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Woo, J.

Publications and source records attributed to Woo, J..

At least 19 recordsLinked to original sources

TFE3 fusions drive expression of CD44 and SPP1 in Translocation Renal Cell Carcinoma

Xp11.2 translocation RCC [Xp11.2 tRCC]) is an underdiagnosed and aggressive subtype of RCC with few specific or targeted therapies. The transmembrane glycoprotein CD44 is an emerging target in many advanced malignancies, and with its ligand OPN (SPP1), is a crucial driver of cancer progression, stemness, metastasis, and immune suppression. Here we show that common TFE3-fusions [ including SFPQ-TFE3, PRCC-TFE3, ASPSCR1-TFE3, and NONO-TFE3] are associated with upregulated expression of CD44 and SPP1, as observed in multiple human and murine bulk transcriptomic studies and a murine tRCC snRNA-Seq dataset. CD44 and/or SPP1 protein expression were also upregulated in murine models of transgenic tRCC kidneys and urine specimens, patient-derived cell lines and human tRCC cases, by immunoblotting and/or IHC. Transient deletion of CD44 was associated with profound and specific suppression of tRCC cell line growth, with decreased mTOR signaling. These data suggest that CD44 and/or SPP1 may potentially drive tumorigenesis in tRCC.

cancer biology↗

Genetically inducible coordinators of cytokine signaling pathways for interrogating T cell motility

Chimeric antigen receptor (CAR) T cell therapy is promising for treating hematologic malignancies, but extending this success to treat solid tumors is challenging. Improving T cell phenotype to address this need is desirable, and one such property is increasing T cell infiltration into tumors. A promising potential approach comprises rewiring cytokine signaling using engineered receptors to change how the T cell responds to environmental cues. However, we currently lack the tools and mechanistic understanding to iterate and improve upon such strategies. Notably, receptors that rewire signaling make it challenging to decouple paracrine effects from those conferred by the signaling inducer. To address this gap, we developed a genetically inducible toolkit of proteins termed Constitutive Activators of Motility-associated Pathways (CAMPs). Building on prior knowledge, CAMPs incorporate domains from IL5R (interleukin-5 receptor) and TNFR (tumor necrosis factor receptor) to place cytokine-associated signaling under direct genetic control, such that expression of a CAMP using a small molecule cue or a condition-responsive promoter induces CAMP signaling. We first identified receptor configurations driving constitutive signaling through targeted pathways. TNFR-based signaling modules drove NF-{kappa}B activation across diverse receptor designs, while IL5R-based signaling modules exhibited stringent requirements for membrane-proximity and organization of subunits. We engineered primary human T cells with inducible CAMP circuits, enabling us to probe pathway-specific effects on motility and transcriptomic responses. Pharmacological induction of motility-associated programs downstream of PKC (protein kinase C) was shown to be feasible and dependent on T cell activation state. CAMP induction drove an inflammatory program, particularly when signaling through both NF-{kappa}B and STAT5, but none of the conditions tested enhanced 3D motility in our assay. Altogether, our findings are consistent with a model in which migratory behavior may be coupled and regulated by multiple stimuli. These findings and new CAMP tools provide a foundation for interrogating and ultimately harnessing motility for improved T cell therapy performance.

synthetic biology↗

Acute stress induces circuit-specific alterations in mesolimbic and nigrostriatal inhibitory transmission and potentiates operant learning

