Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes.

Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.

Somatic genomic changes in single Alzheimer's disease neurons.

Dementia in Alzheimer's disease progresses alongside neurodegeneration1-4, but the specific events that cause neuronal dysfunction and death remain poorly understood. During normal ageing, neurons progressively accumulate somatic mutations5 at rates similar to those of dividing cells6,7 which suggests that genetic factors, environmental exposures or disease states might influence this accumulation5. Here we analysed single-cell whole-genome sequencing data from 319 neurons from the prefrontal cortex and hippocampus of individuals with Alzheimer's disease and neurotypical control individuals. We found that somatic DNA alterations increase in individuals with Alzheimer's disease, with distinct molecular patterns. Normal neurons accumulate mutations primarily in an age-related pattern (signature A), which closely resembles 'clock-like' mutational signatures that have been previously described in healthy and cancerous cells6-10. In neurons affected by Alzheimer's disease, additional DNA alterations are driven by distinct processes (signature C) that highlight C>A and other specific nucleotide changes. These changes potentially implicate nucleotide oxidation4,11, which we show is increased in Alzheimer's-disease-affected neurons in situ. Expressed genes exhibit signature-specific damage, and mutations show a transcriptional strand bias, which suggests that transcription-coupled nucleotide excision repair has a role in the generation of mutations. The alterations in Alzheimer's disease affect coding exons and are predicted to create dysfunctional genetic knockout cells and proteostatic stress. Our results suggest that known pathogenic mechanisms in Alzheimer's disease may lead to genomic damage to neurons that can progressively impair function. The aberrant accumulation of DNA alterations in neurodegeneration provides insight into the cascade of molecular and cellular events that occurs in the development of Alzheimer's disease.

Glial dysregulation in the human brain in fragile X-associated tremor/ataxia syndrome.

Short trinucleotide expansions at the FMR1 locus are associated with the late-onset condition fragile X-associated tremor/ataxia syndrome (FXTAS), which shows very different clinical and pathological features from fragile X syndrome (associated with longer expansions), with no clear molecular explanation for these marked differences. One prevailing theory posits that the shorter, premutation expansion uniquely causes extreme neurotoxic increases in FMR1 mRNA (i.e., four to eightfold increases), but evidence to support this hypothesis is largely derived from analysis of peripheral blood. We applied single-nucleus RNA sequencing to postmortem frontal cortex and cerebellum from 7 individuals with premutation and matched controls (n = 6) to assess cell type-specific molecular neuropathology. We found only modest upregulation (~1.3-fold) of FMR1 in some glial populations associated with premutation expansions. In premutation cases, we also identified decreased astrocyte proportions in the cortex. Differential expression and gene ontology analysis demonstrated altered neuroregulatory roles of glia. Using network analyses, we identified cell type-specific and region-specific patterns of FMR1 protein target gene dysregulation unique to premutation cases, with notable network dysregulation in the cortical oligodendrocyte lineage. We used pseudotime trajectory analysis to determine how oligodendrocyte development was altered and identified differences in early gene expression in oligodendrocyte trajectories in premutation cases specifically, implicating early cortical glial developmental perturbations. These findings challenge dogma regarding extremely elevated FMR1 increases in FXTAS and implicate glial dysregulation as a critical facet of premutation pathophysiology, representing potential unique therapeutic targets directly derived from the human condition.

Brain Somatic Mutation in Aging and Alzheimer's Disease.

Somatic mutations arise postzygotically, producing genetic differences between cells in an organism. Well established as a driver of cancer, somatic mutations also exist in nonneoplastic cells, including in the brain. Technological advances in nucleic acid sequencing have enabled recent breakthroughs that illuminate the roles of somatic mutations in aging and degenerative diseases of the brain. Somatic mutations accumulate during aging in human neurons, a process termed genosenium. A number of recent studies have examined somatic mutations in Alzheimer's disease (AD), primarily from the perspective of genes causing familial AD. We have also gained new information on genome-wide mutations, providing insights into the cellular events driving somatic mutation and cellular dysfunction. This review highlights recent concepts, methods, and findings in the progress to understand the role of brain somatic mutation in aging and AD.

