PIGG variant pathogenicity assessment reveals characteristic features within 19 families.

PURPOSE: Phosphatidylinositol Glycan Anchor Biosynthesis, class G (PIGG) is an ethanolamine phosphate transferase catalyzing the modification of glycosylphosphatidylinositol (GPI). GPI serves as an anchor on the cell membrane for surface proteins called GPI-anchored proteins (GPI-APs). Pathogenic variants in genes involved in the biosynthesis of GPI cause inherited GPI deficiency (IGD), which still needs to be further characterized. METHODS: We describe 22 individuals from 19 unrelated families with biallelic variants in PIGG. We analyzed GPI-AP surface levels on granulocytes and fibroblasts for three and two individuals, respectively. We demonstrated enzymatic activity defects for PIGG variants in vitro in a PIGG/PIGO double knockout system. RESULTS: Phenotypic analysis of reported individuals reveals shared PIGG deficiency-associated features. All tested GPI-APs were unchanged on granulocytes whereas CD73 level in fibroblasts was decreased. In addition to classic IGD symptoms such as hypotonia, intellectual disability/developmental delay (ID/DD), and seizures, individuals with PIGG variants of null or severely decreased activity showed cerebellar atrophy, various neurological manifestations, and mitochondrial dysfunction, a feature increasingly recognized in IGDs. Individuals with mildly decreased activity showed autism spectrum disorder. CONCLUSION: This in vitro system is a useful method to validate the pathogenicity of variants in PIGG and to study PIGG physiological functions.

Exomic variants of an elderly cohort of Brazilians in the ABraOM database.

Brazilians are highly admixed with ancestry from Europe, Africa, America, and Asia and yet still underrepresented in genomic databanks. We hereby present a collection of exomic variants from 609 elderly Brazilians in a census-based cohort (SABE609) with comprehensive phenotyping. Variants were deposited in ABraOM (Online Archive of Brazilian Mutations), a Web-based public database. Population representative phenotype and genotype repositories are essential for variant interpretation through allele frequency filtering; since elderly individuals are less likely to harbor pathogenic mutations for early- and adult-onset diseases, such variant databases are of great interest. Among the over 2.3 million variants from the present cohort, 1,282,008 were high-confidence calls. Importantly, 207,621 variants were absent from major public databases. We found 9,791 potential loss-of-function variants with about 300 mutations per individual. Pathogenic variants on clinically relevant genes (ACMG) were observed in 1.15% of the individuals and were correlated with clinical phenotype. We conducted incidence estimation for prevalent recessive disorders based upon heterozygous frequency and concluded that it relies on appropriate pathogenicity assertion. These observations illustrate the relevance of collecting demographic data from diverse, poorly characterized populations. Census-based datasets of aged individuals with comprehensive phenotyping are an invaluable resource toward the improved understanding of variant pathogenicity.

Morphological affinities of Homo naledi with other Plio-Pleistocene hominins: a phenetic approach.

Recent fossil material found in Dinaledi Chamber, South Africa, was initially described as a new species of genus Homo, namely Homo naledi. The original study of this new material has pointed to a close proximity with Homo erectus. More recent investigations have, to some extent, confirmed this assignment. Here we present a phenetic analysis based on dentocranial metric variables through Principal Components Analysis and Cluster Analysis based on these fossils and other Plio-Pleistocene hominins. Our results concur that the Dinaledi fossil hominins pertain to genus Homo. However, in our case, their nearest neighbors are Homo habilis and Australopithecus sediba. We suggest that Homo naledi is in fact a South African version of Homo habilis, and not a new species. This can also be applied to Australopithecus sediba.

The cranial morphology of the Botocudo Indians, Brazil.

