Biology subjects

Mallach, A.

Publications and source records attributed to Mallach, A..

9 recordsLinked to original sources

bioRxiv2026

Neuronal and glial transcriptional states vary with proximity to tangle-bearing neurons in the human entorhinal cortex

More neurons die in Alzheimer's disease than form tangles, and tangle-bearing neurons can persist for decades, so tangles alone cannot explain degeneration. We combined 6,000-plex spatial transcriptomics with PHF1 immunofluorescence (167,176 cells; 9 donors) and imaging mass cytometry (170,195 cells; 62 donors), measuring each cell's distance to the nearest tangle. Tangle-bearing layer 2-3 excitatory neurons were enriched late along a trajectory of increasing microtubule-associated, synaptic and V-ATPase expression, with elevated p62 and K48-ubiquitin. Tangle-free neurons shared more of this state the closer they lay to a tangle, including higher chaperone and autophagy scores, p62 and nuclear size. Nearby glia had higher disease-associated scores, with astrocytes expressing less GFAP. Excitatory, but not inhibitory, neuron loss was greatest in subtypes closest to tangles and cortical depths richest in phosphorylated tau. Selective neuronal vulnerability may reflect not only a neuron's susceptibility to forming a tangle but also where it lies relative to one.

neuroscience↗

bioRxiv2026

Glial subcellular specialisation resolved with high resolution spatial transcriptomics

Cells in the brain have complex structures with extended processes. This complex morphology supports diverse specialized functions in health and disease, and specifically, cell processes appear to be critical for cellular integration and signalling. Here, we developed a new spatial averaging framework to recover and interrogate molecular phenotypes of glial processes in spatial transcriptomics (ST) data. We characterised cell type specific signatures associated with processes of astrocytes and microglia in both mouse and human brain tissue. Astrocytic processes were enriched for transcripts related to neuronal support relative to their soma, while microglial processes preferentially expressed genes linked to specific microglial states. When investigated in tissue from brains with Alzheimers Disease (AD) pathology, we found that local amyloid-{beta} pathology was associated with subcellular differences in transcriptomes in both an amyloid-{beta} mouse model and human AD patient tissue. Specifically, astrocytic and microglial processes oriented toward amyloid-{beta} plaques exhibited distinct molecular changes in comparison to processes extending away into plaque free areas, suggesting polarized glial responses to pathology. Our work thus outlines a general method for the selective characterisation of transcriptomics of glial processes in mouse and human ST data and provides evidence for differential transcriptomic responses between the soma and processes of glia in health and disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/737168v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@157455corg.highwire.dtl.DTLVardef@8ac0a2org.highwire.dtl.DTLVardef@16ccbf5org.highwire.dtl.DTLVardef@1c24cd0_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Intrinsic molecular susceptibility underlies selective neuronal vulnerability in the Alzheimer's disease entorhinal cortex

Entorhinal cortex (EC) excitatory neurons are lost early in Alzheimers disease (AD), yet the specific subtype and characteristics contributing to this vulnerability are poorly understood. Combining imaging mass cytometry (206,913 cells; 62 donors) and single nucleus RNA sequencing (42,780 nuclei; 36 donors) of post-mortem EC, we found that calbindin-expressing layer 2-3 excitatory neurons accumulate high phospho-tau burden and are preferentially lost in AD. In non-diseased brains, these neurons exhibit elevated tau-modifying kinase expression (ERK1/2, FYN, ROCK), reduced phosphatase expression (PP2A/B, PP5) and low mitochondrial respiratory capacity which together are predicted to promote high vulnerability to tau pathology. Trajectory analysis resolved progression from homeostasis through DNA damage and proteostatic stress to developmental re-entry and death priming. In silico screening suggested histone deacetylase inhibitors and cyclooxygenase inhibitors as candidate resilience-promoting therapeutics. Our work thus reframes intrinsic features of neuronal identity promoting phospho-tau formation as modifiable determinants of the selective vulnerability of EC calbindin neurons.

neuroscience↗

bioRxiv2026

The Alzheimer's disease neurodegenerative cascade reconstructed in human L2/3 excitatory neurons