Neuropathologically directed profiling of PRNP somatic and germline variants in sporadic human prion disease.

Creutzfeldt-Jakob Disease (CJD), the most common human prion disease, is associated with pathologic misfolding of the prion protein (PrP), encoded by the PRNP gene. Of human prion disease cases, < 1% were transmitted by misfolded PrP, ~ 15% are inherited, and ~ 85% are sporadic (sCJD). While familial cases are inherited through germline mutations in PRNP, the cause of sCJD is unknown. Somatic mutations have been hypothesized as a cause of sCJD, and recent studies have revealed that somatic mutations accumulate in neurons during aging. To investigate the hypothesis that somatic mutations in PRNP may underlie sCJD, we performed deep DNA sequencing of PRNP in 205 sCJD cases and 170 age-matched non-disease controls. We included 5 cases of Heidenhain variant sporadic CJD (H-sCJD), where visual symptomatology and neuropathology implicate localized initiation of prion formation, and examined multiple regions across the brain including in the affected occipital cortex. We employed Multiple Independent Primer PCR Sequencing (MIPP-Seq) with a median depth of > 5000× across the PRNP coding region and analyzed for variants using MosaicHunter. An allele mixing experiment showed positive detection of variants in bulk DNA at a variant allele fraction (VAF) as low as 0.2%. We observed multiple polymorphic germline variants among individuals in our cohort. However, we did not identify bona fide somatic variants in sCJD, including across multiple affected regions in H-sCJD, nor in control individuals. Beyond our stringent variant-identification pipeline, we also analyzed VAFs from raw sequencing data, and observed no evidence of prion disease enrichment for the known germline pathogenic variants P102L, D178N, and E200K. The lack of PRNP pathogenic somatic mutations in H-sCJD or the broader cohort of sCJD suggests that clonal somatic mutations may not play a major role in sporadic prion disease. With H-sCJD representing a localized presentation of neurodegeneration, this serves as a test of the potential role of clonal somatic mutations in genes known to cause familial neurodegeneration.

Widespread frontoparietal fMRI activity is greatly affected by changes in criterion placement, not discriminability, during recognition memory and visual detection tests.

Widespread frontoparietal activity is consistently observed in recognition memory tests that compare studied ("target") versus unstudied ("nontarget") responses. However, there are conflicting accounts that ascribe various aspects of frontoparietal activity to mnemonic evidence versus decisional processes. According to Signal Detection Theory, recognition judgments require individuals to decide whether the memory strength of an item exceeds an evidence threshold-the decision criterion-for reporting previously studied items. Yet, most fMRI studies fail to manipulate both memory strength and decision criteria, making it difficult to appropriately identify frontoparietal activity associated with each process. In the current experiment, we manipulated both discriminability and decision criteria across recognition memory and visual detection tests during fMRI scanning to assess how frontoparietal activity is affected by each manipulation. Our findings revealed that maintaining a conservative versus liberal decision criterion drastically affects frontoparietal activity in target versus nontarget response contrasts for both recognition memory and visual detection tests. However, manipulations of discriminability showed virtually no differences in frontoparietal activity in target versus nontarget response or item contrasts. Comparing across task domains, we observed similar modulations of frontoparietal activity across criterion conditions, though the recognition memory task revealed larger activations in both magnitude and spatial extent in these contrasts. Nonetheless, there appears to be some domain specificity in frontoparietal activity associated with the maintenance of a conservative versus liberal criterion. We propose that widespread frontoparietal activity observed in target versus nontarget contrasts is largely attributable to response bias where increased activity may reflect inhibition of a prepotent response, which differs depending on whether a person maintains a conservative versus liberal decision criterion.

A calcium-sensitive antibody isolates soluble amyloid-ß aggregates and fibrils from Alzheimer's disease brain.

