The Deese/Roediger-McDermott (DRM) paradigm induces high false alarm rates for critical words not presented in study lists, an effect typically attributed to false memory. The criterion shift account instead attributes the DRM effect to strategic inferences rather than false memories. Although instructing participants to avoid critical lures reduces the DRM effect, it does not eliminate it on average, a finding often interpreted as evidence against the account. This interpretation, however, overlooks substantial individual differences in people’s willingness to shift decision criteria. We tested whether individual differences in criterion shifting tendencies predict the extent to which criterion manipulations modulate the DRM effect. We developed a novel 100-list DRM paradigm (Experiment 1, N = 47) and examined changes in the DRM effect following monetary incentives in recognition memory (Experiment 2, N = 118) and free recall (Experiments 3 and 4, N = 86 and N = 103), with Experiments 2 and 4 also including an independent recognition test. Monetary incentives altered the DRM effect by up to 70%, and individual differences in this modulation correlated with independently measured criterion shifting tendencies. Moreover, up to 30% of participants eliminated the DRM effect entirely under a conservative criterion. These findings support the criterion shift account, demonstrating that decision criteria substantially influence critical lure susceptibility and that individual differences in criterion shifting predict this influence. Previous group-level assessments have overlooked the possibility that persistent DRM effects reflect insufficient criterion shifting among some individuals rather than enduring false memories.

Although mutations in many genes cause familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), most cases are sporadic (sALS and sFTD) with unclear etiology. Here we tested whether somatic mutations contribute to sALS and sFTD by deep targeted sequencing of 88 neurodegeneration-related genes in postmortem brain and spinal cord samples from 399 sporadic cases and 144 controls. Predicted deleterious somatic variants in ALS/FTD genes were observed in 2.1% of sporadic cases lacking deleterious germline variants. These variants occurred at very low allele fractions (typically <2%) and were often focal and enriched in disease-affected regions. Analysis of bulk RNA-sequencing data from an additional cohort identified deleterious somatic variants in DYNC1H1 and LMNA, genes associated with pediatric motor neuron degeneration. Targeted long-read sequencing further identified one sFTD case with de novo somatic C9orf72 repeat expansions. Together, these findings suggest that rare, focal somatic variants can contribute to sALS and sFTD and drive widespread neurodegeneration.

Somatic mutations are genetic variants that occur after the single-cell phase of development and have been implicated in disease pathogenesis. While most DNA lesions are detected and repaired, examination of healthy tissue has revealed that some lesions escape repair, leading to somatic mutations that accumulate at a consistent rate, including in human brain tissue and postmitotic neurons. Emerging methodological and analytical advances have revealed the presence of persistent mutagenic mechanisms during healthy brain aging as well as mutational pattern shifts in the context of neurodegenerative diseases. Here, we highlight recent methodological advances, summarize our current understanding of somatic mutagenesis in neurotypical brain aging, and examine the role of somatic mutations in neurodegenerative diseases.

Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease (AD) represent two major categories of neurodegenerative disorders—TAR DNA-binding protein 43 (TDP-43) and tau proteinopathies—for which the mechanisms driving neuronal death remain unclear. Single-cell whole-genome sequencing of 469 neurons from C9ORF72 ALS, C9ORF72 FTD, AD, and control brains revealed increased somatic single-nucleotide variants (sSNVs) and insertions/deletions (sIndels) in all three diseases. Mutational signature analysis identified a disease-associated sSNV signature consistent with oxidative damage and an sIndel process affecting 22% of ALS, 76% of FTD, and 61% of AD neurons—but only 2% of control neurons—resembling signature ID4, previously linked to topoisomerase 1 (TOP1)-mediated mutagenesis. Rapid approach to DNA adduct recovery (RADAR) assays confirmed increased TOP1-DNA covalent complexes, and duplex sequencing confirmed the increased sIndels and identified single-strand events as likely precursor lesions. TOP1-associated sIndel mutagenesis and genome instability thus represent a mechanism shared by both TDP-43 and tau neurodegeneration.

