Matthew J. Huentelman

Summary: Amyotrophic lateral sclerosis (ALS) is an age-related neurodegenerative disorder resulting from the loss of motor neurons in the brain and spinal cord. Neuroinflammation, induced by glial cells including microglia (MG) and astrocytes, is an acknowledged aspect of this neurodegeneration. Generating induced pluripotent stem cell (iPSC) neuroinflammatory models of ALS may help elucidate non-neuronal mechanisms of disease. Here, we analyze human postmortem tissue and an iPSC derived glia-crosstalk model identifying a reduction in Golgi enzymes MAN1A1 and MAN1A2 in addition to other glycan enzymes from ALS-associated microglia and astrocytes. Impaired Golgi and glycan metabolism is linked to inflammation and other related ALS disease mechanisms including impaired lysosomal proteostasis, altered extracellular matrix, disrupted secretion, and altered cell-cell signaling.

Background: Handedness is tied to the lateralization of brain functions and significantly affects cognitive function and brain activity. Alzheimer's disease (AD) is a progressive brain disorder that leads to declines in memory, thinking skills, and to behavioral changes, which also exhibits lateralized patterns of brain involvement. Understanding the relationship between handedness and AD may provide useful context for interpreting findings in AD research. Objective: Previous findings on the relationship between AD and handedness are inconsistent. We used the large MindCrowd dataset, comprising with over 150,000 participants, study the association between AD and handedness. Methods: We applied logistic regression models to the data with and without adjustment for other covariates to estimate the association between handedness and AD. We also performed similar analyses for samples stratified by ages. We estimated the unadjusted and adjusted odds ratios (ORs) of having AD among left- and mixed-handed participants compared with right- handed participants. Results: Our results showed that compared with right-handed participants, left- and mixed-handed participants had higher odds of self-reported AD (the overall adjusted OR: 2.08, 95% CI: (1.69, 2.53), p < 0.001)) being larger than that for left-handers (the overall adjusted OR: 1.42, 95% CI: (1.23, 1.64), p < 0.001)). Furthermore, for each age group considered, the estimated adjusted and unadjusted ORs for mixed-handers were consistently greater than that for left-handers; all were greater than 1.0. Conclusions: Our study confirmed that there is a significant association between handedness and AD. Our findings also indicate that mixed-handedness has a stronger association with AD than left-handedness.

Cerebral small vessel disease (SVD) is the most common age-related brain pathology. Magnetic resonance imaging (MRI) is the reference standard for identifying SVD biomarkers, including white matter hyperintensity, recent small subcortical infarcts, lacunes, perivascular spaces, cerebral microbleeds, and cortical superficial siderosis. However, SVD is usually detected only when patients undergo conventional high-field MRI, limiting early identification, longitudinal monitoring, and equitable access to brain health evaluation. Low-field portable MRI systems (<0.1T) offer point-of-care acquisition with reduced infrastructure requirements and have demonstrated concordance with conventional MRI for multiple acute brain pathologies. We review the emerging evidence for portable MRI–based detection of SVD features, with an emphasis on white matter hyperintensity. Future portable MRI work on SVD should prioritize longitudinal validation, standardized reporting, and integration into pragmatic vascular prevention trials.

Pseudotime trajectories can reconstruct latent disease progression from cross-sectional transcriptomic data. However, whether Alzheimer’s disease (AD) progression follows a conserved molecular architecture across brain regions remains unclear. We applied pseudotime analysis to harmonized bulk RNA-seq data from 2,106 postmortem brain samples (1,364 AD, 742 controls) across nine brain regions from three AMP-AD cohorts (ROSMAP, Mayo, MSBB). Pseudotime was significantly associated with AD diagnosis in all nine regions and with Braak stage in seven of nine. We identified 21 genes with concordant pseudotime associations across all regions, increasing to 234 when the cerebellum was excluded. Pathway analysis revealed 1,268 significant associations, with synaptic deregulation as the most conserved process, and immune/ECM programs showing greater regional specificity. The cerebellum followed a distinct pattern, with enrichment for protein refolding and chaperone pathways rather than neurodegeneration. Co-expression network analysis identified six conserved metamodules, including immune/glial (MM1) and excitatory neuronal (MM2) programs spanning all nine regions, and an oligodendrocyte/myelin program (MM3) in seven cortical regions. Key driver analysis identified 76 unique genes across 35 modules, with HCK and LAPTM5 as the most broadly replicated immune regulators in seven regions. Oligodendrocyte-associated key drivers ( MYRF , CNP , MOBP ) increased along pseudotime in cortical regions, supporting active myelin remodeling during AD progression. These findings reveal a conserved transcriptional architecture underlying AD progression, organized around coordinated immune activation, synaptic loss, and myelin remodeling, with the cerebellum following a distinct trajectory.