Acute stress can facilitate learning about stimuli that predict rewarding outcomes, yet whether stress similarly potentiates acquisition of reward-directed actions remains less well understood. Reward learning broadly depends on dopamine signaling within mesolimbic and nigrostriatal pathways. Dopamine transmission in the mesolimbic system is traditionally associated with cue-reward learning, whereas nigrostriatal dopamine signaling has been implicated in movement vigor and the acquisition of instrumental actions. Stress can alter dopamine transmission within these circuits and thereby influence reward learning. Previous work demonstrated that acute stress downregulates the potassium-chloride cotransporter KCC2 in ventral tegmental area GABA neurons. These stress-induced adaptations in inhibitory transmission enhance mesolimbic dopamine signaling and potentiate associative learning. Here, we show that prior exposure to acute restraint stress facilitates acquisition of operant sucrose self-administration in male and female rats. Enhanced learning was associated with increased temporal coincidence of GABA release events onto dopamine neurons and increased excitability of GABAergic inputs, alterations previously linked to enhanced dopamine signaling. These stress-induced adaptations exhibited marked circuit specificity within mesolimbic and nigrostriatal systems, selectively affecting inhibitory transmission onto dopamine neurons projecting to the nucleus accumbens lateral shell and dorsomedial striatum. Importantly, pharmacological enhancement of KCC2 function with CLP290 normalized inhibitory transmission within these pathways and attenuated stress-induced potentiation of operant learning. Together, these findings identify circuit-specific alterations in midbrain inhibitory signaling induced by acute stress that contribute to enhanced reward learning.

neuroscience↗

γδ17 T cell-stromal networks modulate matrix composition and vascularity in foreign body response

Immune-stromal crosstalk governs tissue fibrosis, which is marked by dysregulated extracellular matrix (ECM) production and aberrant vasculature. Here, we investigate how {gamma}{delta} T cell interactions with stromal cells shape fibrosis in the foreign body response. During the acute reaction, type-1 ({gamma}{delta}IFN{gamma}) and type-17 ({gamma}{delta}17) effector subsets accumulated at the implant. While {gamma}{delta}IFN{gamma} decreased as fibrosis progressed, activated {gamma}{delta}17 persisted as dominant interleukin-17 producers. The {gamma}{delta}17 increased with aging and high-fat diet, both factors associated with chronic inflammation and fibrosis. Co-culture with {gamma}{delta}17 stimulated fibroblast expression of collagen genes and intercellular communication inference linked {gamma}{delta} T cell ligands to activation of ECM remodeling and vascular development programs in fibroblasts and endothelial cells. Finally, genetic deletion of {gamma}{delta} T cells altered expression of ECM components and increased vessel size within the fibrotic matrix. Altogether, our findings implicate {gamma}{delta} T cells in regulating stromal behavior to modulate composition and vascularity of fibrotic tissues.

immunology↗

Deep Blood Proteomics Identifies over 12,000 Proteins Providing Valuable Information about the State of the Human Body

Blood is a valuable resource for clinical research, offering insight into physiological and pathological states. However, the specific proteins detectable in blood and the optimal proteomic methods for their detection have not been rigorously investigated and documented. To address this, we conducted various blood proteomic strategies, including directly blood proteomic analysis, high-abundance protein depletion, low-abundance protein enrichment, and extracellular vesicle enrichment using data-independent acquisition or targeted proteomics. These approaches identified 11,679 protein groups in plasma from healthy individuals. In 136 pancreatic ductal adenocarcinoma whole blood samples, 6,956 protein groups were found, including 678 not seen in healthy samples, expanding the total to 12,357 blood proteins. This represents the most comprehensive blood proteome to date. To support broader access and analysis, we developed the Human Blood Proteome (HuBP) database, detailing protein detectability, abundance, and reproducibility across workflows, sample types, and disease contexts.

systems biology↗

High-Sensitive Spatial Proteomics for Pancreatic Cancer Progression Analysis

Pancreatic cancer remains as one of the most challenging malignancies to diagnose and treat due to the late development of symptoms and limited early diagnostic options. Intraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursors to invasive pancreatic ductal adenocarcinoma (PDAC)and an understanding of the changes in patterns of protein expression that accompany the progression from normal ductal (ND) cell, to IPMN to PDAC may provide avenues for improved earlier detection. In this study, we present an optimized spatial tissue proteomics workflow, termed SP-Max (Spatial Proteomics Optimized for Maximum Sensitivity and Reproducibility in Minimal Sample), designed to maximize protein recovery and quantification from limited laser micro dissected (LMD) samples. Our workflow enabled the identification of more than 6,000 proteins and the quantification of over 5,200 protein groups from FFPE tissue contours of pancreatic tissues. Comparative analyses across ND, IPMN, and PDAC revealed critical molecular differences in protein pathways and potential markers of progression. SP-Max provides a systematic, reproducible approach that significantly enhances our ability to study precancerous lesions and cancer progression in pancreatic tissues at unprecedented resolution.

