hypothalamic preoptic area (POA), the brains thermoregulation center, control warm defense, whereas mechanisms by which the POA regulates cold defense remain unclear. Here, we confirmed that the pathway from the lateral parabrachial nucleus (LPB) to the POA, is critical for cold defense. Parallel to this pathway, we uncovered that a pathway from the LPB to the dorsomedial hypothalamus (DMH), namely the LPB[->]DMH pathway, is also essential for cold defense. Projection-specific blockings revealed that both pathways provide an equivalent and cumulative contribution to cold defense, forming a parallel circuit. Specifically, activation of the LPB[->]DMH pathway induced strong cold-defense responses, including increases in thermogenesis of brown adipose tissue (BAT), muscle shivering, heart rate, and physical activity. Further, we identified a subpopulation of somatostatin+ neurons in the LPB that target the DMH to promote BAT thermogenesis. Therefore, we reveal a parabrachial-hypothalamic parallel circuit in governing cold defense in mice. This not only enables resilience to hypothermia but also provides a scalable and robust network in heat production, reshaping our understanding of how neural circuits regulate essential homeostatic behaviors.

neuroscience↗

bioRxiv2023

GPR158 in pyramidal neurons mediates social novelty behavior via modulating synaptic transmission in mice

Social novelty impairment is a hallmark feature of autism spectrum disorder associated with synaptic dysfunction. While G-protein coupled receptor 158 (GPR158) has been shown to be essential for synaptic neurotransmission, its role in modulating social novelty remains unknown. Here, we investigated the impact of GPR158 on social behavior in mice and observed that both constitutive and cell/tissue-specific knockout of Gpr158 in pyramidal neurons or the medial prefrontal cortex (mPFC) result in impaired novelty preference, but not sociability. Notably, we found a significant decline in excitatory synaptic transmission and glutamate vesicles in the mPFC synapses of global Gpr158 knockouts. Mechanistically, we identified that constitutive loss of Gpr158 led to suppressed Vglut1 distribution, possibly resulting from altered expression of vesicular V-ATPases and SNAREs by Gpr158 ablation in pyramidal neurons. Our findings suggest that GPR158 in pyramidal neurons specifically modulates social novelty and may be a potential therapeutic target for treating social disorders. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/536148v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1013ca9org.highwire.dtl.DTLVardef@359faaorg.highwire.dtl.DTLVardef@856371org.highwire.dtl.DTLVardef@143c866_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIKnockout of Gpr158 causes social novelty deficit in mice. C_LIO_LIKnockout of Gpr158 in pyramidal neurons leads to disrupted synaptic transmission and an E-I imbalance in the mPFC. C_LIO_LIDisturbed E-I homeostasis in the mPFC is likely due to reduced density of glutamate vesicles caused by Gpr158 knockout. C_LI

neuroscience↗

bioRxiv2023

Comprehensive Multi-omics Analysis Reveals the Core Role of Glycerophospholipid Metabolism in Rheumatoid Arthritis Development

ObjectivesRheumatoid arthritis (RA) is a chronic autoimmune disease with complex causes and recurrent attacks that can easily develop into chronic arthritis. Our study aims to elucidate potential mechanism among control, new-onset RA (NORA) and chronic RA (CRA) with multi-omics analysis. MethodsA total of 162 subjects were included in our study, 121 subjects were used for 16S rRNA, ITS sequencing and metabolomics analysis and 41 subjects were used for transcriptomics analysis. Enrichment analysis was based on significant difference metabolites and genes. Protein-protein interaction network and correlation analyses were performed to interpret the interactions among intestinal flora, metabolites and genes. We applied three models to distinguish between NORA and CRA using computational OR values, LASSO and random forest, respectively. ResultsOur results demonstrated intestinal flora disturbance in RA development, with significantly increased abundance of Escherichia-Shigella and Proteobacteria in NORA. We also found that the diversity was significantly reduced in CRA compared to NORA through fungi analysis. Moreover, we identified 28 differential metabolites between NORA and CRA. Pathway enrichment analysis revealed significant dysregulation of glycerophospholipid metabolism and phenylalanine metabolism pathways in RA patients. Next, we identified 40 differentially expressed genes between NORA and CRA, which acetylcholinesterase (ACHE) was the core gene and significantly enriched in glycerophospholipid metabolism pathway. Correlation analysis showed a strong negatively correlation between glycerophosphocholine and inflammatory characteristics. ConclusionsThese findings revealed that glycerophospholipid metabolism plays a crucial role in the development and progression of RA, providing new ideas for early clinical diagnosis and optimizing treatment strategies.