Aqueously soluble oligomers of amyloid-ß peptide may be the principal neurotoxic forms of amyloid-ß in Alzheimer's disease, initiating downstream events that include tau hyperphosphorylation, neuritic/synaptic injury, microgliosis and neuron loss. Synthetic oligomeric amyloid-ß has been studied extensively, but little is known about the biochemistry of natural oligomeric amyloid-ß in human brain, even though it is more potent than simple synthetic peptides and comprises truncated and modified amyloid-ß monomers. We hypothesized that monoclonal antibodies specific to neurotoxic oligomeric amyloid-ß could be used to isolate it for further study. Here we report a unique human monoclonal antibody (B24) raised against synthetic oligomeric amyloid-ß that potently prevents Alzheimer's disease brain oligomeric amyloid-ß-induced impairment of hippocampal long-term potentiation. B24 binds natural and synthetic oligomeric amyloid-ß and a subset of amyloid plaques, but only in the presence of Ca2+. The amyloid-ß N terminus is required for B24 binding. Hydroxyapatite chromatography revealed that natural oligomeric amyloid-ß is highly avid for Ca2+. We took advantage of the reversible Ca2+-dependence of B24 binding to perform non-denaturing immunoaffinity isolation of oligomeric amyloid-ß from Alzheimer's disease brain-soluble extracts. Unexpectedly, the immunopurified material contained amyloid fibrils visualized by electron microscopy and amenable to further structural characterization. B24-purified human oligomeric amyloid-ß inhibited mouse hippocampal long-term potentiation. These findings identify a calcium-dependent method for purifying bioactive brain oligomeric amyloid-ß, at least some of which appears fibrillar.

Genome-wide association study identifies 74 loci associated with educational attainment.

Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.

Atraumatic removal of a zirconia-framework fixed partial denture using an Er,Cr:YSGG laser: a case report.

A 3-unit fixed partial denture spanning the maxillary left central incisor, lateral incisor, and canine was fabricated with a zirconia framework and a pontic veneered with porcelain to replace the maxillary left lateral incisor. The prosthesis was attached to the abutment teeth using lingual wings that sat in preparations approximately 1.5 mm deep axially. When the veneering porcelain on the pontic developed a void 5 months after cementation, the patient was offered 3 options to eliminate the defect: (1) restoration with composite resin; (2) destructive removal of the prosthesis followed by fabrication of a replacement; or (3) attempted nondestructive removal of the prosthesis with an erbium, chromium-doped: yttrium-scandium-gallium-garnet (Er,Cr:YSGG) laser followed by laboratory repair of the void with low-fusing porcelain. The patient selected the third option. The laser was set to 3 W, 20 Hz, 50% air, and 50% water using the turbo handpiece with a 700-µm-diameter tip, per the manufacturer's recommendations. The Er,Cr:YSGG laser operates in a noncontact mode at an ideal distance of 3 to 5 mm from the target tissue, in this case, the lingual surfaces of the maxillary left central incisor and canine. No anesthetic was administered to the patient. The laser beam was applied to the wings of the prosthesis intermittently for 8 cycles at a maximum of 60 seconds per cycle. During irradiation, the handpiece moved side-to-side in a scanning motion. Darkening of the cement was observed under the wing on the central incisor, indicating the initial disruption of the adhesive seal. Slight torquing pressure was applied using specially designed crown removal pliers, and the prosthesis was removed atraumatically. The recovered prosthesis was repaired with low-fusing porcelain and adhesively luted. Atraumatic debonding of a high-strength ceramic can be predictably performed with the Er,Cr:YSGG laser when appropriate settings are used.

Functional reorganization of brain networks across the human menstrual cycle.

