Denali Therapeutics (United States)

Mucopolysaccharidoses (MPSs) are characterized by deficient activity of lysosomal hydrolase enzymes, leading to progressive accumulation of glycosaminoglycans. These glycosaminoglycans can be assayed in biofluids as potential markers of disease severity and response to disease-modifying therapies. This study sought to calculate control reference intervals in a largely pediatric population for key MPS biomarkers: heparan sulfate (HS) and dermatan sulfate (DS) in cerebrospinal fluid (CSF) and urine, and CSF monosialic gangliosides GM2 and GM3. We also explored the effect of age on biomarker levels. Biomarker levels were measured using liquid chromatography-tandem mass spectrometry in CSF and urine samples from pediatric and young adult donors and were compared with baseline CSF and urine biomarker levels from an ongoing Phase 1/2 study of children with MPS II. Age-specific reference intervals were estimated for CSF HS, DS, and GM2, and for urine HS, DS, and the sum of HS and DS, after observing that levels of these markers decreased with age. CSF GM3 levels were not found to be age dependent, therefore a single reference interval was estimated for the reference population. In patients with MPS II, levels of HS and DS, respectively, were 6- and 7-fold higher in CSF, and 13- and 30-fold higher in urine than the upper reference interval limits. Establishing age-specific reference intervals will help to optimize biomarker use in clinical studies.

Abstract Magnetic reconnection, a fundamental process in laboratory, space and astrophysical plasmas, can transfer magnetic field energy into particles’ kinetic and thermal energy, leading to many explosive phenomena, such as solar flares and astrophysical jets. It has been believed that reconnection-driven energy transfer typically occurs inside reconnection ejecta, particular reconnection fronts (RFs), which can host localized, ultrastrong energy transfer (UET) directly controlling large-scale energy transport. However, origin of the RF-driven UET remains unclear. Here, using state-of-the-art measurements from NASA’s Magnetospheric Multiscale (MMS) spacecraft, we perform a comprehensive investigation of UET at RFs. We reveal that the UET hosts two different regimes: ion-dominated laminar regime and electron-dominated turbulent regime. The transition between the two regimes is controlled by an electron-ion hybrid instability, which can generate lower hybrid turbulence feeding intense electric fields. We find that Hall term in the generalized Ohm’s law, rather than traditionally-believed electron pressure gradient term, plays a more significant role in balancing the intense electric fields. These results provide novel insights into understanding reconnection-driven energy transport chain widely present in the cosmos.

Goal-directed navigation involves a sequence of planned actions aimed at achieving long-term goals through reinforcement, but detecting hidden states that support this process and their neuronal substrates remains a fundamental challenge. To address this, we developed a complex labyrinth test that mimics naturalistic foraging and implemented a novel hierarchical probabilistic modeling framework, Cognitive Mapping of Planned Actions with State Spaces (CoMPASS). This framework infers a nested state structure, comprising short-term surveillance–ambulation states (Level 1) and long-term goal-oriented navigational states (Level 2). Using CoMPASS, we show that successful navigation in wild-type mice is marked by increased recruitment of both surveillance and goal-oriented states specifically at decision nodes, revealing how sequential behavioral decisions culminate in long-term goals. In contrast, the humanized mouse model of Alzheimer’s disease (AD) exhibited navigational impairments marked by diminished surveillance during decisions, reduced goal-directed states, and increased navigation stochasticity. Importantly, we show that gamma oscillations in the posterior parietal cortex (PPC), a region involved in spatial navigation planning, encode these CoMPASS behavioral states and their dynamic operating modes linking spatial locations to long-term goals. Our findings provide a novel paradigm for assessing hidden goal-directed navigational states and identify gamma oscillations in the PPC as their neural substrates.

High-resolution protein structures are essential for understanding biological mechanisms and drug discovery. While cryoEM has revolutionized structure determination of large protein complexes, most disease-related proteins are small (<50 kDa) and challenging to resolve due to low signal-to-noise ratios and alignment difficulties. Current scaffold protein strategies increase target size but suffer from inherent flexibility, resulting in poorly resolved targets compared to scaffolds. We present an iteratively engineered molecular design transforming antibody fragments (Fabs) into conformationally Rigid Fabs that enable high-resolution structure determination of small proteins (~20 kDa). This design introduces strategic disulfide bonds, creating well-folded, rigidly constrained Fabs applicable across various species, frameworks, and chimeric constructs. Rigid Fabs enabled high-resolution cryoEM structures (2.3-2.5 Å) of two small proteins: Ang2 (26 kDa) and KRAS (21 kDa). Our disulfide-constrained Rigid Fab strategy provides a general approach for overcoming target size limitation of single-particle cryoEM.