cancer biology↗

Selective manipulation of excitatory and inhibitory neurons in top-down and bottom-up visual pathways using ultrasound stimulation

IntroductionTechniques for precise manipulation of neurons in specific neural pathways are crucial for excitatory/inhibitory (E/I) balance and investigation of complex brain circuits. Low-intensity focused ultrasound stimulation (LIFUS) has emerged as a promising tool for noninvasive deep-brain targeting at high spatial resolution. However, there is a lack of studies that extensively investigate the modulation of top-down and bottom-up corticothalamic circuits via selective manipulation of excitatory and inhibitory neurons. Here, a comprehensive methodology using electrophysiological recording and c-Fos staining is employed to demonstrate pulse repetition frequency (PRF)-dependent E/I selectivity of ultrasound stimulation in the top-down and bottom-up corticothalamic pathways of the visual circuit in rodents. Materials and methodsUltrasound stimulation at various PRFs is applied to either the lateral posterior nucleus of the thalamus (LP) or the primary visual cortex (V1), and multi-channel single-unit activity is recorded from the V1 using a silicon probe. Results and conclusionOur results demonstrate that high frequency PRFs, particularly at 3 kHz and 1 kHz, are effective at activating the bidirectional corticothalamic visual pathway. In addition, brain region-specific PRFs modulate E/I cortical signals, corticothalamic projections, and synaptic neurotransmission, which is imperative for circuit-specific applications and behavioral studies.

neuroscience↗

Channel-mediated astrocytic volume transient is required for synaptic plasticity and spatial memory

Astrocytes, known for their support roles, are emerging as active participants in synaptic plasticity and cognitive functions. Astrocytes actively regulate synaptic plasticity and memory through dynamic volume transients. Our previous research identified several key molecules, including TREK-1, TRPA1, and Best1 ion channels, as well as the gliotransmitter BDNF, as critical components of astrocytic volume transients. However, the precise mechanisms by which these volume transients influence synaptic plasticity and memory remain poorly understood. In this study, we investigate the roles of TREK-1 and TRPA1 in astrocytic volume dynamics and their downstream effects. Using intrinsic optical signal imaging, electrophysiology, and behavioral assays, we demonstrate that neuronal stimulation induces astrocytic swelling, initiated by K+ uptake through TREK-1 channels and regulated by Ca2+ influx via TRPA1 channels. This swelling is closely associated short- and long-term potentiation, and is accompanied by the release of BDNF, which restores long-term potentiation under conditions of calcium sequestration during astrocytic calcium clamping experiments. Disruption of astrocytic volume transient associated ion channels results in significant deficits in spatial memory, as evidenced by impairments in object-place recognition and passive avoidance tasks. Furthermore, these channels were found to modulate the synaptic plasticity. These findings reveal astrocytic volume transients and BDNF as pivotal modulators of synaptic plasticity and memory, as well as potential therapeutic targets for addressing memory dysfunctions.

neuroscience↗

AUTO-SP: automated sample preparation for analyzing proteins and protein modifications