Abstract Chronic pain presents a leading challenge in the world today for both clinicians and researchers. Because chronic pain is difficult to explain and treat, it is often managed with opioids despite providing limited relief and contributing to dependence and misuse. Persistent pain can be maintained by altered central nervous system processing even in the absence of distinct tissue damage or disease, which may limit the efficacy of conventional pharmacological therapies that target nociceptive signal transmission rather than maladaptive central nervous system dynamics often present in those with chronic pain. Although neuroimaging studies have identified this shift from nociceptive to emotional circuits during pain chronification, a quantitative framework linking these neural changes to longitudinal pain trajectories or recovery is lacking. We present a parsimonious firing-rate model that can account for the development of and recovery from chronic pain, which is based on the theoretical framework established by Wilson and Cowan. The model provides a quantitative explanation of how sensitization, anxiety, and fear maintain pain even after an injury has healed, and how calming stimulus downregulates these processes to facilitate recovery. A study applying the same principles as the model produced an average pain decrease of 3.5 on the Visual Analog Scale (VAS), with all subjects experiencing a reduction in pain. These results, coupled with our model and findings in prior studies, suggest that increasing calming stimulus can reduce pain without necessitating pharmacological or invasive, resource-intensive interventions.

Mesial (a.k.a., medial) temporal lobe epilepsy (MTLE) is the most common focal epilepsy1,2 and, in drug-resistant cases, is treated by surgical removal of the anterior temporal lobe, which often shows neuronal loss and gliosis consistent with hippocampal sclerosis (HS)2. MTLE with HS has minimal contribution from germline genetic variation3, and is associated with prior precipitating insults such as prolonged childhood seizures and head trauma4-6. Somatic variants in Ras-MAPK pathway genes were recently reported in a few MTLE surgical specimens7,8, but their prevalence, clinical relevance, and underlying biological mechanisms remain unknown. Targeted duplex sequencing of hippocampal DNA from 462 surgical resections revealed significant enrichment of deleterious somatic variants in MTLE versus controls, with >40% of MTLE specimens harboring activating Ras-MAPK variants in PTPN11, NF1, BRAF, KRAS, and twelve genes not previously associated with focal epilepsy. Eight Ras-MAPK genes showed positive clonal selection in MTLE. Increased somatic variant burden predicted worse surgical outcome. Somatic Ras-MAPK variants at ultra-low (<0.5%) variant allele fractions were associated with older seizure onset and HS pathology, supporting a late prenatal or postnatal origin. Ras-MAPK variants in MTLE were enriched in cells derived from hippocampal progenitors-neurons, astrocytes, oligodendrocytes-in line with the known neuronal hyperexcitability and seizures induced by Ras-MAPK overactivation9,10; in contrast, Alzheimer disease hippocampi exhibited microglial enrichment of Ras-MAPK variants, consistent with prior reports11. Single-nucleus RNA sequencing showed increased expression of Ras-MAPK genes in neurons and upregulation of pathways mediating neurogenesis and neural development in MTLE. Functional validation of novel, recurrent PTPN11 variants confirmed gain-of-function, while cellular modeling in induced pluripotent stem cells demonstrated proliferative/survival advantages for mutant cells in mosaic culture. Overall, our data suggest that somatic Ras-MAPK variants and acquired risk factors may converge on clonal competition in the hippocampus to modulate epilepsy risk.