immunology↗

bioRxiv2023

L-type Ca2+ channels mediate regulation of glutamate release by subthreshold potential changes

Subthreshold depolarization enhances neurotransmitter release evoked by action potentials and plays a key role in modulating synaptic transmission by combining analog and digital signals. This process is known to be Ca2+-dependent. However, the underlying mechanism of how small changes in basal Ca2+ caused by subthreshold depolarization can regulate transmitter release triggered by a large increase in local Ca2+ is not well understood. This study aimed to investigate the source and signaling mechanisms of Ca2+ that couple subthreshold depolarization with the enhancement of glutamate release in hippocampal cultures and CA3 pyramidal neurons. Subthreshold depolarization increased presynaptic Ca2+ levels, the frequency of spontaneous release, and the amplitude of evoked release, all of which were abolished by blocking L-type Ca2+ channels. A high concentration of intracellular Ca2+ buffer or blockade of calmodulin and phospholipase C abolished depolarization induced increases in transmitter release. Estimation of the readily releasable pool size using hypertonic sucrose showed depolarization induced increases in readily releasable pool size, and this increase was abolished by blockade of calmodulin or phospholipase C. Our results provide mechanistic insights into the modulation of transmitter release by subthreshold potential change and highlight the role of L-type Ca2+ channels in coupling subthreshold depolarization to the activation of Ca2+-dependent signaling molecules that regulate transmitter release. SIGNIFICANCENeuronal activities are encoded by action potentials, but subthreshold changes in resting membrane potentials also play important roles in regulating neuronal functions including synaptic transmission. It is, however, poorly understood how small changes in basal Ca2+ induced by subthreshold depolarization regulate transmitter release triggered by a large increase in local Ca2+ in presynaptic terminals. We demonstrate that L-type Ca2+ channels are the major source of presynaptic Ca2+ influx at basal state and during subthreshold depolarization, resulting in the activation of signaling molecules such as calmodulin and phospholipase C, which facilitate transmitter release by increasing both release probability and the readily releasable pool size. Our results provide mechanistic insight into how subthreshold potential changes contribute to regulating transmitter release.

neuroscience↗

bioRxiv2022

Regulation of ATAD2B bromodomain binding activity by the histone code

The ATPase family AAA+ domain containing 2 (ATAD2) protein, and its paralog ATAD2B, have a C-terminal bromodomain that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2 and ATAD2B bromodomains to select acetylated lysine among multiple histone post-translational modifications. Isothermal titration calorimetry experiments revealed that the ATAD2 and ATAD2B bromodomains selectively recognize distinct patterns of acetylated lysine residues on the N-terminal tails of histone proteins. Adjacent methylation or phosphorylation marks were found to either enhance or weaken the recognition of acetylated lysine by the ATAD2/B bromodomains. Complementary structural studies provide mechanistic insights into how residues within the bromodomain binding pocket coordinate the acetyllysine group in the context of adjacent post- translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands, either as onco mutations or as histone variants, impact the recognition of an adjacent acetylated lysine residue. In summary, our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2 and ATAD2B bromodomains, resulting in distinct binding modes of the two bromodomains. KEY POINTSO_LIMultiple independent ATAD2 gene duplication events are evident during metazoan evolution, indicating expansion of functionality in the ATAD2 gene family and suggesting distinct functions for ATAD2 and ATAD2B. C_LIO_LIHigh-resolution structures of the ATAD2 and ATAD2B bromodomains in complex with their histone ligands demonstrate how multiple post-translational modifications are coordinated. C_LIO_LIRecognition of different subsets acetylated histone ligands by the ATAD2 and ATAD2B bromodomains is driven by unique features within the binding pockets of these paralogous proteins. C_LIO_LIOnco-histone mutations and histone variants that change the amino acid sequence of the histone tails modulate the ATAD2 and ATAD2B bromodomain activity. C_LIO_LIThis study demonstrates how the combinatorial activity of multiple post- translational modifications forms a histone code and influences the recognition of acetylated lysine by bromodomain-containing proteins. C_LI

biochemistry↗