Liquid chromatography (LC) tandem mass spectrometry (MS/MS) is one of the widely used proteomic techniques to study the alterations occurred at protein expression level as well as post-translation modifications (PTMs) of proteins that are relevant to different physiological or pathological statuses. The mass spectrometric analysis of peptides fragmented from proteins (bottom-up proteomics) has emerged as one of the major approaches for proteomics. In this approach, proteins are first cleaved into peptides for mass spectrometric analysis and peptides with PTMs are further enriched followed by the LC-MS/MS analysis. To achieve a reproducible and quantitative proteomic characterization, a well-established protease digestion and PTM peptide enrichment protocol is critical. In this study, we developed an automated sample preparation (AUTO-SP) for analyzing proteins and protein modifications utilizing Patient-Derived Xenograft (PDX) breast cancer tumors (basal-like and luminal subtypes). The protein amount was quantified and proteins were further digested by using AUTO-SP for each PDX sample. Based on the data-independent acquisition (DIA)-MS data, we observed samples of the same breast cancer subtypes were highly correlated (>0.98). Additionally, >14,000 ubiquitinated peptides were identified in the PDX samples when using AUTO-SP for ubiquitin enrichment, while unique pathways were enriched from the basal-like and luminal subtypes. AUTO-SP demonstrated its efficacy to provide reliable and reproducible sample preparation procedure for MS-based proteomic and PTM analyses.

systems biology↗

The role of inflammation in a humanized mouse model of transthyretin cardiac amyloidosis

BackgroundSystemic amyloidosis represents a group of protein-misfolding diseases that confer significant morbidity and mortality for millions of patients worldwide. Transthyretin cardiac amyloidosis (ATTR) is a particularly devastating amyloid disease that affects middle-aged and elderly individuals and leads to cardiomyopathy (ATTR-CM), which has a median survival of 2.5 to 3.5 years [1, 2]. ATTR-CM can be hereditary, leading to a more aggressive disease course in younger patients. The most prevalent TTR variant in the United States is V122I, which is found in 3-4 % of African Americans [3]. Despite the significant healthcare burden, ATTR-CM remains underdiagnosed due to a lack of disease awareness and limited diagnostic techniques [4]. Informative in vivo models have proven elusive during the past decade [5]. Moreover, there is no available treatment to reverse cardiac dysfunction due to amyloid fibril deposition [1, 6, 7]. Therefore, a better understanding of the molecular mechanisms of ATTR-CM is imperative to developing novel, effective therapies. Method and ResultsTo explore the pathogenesis of ATTR, we created a murine TTR knockout (TTR-KO) model expressing the human V122I TTR variant. To study the gender differences, both male and female TTR-KO mice were utilized in this study. Significant elevations of human TTR were observed in both male and female ATTR murine plasma post-injection 3 months (human TTR level (ng/ml) Male ATTR: 109.9 {+/-} 5.568; Male control: 28.17 {+/-} 7.010; p=0.0008, N=3 mice/group; Female ATTR: 127.5 {+/-} 32.43; Female control: 20.08 {+/-} 8.351; p=0.0327, N=3 mice/group) with preserved cardiac function (FS% Male ATTR: 26.07 {+/-} 3.667; Male control: 22.69 {+/-} 1.585; p=0.3712, N=6-8 mice/group; Female ATTR: 26.62 {+/-} 1.980; Female control: 31.25 {+/-} 4.482;p=0.3397, N=5-6 mice/group). Notably, the mouse model exhibited cardiac amyloid deposits confirmed by amyloidotic-specific Congo Red staining and Thioflavin T Staining. Transmission electron microscopy revealed both immature and mature amyloid fibrils in the extracellular matrix. RNA-sequencing of the ATTR mouse heart identified distinct transcriptomic patterns and conserved inflammation pathways similar to those seen in a cohort of human ATTR heart samples, including leukocyte transendothelial migration, T-cell receptor signaling, and apoptosis, along with upregulation of inflammatory markers CXCL-1/2/3 and CCL20, were observed in ATTR murine hearts. At the posttranslational level, we confirmed an increased level of CCL5 (MFI ATTR: 801 {+/-} 105; Control: 426{+/-} 64; p=0.0061, N=3 mice/group) in murine plasma post-injection 3 months by a luminance-based immunoassay. The CXCL- and CCL-chemokines family are critical for directing leukocytes to inflammation sites. ConclusionIn this study, we developed a humanized V122I ATTR mouse model with elevated circulating human TTR level and Congophilic amyloid deposits in the murine heart and kidneys. Our transcriptomic study suggested that inflammation may contribute to the ATTR-CM pathogenesis. Further studies are needed to decipher the precise interactions between inflammation and ATTR-CM. Highlights/Whats new/Clinical relevanceO_LIWe developed a humanized mouse model to replicate the multisystem complexity and clinical diversity associated with V122I ATTR-CM. C_LIO_LIOur study unveiled the pathogenic molecular mechanisms of amyloid deposition in ATTR-CM via a novel mouse model. C_LIO_LIWe identified signature inflammatory pathways that uncover potential therapeutic targets for ATTR-CM. C_LIO_LIOur ATTR mouse model allows for preclinical pharmacogenomic assessments of novel therapeutics, which will undoubtedly improve outcomes for ATTR-CM patients. C_LI