Identifying the molecular cascade underlying neuronal degeneration in Alzheimers disease has been hampered by cellular heterogeneity and the limitations of donor-level classification. By integrating 851,682 cortical layer 2 and 3 excitatory neuron transcriptomes from 557 individuals across four independent snRNA-seq datasets of the human prefrontal cortex, we reconstruct neuronal degeneration as a continuous, stage-resolved transcriptional trajectory. Ordering neurons by collective pathological burden and clinical manifestation reveals that degeneration unfolds asynchronously within individual brains. Neurons in a single brain can simultaneously occupy early, intermediate, and late pathological states, a continuum entirely obscured by conventional approaches. The trajectory captures discrete transcriptional inflection points defining successive stages of vulnerability linked to development of neuropathology. Systematic analysis of the complete human kinome and phosphatome along this trajectory identifies a temporal hierarchy of phosphorylation dysregulation which collectively creates a permissive environment for tau pathology to escalate, defining stage-specific molecular nodes in the degenerative cascade.

neuroscience↗

bioRxiv2023

Differential LRRK2 signalling and gene expression in WT-LRRK2 and G2019S-LRRK2 mouse microglia treated with zymosan and MLi2.

IntroductionMutations in the Leucine Rich Repeat Kinase 2 (LRRK2) gene cause autosomal dominant Parkinsons disease (PD) with the most common causative mutation being the LRRK2 p.G2019S within the kinase domain. LRRK2 protein is highly expressed in the human brain and also in the periphery, and high expression of dominant PD genes in immune cells suggest involvement of microglia and macrophages in inflammation related to PD. LRRK2 is known to respond to extracellular signalling including TLR4 resulting in alterations in gene expression, with the response to TLR2 signalling through zymosan being less known. MethodsHere, we investigated the effects of zymosan, a TLR2 agonist and the potent and specific LRRK2 kinase inhibitor MLi-2 on gene expression in microglia from LRRK2-WT and LRRK2 p.G2019S knock-in mice by RNA-Sequencing analysis. ResultsWe observed both overlapping and distinct zymosan and MLi-2 mediated gene expression profiles in microglia. At least two candidate Genome-Wide Association (GWAS) hits for PD, CathepsinB (Ctsb) and Glycoprotein-nmb (Gpnmb), were notably downregulated by zymosan treatment. Genes involved in inflammatory response and nervous system development were up and downregulated respectively with zymosan treatment while MLi-2 treatment particularly exhibited upregulated genes for ion transmembrane transport regulation. Furthermore, we observed the top twenty most significantly differentially expressed genes in LRRK2 p.G2019S microglia show enriched biological processes in iron transport and response to oxidative stress. DiscussionOverall, these results suggest that microglial LRRK2 may contribute to PD pathogenesis through altered inflammatory pathways. Our findings should encourage future investigations of these putative avenues in the context of PD pathogenesis.

neuroscience↗

bioRxiv2023

Applying high-resolution spatial transcriptomics to characterise the amyloid plaque cell niche in Alzheimer's Disease

The amyloid plaque cell niche is a pivotal hallmark of Alzheimers disease (AD). Where early spatial transcriptomics (ST) technologies have provided valuable information on transcriptomic alterations in the small tissue domains overlaying with amyloid plaques, they lacked cellular resolution. Here we compare two novel high-resolution ST platforms, CosMx and Stereo-seq, in their ability to characterize the cellular response in the amyloid plaque niche in an AD mouse model. Combining the results from both techniques empowered us to survey the highly variable microglial-astrocytic response across the amyloid plaque micro-environment and provided a first insight into how these responses could relate to neuronal transcriptomic alterations. This pilot study demonstrates the great potential of high-resolution ST, while simultaneously highlighting limitations that, when addressed, will unleash the full power of these techniques to map the progression of molecular and cellular changes in the brains of AD patients.

neuroscience↗

bioRxiv2021

Differential stimulation of pluripotent stem cell-derived human microglia leads to exosomal proteomic changes affecting neurons

