Biology subjects

Blackburn, E.

Publications and source records attributed to Blackburn, E..

8 recordsLinked to original sources

bioRxiv2026

Glycogen-Dependent Metabolic Reprogramming Regulates Microglial Activation and Dysfunction in Neurodegenerative Disease

Microglia are central regulators of neuroinflammation in Alzheimers disease (AD), yet how metabolic states modulate function remains unclear. Here we show that microglia from the APPNL-G-F mouse model revealed upregulation of glycolytic enzymes coinciding with onset of microglial activation. Surprisingly, this glycolytic shift occurred alongside reduced expression of glucose transporters, suggesting that extracellular glucose may not be the primary fuel source, implicating glycogenolysis as the potential metabolic driver. Consistent with this, significant microglial glycogen accumulation was noted in late disease, when cells exhibited features of metabolic exhaustion and functional impairment. Pharmacological inhibition of glycogenolysis blunted microglia responses to Abeta aggregates and markedly reduced Abeta uptake, confirming a functional role for glycogen metabolism in shaping microglial states. Together, these findings identify glycogen as a central regulator of microglial metabolic health and function, highlighting glycogen homeostasis as a potential therapeutic target for promoting Abeta clearance and preserving protective microglial functions in AD.

neuroscience↗

bioRxiv2025

Reduced 4E-BP1 activity leads to acquired capivasertib resistance via increased cap-dependent protein synthesis.

BackgroundThe PI3K/AKT/mTOR (PAM) pathway is frequently dysregulated in human cancers and is a major target of therapeutic intervention, exemplified by the newly approved AKT inhibitor capivasertib. However, clinical responses are often limited by the emergence of acquired drug resistance. MethodsTo uncover potential mechanisms underlying acquired resistance to capivasertib, we developed a drug-resistant ovarian cancer model (A2780 254R) through chronic exposure to the capivasertib precursor CCT129254. ResultsThe 254R cells exhibit broad cross-resistance to AKT inhibitors, including capivasertib, along with mTORC1 and PI3K inhibitors, in the absence of AKT mutations or elevated kinase activity. A defining feature of resistance is the reduced expression and phosphorylation of 4E-BP1, a key negative regulator of cap-dependent protein synthesis (CDPS). mcGTP pull-down assays revealed impaired 4E-BP1-eIF4E binding and persistent eIF4F complex formation, which was consistent with enhanced CDPS. An [~]9-fold increase in CDPS activity was observed in 254R cells, without corresponding increases in global protein synthesis or the expression of canonical eIF4E targets. Strikingly, ectopic expression of wild-type or constitutively active 4E-BP1 restored capivasertib sensitivity, re-established the 4E-BP1-eIF4E interaction, and significantly reduced resistance to capivasertib. These findings identify impaired 4E-BP1 function and elevated CDPS as central mediators of acquired resistance to capivasertib. ConclusionOverall, this work underscores the therapeutic vulnerability of the translational machinery to AKT inhibitor resistance. Targeting the eIF4F complex may offer a promising strategy to overcome acquired resistance, and the expression or phosphorylation of 4E-BP1 and eIF4E may serve as predictive biomarkers to guide use of capivasertib in the clinic.

cancer biology↗

bioRxiv2025

Fast segmentation with the NextBrain histological atlas

Structural brain analysis at the subregion level offers critical insights into healthy aging and neurodegenerative diseases. The NextBrain histological atlas was recently introduced to support such fine-grained investigations, but its existing Bayesian segmentation framework remains computationally prohibitive, particularly for large-scale studies. We present a new, open-source tool that dramatically accelerates segmentation using a hybrid approach combining: machine learning, contrast-adaptive segmentation; target-specific image synthesis; and fast diffeomorphic registration (all three with GPU support). Our method enables highly granular segmentation of brain MRI scans of any resolution and contrast (in vivo or ex vivo) at a fraction of the computational cost of the original method (<5 minutes on a GPU). We validate our tool on four different modalities (in vivo MRI, ex vivo MRI, HiP-CT, and photography) across a total of approximately 4,000 brain scans. Our results demonstrate that the accelerated approach achieves comparable accuracy to the original method in terms of Dice scores, while reducing runtime by over an order of magnitude. This work enables high-resolution anatomical analysis at unprecedented scale and flexibility, providing a practical solution for large neuroimaging studies. Our tool is publicly available in FreeSurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/HistoAtlasSegmentation).

neuroscience↗

bioRxiv2025

Impaired BDNF-TrkB trafficking and signalling in Down syndrome basal forebrain neurons

Brain derived neurotrophic factor (BDNF) and its receptor tropomyosin-related kinase B (TrkB) play crucial roles in neuronal development, synaptic transmission, and neuroplasticity. Deficits in BDNF/TrkB signalling and trafficking have been identified in several neurodegenerative diseases, including Alzheimers disease (AD). Individuals with Down syndrome (DS) are at an increased risk of developing AD compared to the general population. Basal forebrain neurons (BFNs) are among the first to degenerate in AD and DS, but the mechanisms underlying their vulnerability remain unclear. Using BFNs derived from the Dp1Tyb mouse model of DS, we investigated neurotrophic signalling and trafficking deficits in AD-DS. We found enlarged early endosomes and elevated levels of active Rab5, a GTPase critical for early endosome formation, in Dp1Tyb BFNs. These abnormalities were associated with impaired transport of internalised TrkB from axon terminals to the soma. Using microfluidic devices, we demonstrated that axonal BDNF stimulation enhanced signalling endosome dynamics in wild-type but not Dp1Tyb BFNs, which is likely due to impaired axonal ERK1/2 signalling. Our findings establish a link between Rab5 hyperactivation, endosomal dysfunction, and impaired ERK1/2 signalling, highlighting the interplay between trafficking and neurotrophic signalling, and underscore the importance of targeting endolysosomal and signalling pathways to mitigate neuronal dysfunction in AD-DS.