The term Precision Aging describes an approach that focuses on multi-domain profiles of risks impacting individual trajectories of age-related cognitive functioning. The goal of the present study was to identify profiles of risk within a sample of 555 adults, ages 50 to 79, without diagnosis of dementia. Using cluster analyses, we considered 38 risk factors associated with five categories of risk known to negatively impact cognitive aging – cardiovascular insufficiency, glucose dysregulation, inflammation, immune dysfunction, and neuropathology. Results yielded five profiles, including a group with low risk in all five risk categories, and four groups with prominent risks in specific domains. Importantly, all four high risk groups performed more poorly relative to the low risk group on multiple memory measures from a well-established neuropsychological test, the Auditory Verbal Learning Test. The results highlight the importance of considering multiple domains of risk within the same cohort to predict age-related cognitive functioning.

Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS) are linked neurodegenerative diseases characterized by both synaptic dysfunction and TDP-43 pathology. A hexanucleotide repeat expansion (HRE) in the C9ORF72 (C9) gene represents the most common genetic cause of FTD and ALS, yet the synapse-specific mechanisms underlying disease pathogenesis remain poorly understood. Here, we performed integrated multi-omic profiling of synaptosomes enriched from postmortem frontal cortex and patient-derived induced pluripotent stem cell (iPSC)-derived cortical neurons to define molecular alterations associated with C9-FTD-mediated synaptic dysfunction. Proteomic profiling of frontal cortex-derived synaptosomes identified 1,324 differentially abundant proteins (p<0.05) enriched in pathways regulating synaptic vesicle transport and synapse organization, while synaptosomal RNA sequencing revealed 2,835 differentially expressed protein-coding genes. C9-FTD iPSC-cortical neurons exhibited reductions in excitatory and inhibitory postsynaptic markers, accompanied by progressive impairment of neuronal network activity, supporting both structural and functional deficits. iPSC-derived synaptosomes recapitulated key molecular pathways observed in patient brain, revealing convergent dysregulation of synaptic signaling pathways. Comparative analyses revealed divergence between protein and RNA alterations, consistent with the disruption of regulatory processes that link RNA and protein abundance diseased synapses. Consistent with TDP-43 loss-of-function pathology we identified cryptic exon (CE)-containing transcripts within C9-FTD frontal cortex-derived synaptosomes, including KALRN and STMN2, providing evidence that aberrantly spliced RNAs localize to synaptic compartments. Together, these findings define convergent molecular pathways underlying synapse vulnerability in both C9-FTD model systems and identify synaptic localization of CE-containing transcripts as a previously unrecognized feature of TDP-43 proteinopathy.

Background: Vascular contributions to cognitive impairment and dementia (VCID) are thought to arise from distributed neurovascular unit (NVU) dysfunction rather than focal pathology, yet the transcriptional architecture of human VCID brain tissue and the status of endogenous counter-regulatory signaling within it remain incompletely characterized. Defining whether protective pathways are engaged and why they may be insufficient is critical for identifying therapeutic entry points in a disease lacking approved treatments. Methods: We performed differential gene expression analysis (DESeq2 v1.38.0) and pre-ranked gene set enrichment analysis (fgsea v1.24.0) on bulk RNA-sequencing data from superior parietal lobe tissue (GEO:GSE303449; n = 40; 19 VCID, 21 controls; model: age_scaled + Sex + condition), followed by Spearman correlation analysis, PI3K-Akt pathway level, leading-edge decomposition, and single-nucleus RNA-seq endothelial cell characterization (GEO:GSE282111). Results: No individual gene reached FDR < 0.05 for differential expression between VCID and control across 51,962 genes tested. Gene set enrichment analysis nonetheless identified eight significantly enriched pathway programs (all FDR < 0.05) that were upregulated, encompassing inflammatory, stress-response, cytoskeletal, and apoptotic signaling, consistent with distributed network-level dysregulation rather than dominant single-gene effects. The MAS1/ANG1-7 associated signaling gene set (54 genes) was the only counter-regulatory pathway achieving significance (NES = 1.381, FDR = 0.0127). MAS1 receptor expression was strongly (absolute Spearman’s rho ≥ 0.64) and inversely associated with NF-κB pathway drivers TLR4 (Spearman’s rho = -0.804) and IKBKB (Spearman’s rho = -0.797; both FDR = 4.73 × 10^-9). Further, 9 of 12 correlations between MAS1 downstream effectors and endothelial activation markers were FDR-significant and positive, indicating that the downstream protective effector program is co-activated by inflammatory stress rather than directed by its receptor. Single-nucleus RNA-seq supports endothelial enrichment of the MAS1 pathway enrichment signal in VCID brain tissue. PI3K-Akt leading-edge decomposition revealed 96% gene-level non-overlap between inflammatory and vasoprotective arms. Conclusions: Human VCID brain tissue exhibits coordinated pathway-level dysregulation in the absence of dominant individual-gene effects, consistent with a disease driven by distributed transcriptional network stress. The MAS1/ANG1-7 vasoprotective axis is transcriptionally engaged and endothelially enriched, yet receptor expression is inversely associated with inflammatory signaling while downstream effectors remain transcriptionally engaged. This pattern suggests a failed compensatory state in the VCID superior parietal lobe. This architecture is consistent with a transcriptionally primed but receptor-constrained protective program. These findings suggest that therapeutic strategies restoring MAS1 receptor-level input to an already engaged downstream program may represent a plausible therapeutic strategy for VCID, pending experimental validation.