Alzheimer’s disease (AD) is a neurodegenerative condition characterized by microglia-mediated neuroinflammation. Deep (>1,000×) panel sequencing of 311 brain samples revealed enrichment of somatic single-nucleotide variants (sSNVs) in cancer driver genes in AD brains, especially in genes associated with clonal hematopoiesis (CH). These sSNVs were associated with clonal expansion and carried by both microglia-like brain macrophages (MLBMs) in multiple brain regions as well as paired blood, suggesting a likely hematopoietic origin. Single-nucleus RNA sequencing data from 62 additional AD and control brains revealed increased somatic copy number variants (sCNVs) associated with CH in AD MLBMs, whereas single-cell multi-omic analyses demonstrated that sSNV- and sCNV-carrying MLBMs exhibited inflammatory and proliferative transcriptional signatures characteristic of disease-associated microglia. These signatures were recapitulated in induced pluripotent stem cell-derived microglia-like cells with TET2, ASXL1, and DNMT3A variants. These findings suggest that clonal somatic driver variants in MLBMs are enriched in AD, potentially promoting neuroinflammation and neurodegeneration.

Abstract The decision criterion is foundational to theories of decision-making, yet little is known about its neural underpinnings. In memory-based decision making, the criterion sets the minimal memory strength for something to be familiar, but whether or how it is distinctly represented from memory strength is unknown. We recorded single neurons in the medial frontal cortex (MFC) and medial temporal lobe (MTL), both implicated in memory-based decisions, while participants made decisions under different decision criteria. We identified criterion-selective (CS) neurons in the MFC that tracked the criterion regardless of memory strength, and memory-selective (MS) neurons in both regions that tracked memory strength regardless of the criterion. CS neurons signaled the criterion before MS neurons signaled memory strength, and a race model incorporating both neuron types outperformed one using MS neurons alone. These findings reveal two independent cellular substrates, one for the decision criterion and one for memory strength, whose joint activity underlies memory-based decisions.

Alzheimer disease neuropathologic change (ADNC) is considered to be the most common cause of cognitive decline and dementia worldwide. ADNC level is determined using the density of neuritic plaques in combination with the topographical distribution of β-amyloid (Aβ) plaques and hyperphosphorylated tau (p-tau)-positive neurofibrillary tangles (NFTs). While cognitive decline correlates with the level of ADNC, there remains a great deal of variation in cognitive outcomes between individuals that is unaccounted for by current neuropathologic evaluation metrics. We leveraged quantitative computer-assisted positive pixel assessments to establish the neocortical p-tau burden in the middle frontal and superior temporal gyri of 61 individuals with Braak NFT stage V who had a wide range of cognitive outcomes and trajectories. Frontal and temporal neocortical p-tau burden varied between 0.2

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by the deposition of amyloid-beta and hyperphosphorylated tau (P-tau) proteins in the brain. P-tau accumulates in neurons and is strongly associated with AD severity and affected brain regions. However, only a subset of neurons in AD exhibit tau pathology. The molecular mechanisms behind heterogeneous tau pathology and how it contributes to AD are not well understood. We developed a fluorescence-activated nuclear sorting (FANS) method to separate P-tau+ neuronal nuclei from P-tau- neuronal nuclei from the same brain tissue. To validate the specificity of P-tau+ neurons, we mixed non-AD control tissue with AD tissue and examined the origin of neuronal nuclei based on their genotype. We also subjected nuclei with P-tau signal from FANS to immunofluorescence microscopy to examine the morphology and localization of P-tau aggregates. We observed disease-specific P-tau signal for nuclei in advanced AD (Braak stage V-VI) cases. These P-tau+ nuclei are highly distinguished from the P-tau-free nuclei. Confocal immunofluorescence microscopy showed P-tau adherent to the outside of nuclei that exhibited P-tau signal by FANS. We demonstrated that the nuclei sorting method based on P-tau levels can highly enrich for P-tau+ nuclei (>380 fold) and has a high accuracy of 98% based on the mixing experiments. In addition, we were able to obtain high-quality single-cell genome amplification for P-tau-sorted nuclei using primary template-directed amplification (PTA), permitting single-nucleus genome interrogation. We developed a highly efficient method using fluorescence-activated nuclear sorting (FANS) to separate the population of P-tau+ neuronal nuclei in AD brains. This method allows interrogation of human neuronal nuclei based on single-cell tau pathology and enables single-cell genomic studies of heterogeneous tau pathology in AD, toward insight into disease pathogenesis and therapeutic targets.