pathology↗

SFPQ-TFE3 gene fusion reciprocally regulates mTORC1 activity and induces lineage plasticity in a novel mouse model of renal tumorigenesis

The MiT/TFE family gene fusion proteins, such as SFPQ-TFE3, drive both epithelial (eg, translocation renal cell carcinoma, tRCC) and mesenchymal (eg, perivascular epithelioid cell tumor, PEComa) neoplasms with aggressive behavior. However, no prior mouse models for SFPQ-TFE3-related tumors exist and the mechanisms of lineage plasticity induced by this fusion remain unclear. Here, we demonstrate that constitutive murine renal expression of human SFPQ-TFE3 using Ksp Cadherin-Cre as a driver disrupts kidney development leading to early neonatal renal failure and death. In contrast, post-natal induction of SFPQ-TFE3 in renal tubular epithelial cells using Pax8 ERT-Cre induces infiltrative epithelioid tumors, which morphologically and transcriptionally resemble human PEComas. As seen in MiT/TFE fusion-driven human tumors, SFPQ-TFE3 expression is accompanied by the strong induction of mTORC1 signaling, which is partially amino acid-sensitive and dependent on increased SFPQ-TFE3-mediated RRAGC/D transcription. Remarkably, SFPQ-TFE3 expression is sufficient to induce lineage plasticity in renal tubular epithelial cells, with rapid down-regulation of the critical PAX2/PAX8 nephric lineage factors and tubular epithelial markers, and concomitant up-regulation of PEComa differentiation markers in transgenic mice, human cell line models and human tRCC. Pharmacologic or genetic inhibition of mTOR signaling downregulates expression of the SFPQ-TFE3 fusion protein and rescues nephric lineage marker expression and transcriptional activity in vitro. These data provide evidence of a potential epithelial cell-of-origin for TFE3-driven PEComas and highlight a reciprocal role for SFPQ-TFE3 and mTOR in driving lineage plasticity in the kidney, expanding our understanding of the pathogenesis of MiT/TFE-driven tumors.

cancer biology↗

Dynamic Changes in Chloride Homeostasis Coordinate Midbrain Inhibitory Network Activity during Reward Learning

The ability to associate environmental stimuli with positive outcomes is a fundamental form of learning. While extensive research has focused on the response profiles of midbrain dopamine neurons during associative learning, less is known about learning-mediated changes in the afferents that shape their responses. We demonstrate that during critical phases of learning, anion homeostasis in midbrain GABA neurons - a primary source of input to dopamine neurons - is disrupted due to downregulation of the chloride transporter KCC2. This alteration in GABA neurons preferentially impacted lateral mesoaccumbal dopamine pathways and was not observed after learning was established. At the network level, learning-mediated KCC2 downregulation was associated with enhanced synchronization between individual GABA neurons and increased dopamine responses to reward-related stimuli. Conversely, enhancing KCC2 function during learning reduced GABA synchronization, diminished relevant dopamine signaling, and prevented cue-reward associations. Thus, circuit-specific adaptations in midbrain GABA neurons are crucial for forming new reward-related behaviors.