Frontotemporal lobar degeneration TDP43 type C (TDP-C) is a rare and unique neurodegenerative disease that attacks the anterior temporal lobe. Recently, it was shown that Annexin-A11 and TDP-43 coaggregate specifically in TDP-C. Current literature on the genetic associations with TDP-C, reviewed here, lacks a discernible corpus of robust or replicated findings. In this study, using blood tissue, we completed whole genome sequencing to investigate ANXA11 and TARDBP genetic variants for their association with TDP-C. Then, we completed genome-wide hypothesis-free analyses using artificial intelligence to identify rare pathogenic variants associated with TDP-C. (1) We tested common variants in ANXA11 and TARDBP for their association with 37 TDP-C cases vs 290 controls. We attempted to replicate our findings in a different cohort of 467 TDP-C cases vs 3,153 controls and contrasted them with cohorts of TDP-A and TDP-B. (2) AI-guided analyses were completed to prioritize pathogenic rare variants associated with TDP-C in our cohort. (1) Four common variants in ANXA11 (rs113772135, rs2789686, rs1079242, rs61860017) were significantly associated with TDP-C in the discovery cohort and replicated in the other cohort of TDP-C but not in TDP-A or TDP-B, providing evidence for ANXA11 specific association with TDP-C. Rs1079242-A showed the most robust replication (p = 7.35 × 10⁻⁰⁵) and correlates with higher ANXA11 level in CSF (p = 4 × 10⁻¹¹). No associations were found between TARDBP and TDP-C (p > 0.05). Using AI-guided rare variant analyses, we identified a pathogenic variant in FIG4, a gene that has been implicated in amyotrophic lateral sclerosis (ALS). Because of the observed potential genetic overlap between some ALS genes and TDP-C, we leveraged mendelian randomization and found that ALS genetic load is associated with TDP-C risk (p = 0.0046). This study provides replicated evidence for the association between common variants in ANXA11 with TDP-C. Knowing rs1079242-A affects ANXA11 level in CSF, future studies may aim to investigate ANXA11 level as potential CSF biomarker for TDP-C. Moreover, FIG4 and ANXA11 have been implicated in the inositol pathway. Our results provide novel insights into the genetic risk of TDP-C and offer new clues about its underpinning mechanisms.

Recent genetic studies highlight microglia as central drivers of Alzheimer’s disease (AD), yet how specific risk variants like TREM2-R47H influence broader neurocellular networks remains elusive. Here, we utilize an iPSC-derived forebrain organoid co-culture system to investigate the multi-lineage impact of the TREM2-R47H variant. High-resolution transcriptomic profiling, paired with confocal imaging, demonstrate that mutant organoids recapitulate AD-specific pathological signatures. Representative confocal imaging revealed phosphorylated-Tau (pTau) and amyloid-beta (Aβ) internalization by WT microglia, while R47H variants showed a qualitative reduction in pTau accumulation. Single-cell RNA sequencing (scRNA-seq) revealed neurodegenerative transcriptional profiles in TREM2-R47H neurons as early as day 139, occurring independently of microglia presence. By day 173, these cell-intrinsic signatures intensified, characterized by disrupted oxidative phosphorylation and impaired maturation trajectories. Interaction analysis further demonstrated that the addition of microglia exacerbated this phenotype; while WT cells adapted to the microglia niche by activating homeostatic, neuro-supportive programs, TREM2-R47H cells underwent ‘identity erosion’ and failed to transition into HLA-enriched activation states. This state was characterized by a failure to adopt brain-resident signatures and a divergent shift toward inflammatory myeloid phenotypes. These findings reveal that the TREM2-R47H mutation exerts a dual burden: it drives a baseline neurodegenerative state in neural lineages and renders them incapable of proper niche integration. Our study provides an in vitro human platform to dissect the interplay between genetic risk and multi-cellular dysfunction, establishing a scalable system for evaluating novel therapeutic interventions and drug screening aimed at restoring neuro-immune homeostasis in AD.