Alzheimer’s disease (AD), an age-associated neurodegenerative disorder, is characterized by progressive neuronal loss and the accumulation of misfolded proteins such as amyloid-β and tau. While neuroinflammation, mediated by microglia and brain-resident macrophages, plays a pivotal role in AD pathogenesis, the intricate interactions among age, genes, and other risk factors remain elusive. Somatic mutations, known to accumulate with age, instigate clonal expansion across diverse cell types, impacting both cancer and non-cancerous conditions. Utilizing molecular-barcoded deep panel sequencing, which enables sensitive detection of somatic mutations with allele fractions as low as 0.1%, we profiled clonal somatic mutations among 149 cancer driver genes in 311 prefrontal cortex samples from AD patients and matched controls. Fluorescence-activated nuclei sorting and single-nucleus RNA sequencing were further used to study the cell-type composition and transcriptomic impact of somatic mutations. Our study unveiled an elevated occurrence of somatic single-nucleotide variants and insertions/deletions within cancer driver genes in AD brains. Recurrent somatic mutations, often multiple, were observed in genes associated with clonal hematopoiesis (CH). Remarkably, these somatic mutations were specifically enriched in CSF1R+ microglia and exhibited signals of positive selection, suggesting mutation-driven microglial clonal expansion (MiCE) in AD brains. Single-nucleus RNA sequencing of temporal neocortex samples from an additional 62 AD patients and matched controls revealed a nominal increase in mosaic chromosomal alterations (mCAs) associated with CH in AD microglia, with microglia carrying mCA exhibiting upregulated pro-inflammatory genes, resembling the transcriptomic features of the disease-associated state in AD. Our findings indicate that proliferation-related somatic mutations in microglia are prevalent in normal aging but further enriched in AD, driving MiCE and promoting inflammatory, disease-related microglial signatures. This study provides crucial insights into microglial clonal dynamics in AD, potentially paving the way for novel approaches to AD diagnosis and therapy.

The human cerebral cortex is composed of six layers and dozens of areas that are molecularly and structurally distinct 1–4 . Although single-cell transcriptomic studies have advanced the molecular characterization of human cortical development, a substantial gap exists owing to the loss of spatial context during cell dissociation 5–8 . Here we used multiplexed error-robust fluorescence in situ hybridization (MERFISH) 9 , augmented with deep-learning-based nucleus segmentation, to examine the molecular, cellular and cytoarchitectural development of the human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing more than 18 million single cells, spans eight cortical areas across seven developmental time points. We uncovered the early establishment of the six-layer structure, identifiable by the laminar distribution of excitatory neuron subtypes, 3 months before the emergence of cytoarchitectural layers. Notably, we discovered two distinct modes of cortical areal specification during mid-gestation: (1) a continuous, gradual transition observed across most cortical areas along the anterior–posterior axis and (2) a discrete, abrupt boundary specifically identified between the primary (V1) and secondary (V2) visual cortices as early as gestational week 20. This sharp binary transition in V1–V2 neuronal subtypes challenges the notion that mid-gestation cortical arealization involves only gradient-like transitions 6,10 . Furthermore, integrating single-nucleus RNA sequencing with MERFISH revealed an early upregulation of synaptogenesis in V1-specific layer 4 neurons. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This study establishes a spatially resolved single-cell analysis paradigm and paves the way for the construction of a comprehensive developmental atlas of the human brain.