neuroscience↗

Single-molecule imaging reveals the role of membrane-binding motif and C-terminal domain of RNase E in its localization and diffusion in Escherichia coli

In Escherichia coli, RNase E, a central enzyme in RNA processing and mRNA degradation, contains a catalytic N-terminal domain (NTD), a membrane-targeting sequence (MTS), and a C-terminal domain (CTD). We investigated how MTS and CTD influence RNase E localization, diffusion, and function. Super-resolution microscopy revealed that [~]93% of RNase E localizes to the inner membrane and exhibits slow diffusion similar to polysomes. Comparing the native amphipathic MTS with a transmembrane motif showed that the MTS confers slower diffusion and stronger membrane binding. The CTD further slows diffusion by increasing mass but unexpectedly weakens membrane association. RNase E mutants with partial cytoplasmic localization displayed enhanced co-transcriptional degradation of lacZ mRNA. These findings indicate that variations in the MTS and the presence of the CTD shape the spatiotemporal organization of RNA processing in bacterial cells, providing mechanistic insight into how RNase E domain architecture influences its cellular function.

microbiology↗

Single-Cell Proteomic and Transcriptomic Characterization of Drug-Resistant Prostate Cancer Cells Reveals Molecular Signatures Associated with Morphological Changes

This study delves into the proteomic intricacies of drug-resistant cells (DRCs) within prostate cancer, which are known for their pivotal roles in therapeutic resistance, relapse, and metastasis. Utilizing single-cell proteomics (SCP) with an optimized high-throughput Data Independent Acquisition (DIA) approach with the throughput of 60 sample per day, we characterized the proteomic landscape of DRCs in comparison to parental PC3 cells. This optimized DIA method allowed for robust and reproducible protein quantification at the single-cell level, enabling the identification and quantification of over 1,300 proteins per cell on average. Distinct proteomic sub-clusters within the DRC population were identified, closely linked to variations in cell size. The study uncovered novel protein signatures, including the regulation of proteins critical for cell adhesion and metabolic processes, as well as the upregulation of surface proteins and transcription factors pivotal for cancer progression. Furthermore, by integrating SCP and single-cell RNA-seq (scRNA-seq) data, we identified six upregulated and ten downregulated genes consistently altered in drug-treated cells across both SCP and scRNA-seq platforms. These findings underscore the heterogeneity of DRCs and their unique molecular signatures, providing valuable insights into their biological behavior and potential therapeutic targets.

cancer biology↗

Refined Myocardium Segmentation from CT Using a Hybrid-Fusion Transformer

1.Accurate segmentation of the left ventricle (LV) in cardiac CT images is crucial for assessing ventricular function and diagnosing cardiovascular diseases. Creating a sufficiently large training set with accurate manual labels of LV can be cumbersome. More efficient semi-automatic segmentation, however, often includes unwanted structures, such as papillary muscles, due to low contrast between the LV wall and surrounding tissues. This study introduces a two-input-channel method within a Hybrid-Fusion Transformer deep-learning framework to produce refined LV labels from a combination of CT images and semi-automatic rough labels, effectively removing papillary muscles. By leveraging the efficiency of semi-automatic LV segmentation, we train an automatic refined segmentation model on a small set of images with both refined manual and rough semi-automatic labels. Evaluated through quantitative cross-validation, our method outperformed models that used only either CT images or rough masks as input.