Microglial exosomes are an emerging communication pathway, implicated in fulfilling homeostatic microglial functions and transmitting neurodegenerative signals. Gene variants of the triggering receptor expressed myeloid cells-2 (TREM2) are associated with an increased risk of developing dementia. We investigated the influence of the TREM2 Alzheimers disease risk variant, R47Hhet, on the microglial exosomal proteome consisting of 3019 proteins secreted from human iPS-derived microglia (iPS-Mg). Exosomal protein content changed according to how iPS-Mg were stimulated. Thus lipopolysaccharide (LPS) induced microglial exosomes to contain more inflammatory signals, whilst stimulation with the TREM2 ligand phosphatidylserine (PS+) increased metabolic signals within the microglial exosomes. We tested the effect of these exosomes on neurons and found that the exosomal protein changes were functionally relevant and influenced downstream functions in both neurons and microglia. Exosomes from R47Hhet iPS-Mg contained disease-associated microglial (DAM) signature proteins, and were less able to promote outgrowth of neuronal processes and increase mitochondrial metabolism in neurons compared with exosomes from TREM2 common variant iPS-Mg. Taken together these data highlight the importance of microglial exosomes in fulfilling microglial functions. Additionally, variations in the exosomal proteome influenced by the R47Hhet TREM2 variant may underlie the increased risk of Alzheimers disease associated with this variant. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/452610v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@3dd1eborg.highwire.dtl.DTLVardef@a0b1feorg.highwire.dtl.DTLVardef@5a232org.highwire.dtl.DTLVardef@1dbadc3_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2020

Microglial signalling pathway deficits associated with the R47H TREM2 variant linked to AD indicate inability to activate inflammasome

The R47H variant of the microglial membrane receptor TREM2 is linked to increased risk of late onset Alzheimers disease. Human induced pluripotent stem cell derived microglia (iPS-Mg) from patient iPSC lines expressing the AD-linked R47Hhet TREM2 variant, common variant (Cv) or an R47Hhom CRISPR edited line and its isogeneic control, demonstrated that R47H-expressing iPS-Mg expressed a deficit in signal transduction in response to the TREM2 endogenous ligand phosphatidylserine with reduced pSYK-pERK1/2 signalling and a reduced NLRP3 inflammasome response, (including ASC speck formation, Caspase-1 activation and IL-1beta secretion). Apoptotic cell phagocytosis and soluble TREM2 shedding were unaltered, suggesting a disjoint between these pathways and the signalling cascades downstream of TREM2 in R47H-expressing iPS-Mg, whilst metabolic deficits in glycolytic capacity and maximum respiration were reversed when R47H expressing iPS-Mg were exposed to PS+ expressing cells. These findings suggest that R47H-expressing microglia are unable to respond fully to cell damage signals such as phosphatidylserine, which may contribute to the progression of neurodegeneration in late-onset AD.

neuroscience↗

bioRxiv2019

A locked immunometabolic switch underlies TREM2 R47H loss of function in human iPSC--derived microglia

Loss-of-function genetic variants of triggering receptor expressed on myeloid cells 2 (TREM2) are linked with an enhanced risk of developing dementias. Microglia, the resident immune cell of the brain, express TREM2 and microglial responses are implicated in dementia pathways. In a normal surveillance state, microglia use oxidative phosphorylation for their energy supply, but rely on the ability to undergo a metabolic switch to glycolysis to allow them to perform rapid plastic responses. We investigated the role of TREM2 on microglial metabolic function in human patient iPSC-derived-microglia expressing loss of function variants in TREM2. We show that these TREM2 variant iPSC-microglia, including the Alzheimers disease R47H risk variant, exhibit significant metabolic deficits including a reduced mitochondrial respiratory capacity and an inability to perform a glycolytic immunometabolic switch. We determined that dysregulated PPAR{gamma}/p38MAPK signalling underlies the observed phenotypic deficits in TREM2 variants and that activation of these pathways can ameliorate the metabolic deficit in these cells and consequently rescue critical microglial cellular function such as {beta}-Amyloid phagocytosis. These findings have ramifications for microglial focussed-treatments in AD.

neuroscience↗