The brain is an endocrine organ, sensitive to the rhythmic changes in sex hormone production that occurs in most mammalian species. In rodents and nonhuman primates, estrogen and progesterone's impact on the brain is evident across a range of spatiotemporal scales. Yet, the influence of sex hormones on the functional architecture of the human brain is largely unknown. In this dense-sampling, deep phenotyping study, we examine the extent to which endogenous fluctuations in sex hormones alter intrinsic brain networks at rest in a woman who underwent brain imaging and venipuncture for 30 consecutive days. Standardized regression analyses illustrate estrogen and progesterone's widespread associations with functional connectivity. Time-lagged analyses examined the temporal directionality of these relationships and suggest that cortical network dynamics (particularly in the Default Mode and Dorsal Attention Networks, whose hubs are densely populated with estrogen receptors) are preceded-and perhaps driven-by hormonal fluctuations. A similar pattern of associations was observed in a follow-up study one year later. Together, these results reveal the rhythmic nature in which brain networks reorganize across the human menstrual cycle. Neuroimaging studies that densely sample the individual connectome have begun to transform our understanding of the brain's functional organization. As these results indicate, taking endocrine factors into account is critical for fully understanding the intrinsic dynamics of the human brain.

Identification of Common Genetic Variants Influencing Spontaneous Dizygotic Twinning and Female Fertility.

Spontaneous dizygotic (DZ) twinning occurs in 1%-4% of women, with familial clustering and unknown physiological pathways and genetic origin. DZ twinning might index increased fertility and has distinct health implications for mother and child. We performed a GWAS in 1,980 mothers of spontaneous DZ twins and 12,953 control subjects. Findings were replicated in a large Icelandic cohort and tested for association across a broad range of fertility traits in women. Two SNPs were identified (rs11031006 near FSHB, p = 1.54 × 10(-9), and rs17293443 in SMAD3, p = 1.57 × 10(-8)) and replicated (p = 3 × 10(-3) and p = 1.44 × 10(-4), respectively). Based on ∼90,000 births in Iceland, the risk of a mother delivering twins increased by 18% for each copy of allele rs11031006-G and 9% for rs17293443-C. A higher polygenic risk score (PRS) for DZ twinning, calculated based on the results of the DZ twinning GWAS, was significantly associated with DZ twinning in Iceland (p = 0.001). A higher PRS was also associated with having children (p = 0.01), greater lifetime parity (p = 0.03), and earlier age at first child (p = 0.02). Allele rs11031006-G was associated with higher serum FSH levels, earlier age at menarche, earlier age at first child, higher lifetime parity, lower PCOS risk, and earlier age at menopause. Conversely, rs17293443-C was associated with later age at last child. We identified robust genetic risk variants for DZ twinning: one near FSHB and a second within SMAD3, the product of which plays an important role in gonadal responsiveness to FSH. These loci contribute to crucial aspects of reproductive capacity and health.

Does intrinsic reward motivate cognitive control? a naturalistic-fMRI study based on the synchronization theory of flow.

Cognitive control is a framework for understanding the neuropsychological processes that underlie the successful completion of everyday tasks. Only recently has research in this area investigated motivational contributions to control allocation. An important gap in our understanding is the way in which intrinsic rewards associated with a task motivate the sustained allocation of control. To address this issue, we draw on flow theory, which predicts that a balance between task difficulty and individual ability results in the highest levels of intrinsic reward. In three behavioral and one functional magnetic resonance imaging studies, we used a naturalistic and open-source video game stimulus to show that changes in the balance between task difficulty and an individual's ability to perform the task resulted in different levels of intrinsic reward, which is associated with different brain states. Specifically, psychophysiological interaction analyses show that high levels of intrinsic reward associated with a balance between task difficulty and individual ability are associated with increased functional connectivity between key structures within cognitive control and reward networks. By comparison, a mismatch between task difficulty and individual ability is associated with lower levels of intrinsic reward and corresponds to increased activity within the default mode network. These results suggest that intrinsic reward motivates cognitive control allocation.

Cross-task and cross-manipulation stability in shifting the decision criterion.