bioengineering↗

Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo approach

Genome-wide identification of binding profiles for DNA-binding proteins in Salmonella Typhimurium within macrophages is crucial for understanding virulence gene expression and cellular processes. However, this task remains challenging due to the limited amount of intracellular bacterial cells. Here, we present ChIP-mini, a low-input ChIP-exo utilizing 5,000-fold reduced number of initial bacterial cells and analysis pipeline (DiffExo), to identify genome-wide binding dynamics of DNA-binding proteins in host-infected pathogens. Applying ChIP-mini to intracellular S. Typhimurium, we identified 642 and 1,837 binding sites of H-NS and RpoD, respectively, with near-base pair resolution, elucidating their roles in transcriptional initiation. Post-infection, we observed 21 significant reductions in H-NS binding at intergenic regions, exposing the promoter region of virulence genes, such that those in Salmonella pathogenicity islands-2, 3 and effectors, facilitating RpoD binding for transcription initiation. Furthermore, we identified 24 novel RpoD binding sites and 19 significantly increased RpoD bindings at the transcription start sites of virulence genes. These findings substantially enhance our understanding of how H-NS and RpoD simultaneously coordinate the transcription initiation of virulence genes within macrophages. Collectively, this optimized method demonstrates a tool that can be broadly adapted to elucidate transcriptional regulatory networks of host-infected pathogens, revealing critical interactions between host and microbe.

systems biology↗

Critical assessment of missense variant effect predictors on disease-relevant variant data

Regular, systematic, and independent assessment of computational tools used to predict the pathogenicity of missense variants is necessary to evaluate their clinical and research utility and suggest directions for future improvement. Here, as part of the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, we assess missense variant effect predictors (or variant impact predictors) on an evaluation dataset of rare missense variants from disease-relevant databases. Our assessment evaluates predictors submitted to the CAGI6 Annotate-All-Missense challenge, predictors commonly used by the clinical genetics community, and recently developed deep learning methods for variant effect prediction. To explore a variety of settings that are relevant for different clinical and research applications, we assess performance within different subsets of the evaluation data and within high-specificity and high-sensitivity regimes. We find strong performance of many predictors across multiple settings. Meta-predictors tend to outperform their constituent individual predictors; however, several individual predictors have performance similar to that of commonly used meta-predictors. The relative performance of predictors differs in high-specificity and high-sensitivity regimes, suggesting that different methods may be best suited to different use cases. We also characterize two potential sources of bias. Predictors that incorporate allele frequency as a predictive feature tend to have reduced performance when distinguishing pathogenic variants from very rare benign variants, and predictors supervised on pathogenicity labels from curated variant databases often learn label imbalances within genes. Overall, we find notable advances over the oldest and most cited missense variant effect predictors and continued improvements among the most recently developed tools, and the CAGI Annotate-All-Missense challenge (also termed the Missense Marathon) will continue to assess state-of-the-art methods as the field progresses. Together, our results help illuminate the current clinical and research utility of missense variant effect predictors and identify potential areas for future development.

genetics↗

Cerebellar tonic inhibition orchestrates the maturation of information processing and motor coordination

Tonic inhibition in cerebellar granule cells (GC) is crucial in information coding fidelity for motor coordination. It emerges in activity-dependent and-independent manners, and their interplay evolves with age. However, specific molecular and cellular mechanisms and how their change affects network-level computation and motor behavior remain unclear. Here we show that, while net tonic inhibitory current remains unchanged, the main source of tonic GABA switches from synaptic spillover (neuronal activity-dependent) to astrocytic Best1 (activity-independent) throughout adolescence (4-8 weeks) in mice. Computational modeling based on experimental data demonstrated that this switch down-regulates the internally generated network activity mediating mutual inhibition between GC clusters receiving different inputs, thereby enhancing their independence. Consistent with simulations, 3D-posture analysis revealed an age-dependent increase in independent limb movements during spontaneous motion, which was impaired in Best1 knockout mice. Our findings highlight the late-stage development of complex motor coordination driven by the emergence of astrocyte-mediated tonic inhibition. O_LI6 main figures, 58 references, 5,924 words in the manuscript (excluding the abstract, tables, figure legends and references). C_LIO_LISupplementary information: 1 text (supplementary methods), 9 figures, 4 movies, and 1 table. C_LI

neuroscience↗