neuroscience↗

bioRxiv2024

A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation

Magnetic resonance imaging (MRI) is the standard tool to image the human brain in vivo. In this domain, digital brain atlases are essential for subject-specific segmentation of anatomical regions of interest (ROIs) and spatial comparison of neuroanatomy from different subjects in a common coordinate frame. High-resolution, digital atlases derived from histology (e.g., Allen atlas [7], BigBrain [13], Julich [15]), are currently the state of the art and provide exquisite 3D cytoarchitectural maps, but lack probabilistic labels throughout the whole brain. Here we present NextBrain, a next - generation probabilistic atlas of human brain anatomy built from serial 3D histology and corresponding highly granular delineations of five whole brain hemispheres. We developed AI techniques to align and reconstruct [~]10,000 histological sections into coherent 3D volumes with joint geometric constraints (no overlap or gaps between sections), as well as to semi-automatically trace the boundaries of 333 distinct anatomical ROIs on all these sections. Comprehensive delineation on multiple cases enabled us to build the first probabilistic histological atlas of the whole human brain. Further, we created a companion Bayesian tool for automated segmentation of the 333 ROIs in any in vivo or ex vivo brain MRI scan using the NextBrain atlas. We showcase two applications of the atlas: automated segmentation of ultra-high-resolution ex vivo MRI and volumetric analysis of Alzheimers disease and healthy brain ageing based on [~]4,000 publicly available in vivo MRI scans. We publicly release: the raw and aligned data (including an online visualisation tool); the probabilistic atlas; the segmentation tool; and ground truth delineations for a 100 m isotropic ex vivo hemisphere (that we use for quantitative evaluation of our segmentation method in this paper). By enabling researchers worldwide to analyse brain MRI scans at a superior level of granularity without manual effort or highly specific neuroanatomical knowledge, NextBrain holds promise to increase the specificity of MRI findings and ultimately accelerate our quest to understand the human brain in health and disease.

neuroscience↗

bioRxiv2023

3D analysis of dissection photographs with surface scanning and machine learning for quantitative neuropathology

We present open-source tools for 3D analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (i) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (ii) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimers Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between post mortem confirmed Alzheimers disease cases and controls. The tools are available in our widespread neuroimaging suite "FreeSurfer" (https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools).

neuroscience↗

bioRxiv2021

Molecular Basis for CPC-Sgo1 Interaction: Implications for Centromere Localisation and Function of the CPC

The Chromosomal Passenger Complex (CPC; consisting of Borealin, Survivin, INCENP and Aurora B kinase) and Shugoshin 1 (Sgo1) are key regulators of chromosome bi-orientation, a process essential for error-free chromosome segregation. Their functions rely on their ability to associate with centromeres. Two histone phosphorylations, histone H3 Thr3 (H3T3ph; directly recognised by Survivin) and histone H2A Thr120 (H2AT120ph; indirectly recognised via Sgo1), together with CPCs intrinsic ability to bind nucleosome, facilitate CPC centromere recruitment. The molecular basis for CPC-Sgo1 binding and how their direct interaction influences CPC centromere localisation and function are lacking. Here, using an integrative structure-function approach, we show that the histone H3-like Sgo1 N-terminal tail interacts with Survivin acting as a hot-spot for CPC-Sgo1 assembly, while downstream Sgo1 residues, mainly with Borealin contributes for high affinity interaction. Disruption of the Sgo1 N-terminal tail-Survivin interaction abolished CPC-Sgo1 assembly in vitro and perturbed centromere localisation and function of CPC. Our findings provide evidence that CPC binding to Sgo1 and histone H3 N-terminal tail are mutually exclusive, suggesting that these interactions will likely take place in a spatially/temporally restricted manner and provide a rationale for the Sgo1-mediated kinetochore proximal centromere pool of CPC.

cell biology↗

bioRxiv2019

A New Role for Telomerase in Promoting Meiotic Homolog Pairing Fidelity

We report a role for telomerase, beyond its known function of telomeric DNA end extension, in maintaining normal chromosome dynamics during meiosis in Saccharomyces cerevisiae. When telomerase at telomeres was reduced by various genetic means, increased frequencies of crossover and noncrossover recombination events occurred. To investigate the mechanism of this increased meiotic recombination, we examined the kinetics of meiosis events, and tracked the movement of chromosomes in live cells during meiotic prophase. Cytoskeletal forces acting on telomeres during meiosis have been shown to promote active chromosome motion needed to pair homologous chromosomes. Here we show that changes in telomerase interaction with telomeres using a tlc1-11 mutant result in altered meiotic motion. Specifically, reduction in telomerase at telomeres leads to a decreased frequency of high velocity chromosome pulls. In the tlc1-11 mutant, we see earlier synapsis and increased genome-wide recombination for the majority of the cells and lower gamete viability. Notably, homologous pairing is not delayed unlike other telomere binding mutants. Although synapsis initiates earlier, the overall timing of synapsis remains the same, except for a subset of cells that do not exit meiosis I. Together, these results suggest that the strong pulling component of the active chromosome motion promotes homolog pairing fidelity, likely by pulling apart improperly associated regions. Our combined observations are consistent with a model in which telomerase-mediated telomeric anchoring to the nuclear envelope helps engage and properly transmit cytoskeletal forces to chromosomes. Thus, telomerase contributes to efficient chromosome movements leading to normal gamete viability.

cell biology↗