Anti-amyloid β-peptide (Aβ) immunotherapy was developed to reduce amyloid plaque pathology and slow cognitive decline during progression of Alzheimer’s disease. Efficient amyloid clearance has been proven in clinical trials testing anti-Aβ antibodies, by their impact on cognitive endpoints correlating with the extent of amyloid removal. However, treatment is associated with adverse side effects, such as oedema and haemorrhages, which are potentially linked to the induced immune response. To improve the safety profile of these molecules, it is imperative to understand the consequences of anti-Aβ antibody treatment on immune cell function. Here, we investigated the effects of long-term chronic anti-Aβ treatment on amyloid plaque pathology and microglial response in the APP-SAA triple knock-in mouse model with an intervention paradigm early during amyloidogenesis. Long-term treatment with anti-Aβ results in a robust and dose-dependent lowering of amyloid plaque pathology, with a higher efficiency for reducing diffuse over dense-core plaque deposition. Analysis of the CSF proteome indicates a reduction of markers for neurodegeneration including Tau and α-Synuclein, as well as immune-cell-related proteins. Bulk RNA-seq revealed a dose-dependent attenuation of disease-associated microglial (DAM) and glycolytic gene expression, which is supported by a parallel decrease of glucose uptake and protein levels of Triggering Receptor Expressed on Myeloid cells 2 (Trem2) protein, a major immune receptor involved in DAM activation of microglia. In contrast, DAM activation around residual plaques remains high, regardless of treatment dose. In addition, microglia surrounding residual plaques display a dose-dependent increase in microglial clustering and a selective increase in antigen-presenting and immune signalling proteins. These findings demonstrate that chronic early intervention by an anti-amyloid immunotherapy leads to a dose-dependent decrease in plaque formation, which is associated with lower brain-wide microglial DAM activation and neurodegeneration. Microglia at residual plaques still display a combined DAM and antigen-presenting phenotype that suggests a continued treatment response.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13024-025-00878-1.

Diffuse hemispheric glioma H3 G34-mutant is primarily diagnosed in adolescents/young adults. While molecular diagnostics have improved, cellular mechanisms that drive tumor progression and therapy resistance are poorly understood. Combining previous published studies with findings from the 2024 NIH G34-mutant symposium aid in summarizing translational and clinical updates on disease development, cellular repair processes, and the immune microenvironment. This collective work is meant to outline opportunities for treatment and prolonged survival.

The triggering receptor expressed on myeloid cells 2 (TREM2) plays a pivotal role in the activation of myeloid cells and is currently being investigated as a potential therapeutic target in several diseases. In this study, we established enhanced quantification of PET images of a 64Cu-labeled antibody-based PET radiotracer as a noninvasive tool for the assessment of TREM2 expression in the brain and peripheral organs of mice. We used TREM2 knockout mice that lack target expression to investigate data-driven blood normalization of PET images against percentage of injected dose normalization. Methods: TREM2 knockout and wild-type mice (n = 11 each) were injected with the radiotracer [64Cu]Cu-NODAGA-ATV:4D9 (ATV is antibody transport vehicle). Twenty hours after injection, TREM2 PET was conducted and blood samples were collected. A voxelwise analysis with statistical parametric mapping served to determine voxels that correlate with ex vivo blood radioactivity levels. Furthermore, TREM2 PET signals were compared between mice with and those without TREM2 expression using image-derived blood normalization. Correlation with TREM2 protein expression levels in the lung, liver, spleen, and bone marrow was used to validate organ-specific PET results. Disease models of brain amyloidosis and myocardial infarction were investigated to test for the value of image-derived normalization in mice. Results: Blood radioactivity levels derived from a statistical parametric mapping-derived region of interest demonstrated a robust correlation with radioactivity measurements obtained from ex vivo blood samples. Voxelwise clusters of TREM2 PET signals were more robustly detected after blood normalization of the PET images. Significant voxelwise clusters of TREM2 PET signals in peripheral organs correlated with TREM2 protein expression levels. Furthermore, image-derived normalization enhanced the significance of voxelwise clusters of TREM2 in the brains of App SAA;TfRmu/hu mice, as well as the TREM2 signal in the myocardial infarct region. Both strongly correlated with ex vivo autoradiography. Conclusion: Normalization of PET images to account for blood levels enhanced the detection of TREM2. This improved methodology for TREM2 PET analysis provides a promising basis for future assessments of TREM2 imaging.

Abstract BackgroundMacrophages and microglia are myeloid cells that play critical roles in the surveillance of the local environment of the tissues in which they reside. The ability of these phagocytes to perform key functions is contingent on their capacity to sense extracellular cues and mount responses that involve chemotaxis, proliferation, cytokine secretion, and phagocytosis of various cargos for lysosomal clearance. Our overarching hypothesis is that lysosomal degradation of phagocytic cargoes is critical for the resolution of cellular/tissue damage, as well as of inflammation, and that failure to accomplish this step affects myeloid cell states and immune responses.MethodTo test this hypothesis, we examined the consequences of disrupting lysosomal function on myeloid cell state, using GRN deficiency as a model of primary lysosomal dysfunction.ResultGRN is highly expressed in these cells and encodes progranulin, a frontotemporal dementia‐linked protein critical for the regulation of lysosomal degradative processes. We first performed single‐nucleus RNA‐sequencing of purified microglia from aged wild‐type and Grn knockout (KO) mice, defining the diverse subpopulations that emerge with disease in this context. Next, we characterized primary microglia and macrophages from Grn KO mice cultured in the absence of other cell types, which revealed robust cell autonomous transcriptional and functional alterations resulting from Grn deficiency. To further examine how specific forms of lysosomal dysfunction impact myeloid cell state, we induced pharmacological and genetic perturbations of various lysosomal properties, which uncovered a robust response of myeloid cells to lysosomal deacidification that largely overlaps with that observed in Grn KO myeloid cells. Finally, we identified putative transcription factors that mediate the transcriptional remodeling of myeloid cells in response to lysosomal stress.ConclusionOverall, these data reveal a novel link between lysosomal health and myeloid cell transcriptional and functional states.