In recognition memory experiments participants must discriminate between old and new items, a judgment influenced by response bias. Research has shown substantial individual differences in the extent to which people will strategically adjust their response bias to diagnostic cues such as the prior probability of an old item. Despite this significant between subject variability, shifts in bias have been found to be relatively predictive within individuals across memory tests. Experiment 1 sought to determine whether this predictability extends beyond memory. Results revealed that the amount a subject shifted response bias in a recognition memory task was significantly predictive of shifting in a visual perception task, suggesting that shifting can generalise outside of a specific testing domain. Experiment 2 sought to determine how predictive shifting would be across two manipulations well known to induce shifts in bias: a probability manipulation and a response payoff manipulation. A modest positive relationship between these two methods was observed, suggesting that shifting behaviour is relatively predictive across different manipulations of shifting. Overall, results from both experiments suggest that response bias shifting, like response bias setting, is a relatively stable behaviour within individuals despite changes in test domain and test manipulation.

Age-dependent changes in task-based modular organization of the human brain.

As humans age, cognition and behavior change significantly, along with associated brain function and organization. Aging has been shown to decrease variability in functional magnetic resonance imaging (fMRI) signals, and to affect the modular organization of human brain function. In this work, we use complex network analysis to investigate the dynamic community structure of large-scale brain function, asking how evolving communities interact with known brain systems, and how the dynamics of communities and brain systems are affected by age. We analyze dynamic networks derived from fMRI scans of 104 human subjects performing a word memory task, and determine the time-evolving modular structure of these networks by maximizing the multislice modularity, thereby identifying distinct communities, or sets of brain regions with strong intra-set functional coherence. To understand how community structure changes over time, we examine the number of communities as well as the flexibility, or the likelihood that brain regions will switch between communities. We find a significant positive correlation between age and both these measures: younger subjects tend to have less fragmented and more coherent communities, and their brain regions tend to change communities less often during the memory task. We characterize the relationship of community structure to known brain systems by the recruitment coefficient, or the probability of a brain region being grouped in the same community as other regions in the same system. We find that regions associated with cingulo-opercular, somatosensory, ventral attention, and subcortical circuits have a significantly higher recruitment coefficient in younger subjects. This indicates that the within-system functional coherence of these specific systems during the memory task declines with age. Such a correspondence does not exist for other systems (e.g. visual and default mode), whose recruitment coefficients remain relatively uniform across ages. These results confirm that the dynamics of functional community structure vary with age, and demonstrate methods for investigating how aging differentially impacts the functional organization of different brain systems.

A Structural and Functional Comparison Between Infectious and Non-Infectious Autocatalytic Recombinant PrP Conformers.

Infectious prions contain a self-propagating, misfolded conformer of the prion protein termed PrPSc. A critical prediction of the protein-only hypothesis is that autocatalytic PrPSc molecules should be infectious. However, some autocatalytic recombinant PrPSc molecules have low or undetectable levels of specific infectivity in bioassays, and the essential determinants of recombinant prion infectivity remain obscure. To identify structural and functional features specifically associated with infectivity, we compared the properties of two autocatalytic recombinant PrP conformers derived from the same original template, which differ by >105-fold in specific infectivity for wild-type mice. Structurally, hydrogen/deuterium exchange mass spectrometry (DXMS) studies revealed that solvent accessibility profiles of infectious and non-infectious autocatalytic recombinant PrP conformers are remarkably similar throughout their protease-resistant cores, except for two domains encompassing residues 91-115 and 144-163. Raman spectroscopy and immunoprecipitation studies confirm that these domains adopt distinct conformations within infectious versus non-infectious autocatalytic recombinant PrP conformers. Functionally, in vitro prion propagation experiments show that the non-infectious conformer is unable to seed mouse PrPC substrates containing a glycosylphosphatidylinositol (GPI) anchor, including native PrPC. Taken together, these results indicate that having a conformation that can be specifically adopted by post-translationally modified PrPC molecules is an essential determinant of biological infectivity for recombinant prions, and suggest that this ability is associated with discrete features of PrPSc structure.

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan.

Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task") consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory"), in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.