Genetic information in cells flows from DNA to RNA to proteins, which form molecular machines. During normal ageing, cell intrinsic and environmental factors alter this flow of information by damaging DNA in cells, including postmitotic neurons. Damage to DNA is associated with age-related neurodegenerative diseases such as Alzheimer’s disease (AD). We previously reported an increase in DNA repair mechanisms in a fly model of AD. However, the causal mechanisms underlying somatic mutations in AD remain unclear. Here, we combine in silico methods from single-cell genomics of patients with AD with experimental validation in a Drosophila model of AD to elucidate the DNA repair processes in AD. We show that the levels of poly(ADP‒ribose) polymerase 1 (PARP1), which mediates multiple DNA damage repair pathways, are increased in the brains of patients with AD. We found that higher PARP1 levels in neurons from patients with AD are linked to increased disease risk and a greater burden of somatic mutations. Nucleotide imbalance can increase the frequency of somatic mutations upon activation of DNA repair processes. Using a fly model of AD, we identified a metabolic signature in AD animals characterised by decreased levels of phosphorylated nucleotides. Enhancing nucleotide metabolism via dietary supplementation or genetic manipulation protects against AD pathology in animals. Finally, Mendelian randomisation revealed that higher expression of human deoxyguanosine kinase (DGUOK) is linked to a lower risk of developing AD. Our results suggest that enhancing nucleotide metabolism could improve DNA repair and serve as an adjunct therapy to delay AD progression.

Background:Alternative splicing of the MAPT gene produces distinct tau isoforms in the central and peripheral nervous systems (CNS and PNS), yet their respective biological and pathological roles remain poorly understood. Recent studies suggest that CNS-tau may play a key role in amyloid-β associated neurodegeneration in Alzheimer's disease (AD), but the absence of isoform-specific tools has limited both mechanistic insight and biomarker development. We aimed to develop and validate CNS-tau-specific monoclonal antibodies and assess their utility in neuropathology and fluid-based biomarker assays across AD and primary tauopathies. Methods:We generated six recombinant rabbit monoclonal antibodies targeting a CNS-tau-specific sequence encoded by exons 4 and 5. Specificity and affinity were evaluated via biolayer interferometry, immunoblotting, and tau-expressing HEK293 models. The lead clone, LL-T-1-1, was tested in postmortem brain sections from AD (n = 23), progressive supranuclear palsy (PSP, n = 3), and corticobasal degeneration (CBD, n = 3). A second clone, LL-T-1-5, was optimized for use in plasma assays via an ultrasensitive nanoneedle platform, LoD < 1 pg/ml. Results:LL-T-1-1 showed nanomolar affinity for CNS-tau and no cross-reactivity with PNS-tau. It selectively labeled dystrophic neurites in AD and all hallmark tau lesions in PSP and CBD without antigen retrieval. LL-T-1-5-based plasma assays revealed CNS-tau levels significantly correlated with cognitive scores (MMSE and QDRS) and differentiated impaired from unimpaired individuals. Conclusions:CNS-tau-specific antibodies LL-T-1-1 and LL-T-1-5 provide new tools for neuropathology and fluid biomarker development across tauopathies.

The dynamic integration of the lateralized and specialized capacities of the two cerebral hemispheres constitutes a hallmark feature of human brain function. This interhemispheric exchange of information critically depends upon the corpus callosum. Classical anatomical descriptions of callosal organization outline a topographic gradient from front to back, such that specific transcallosal fibers support distinct aspects of integrated brain function. Here, we present a challenge to this conventional model. Using neuroimaging data obtained from a new cohort of adult corpus callosotomy patients, we leverage modern network neuroscience techniques to show that full interhemispheric integration can be achieved via a small proportion of posterior callosal fibers. Partial callosotomy patients with spared callosal fibers retained widespread patterns of interhemispheric functional connectivity and showed no signs of behavioral disconnection, even with only 1 cm of the splenium intact. Conversely, only complete callosotomy patients demonstrated sweeping disruptions of interhemispheric network architectures, aligning with disconnection syndromes long-thought to reflect diminished information propagation and communication across the brain. These findings motivate an evolving mechanistic understanding of synchronized interhemispheric neural activity for large-scale human brain function and behavior.