The Botocudo Indians were hunter-gatherer groups that occupied the East-Central regions of Brazil decimated during the colonial period in the country. During the 19th century, craniometric studies suggested that the Botocudo resembled more the Paleoamerican population of Lagoa Santa than typical Native Americans groups. These results suggest that the Botocudo Indians might represent a population that retained the biological characteristics of early groups of the continent, remaining largely isolated from groups that gave origin to the modern Native South American variation. Moreover, recently, some of the Botocudo remains have been shown to have mitochondrial and autosomal DNA lineages currently found in Polynesian populations. Here, we explore the morphological affinities of Botocudo skulls within a worldwide context. Distinct multivariate analyses based on 32 craniometric variables show that 1) the two individuals with Polynesian DNA sequences have morphological characteristics that fall within the Polynesian and Botocudo variation, making their assignation as Native American specimens problematic, and 2) there are high morphological affinities between Botocudo, Early Americans, and the Polynesian series of Easter Island, which support the early observations that the Botocudo can be seen as retaining the Paleoamerican morphology, particularly when the neurocranium is considered. Although these results do not elucidate the origin of the Polynesian DNA lineages among the Botocudo, they support the hypothesis that the Botocudo represent a case of late survival of ancient Paleoamerican populations, retaining the morphological characteristics of ancestral Late Pleistocene populations from Asia.

Cranial morphological diversity of early, middle, and late Holocene Brazilian groups: implications for human dispersion in Brazil.

The history of human occupation in Brazil dates to at least 14 kyr BP, and the country has the largest record of early human remains from the continent. Despite the importance and richness of Brazilian human skeletal collections, the biological relationships between groups and their implications for knowledge about human dispersion in the country have not been properly explored. Here, we present a comprehensive assessment of the morphological affinities of human groups from East-Central, Coastal, Northeast, and South Brazil from distinct periods and test for the best dispersion scenarios to explain the observed diversity across time. Our results, based on multivariate assessments of shape and goodness of fit tests of dispersion and adaptation models, favor the idea that Brazil experienced at least two large dispersion waves. The first dispersive event brought the morphological pattern that characterize Late Pleistocene groups continent-wide and that persisted among East-Central Brazil groups until recently. Within the area covered by our samples, the second wave was probably restricted to the coast and is associated with a distinct morphological pattern. Inland and coastal populations apparently did not interact significantly during the Holocene, as there is no clear signal of admixture between groups sharing the two morphological patterns. However, these results cannot be extended to the interior part of the country (Amazonia and Central Brazil), given the lack of skeletal samples in these regions.

Automated preprocessing and phase-amplitude coupling analysis of scalp EEG discriminates infantile spasms from controls during wakefulness.

OBJECTIVE: Delta-gamma phase-amplitude coupling in EEG is useful for localizing epileptic sources and to evaluate severity in children with infantile spasms. We (1) develop an automated EEG preprocessing pipeline to clean data using artifact subspace reconstruction (ASR) and independent component (IC) analysis (ICA) and (2) evaluate delta-gamma modulation index (MI) as a method to distinguish children with epileptic spasms (cases) from normal controls during sleep and awake. METHODS: Using 400 scalp EEG datasets (200 sleep, 200 awake) from 100 subjects, we calculated MI after applying high-pass and line-noise filters (Clean 0), and after ASR followed by either conservative (Clean 1) or stringent (Clean 2) artifactual IC rejection. Classification of cases and controls using MI was evaluated with Receiver Operating Characteristics (ROC) to obtain area under curve (AUC). RESULTS: The artifact rejection algorithm reduced raw signal variance by 29-45% and 38-60% for Clean 1 and Clean 2, respectively. MI derived from sleep data, with or without preprocessing, robustly classified the groups (all AUC > 0.98). In contrast, group classification using MI derived from awake data was successful only after Clean 2 (AUC = 0.85). CONCLUSIONS: We have developed an automated EEG preprocessing pipeline to perform artifact rejection and quantify delta-gamma modulation index.

Interictal scalp fast ripple occurrence and high frequency oscillation slow wave coupling in epileptic spasms.

OBJECTIVE: Intracranial high frequency oscillation (HFO) occurrence rate (OR) and slow wave activity (SWA) coupling are potential markers of epileptogenicity in epileptic spasms (ES). Scalp ripple (R) detection and SWA coupling have been described in ES; however, the feasibility of scalp fast ripple (FR) detection and measurement of scalp FR coupling to SWA is not known. We evaluated interictal scalp R and FR OR and SWA coupling in pre-treatment EEG in children with short-term treatment-refractory ES compared to short-term treatment non-refractory ES. METHODS: We retrospectively identified children with ES and identified HFOs using a semi-automated HFO detector on pre-treatment scalp EEG during sleep. We evaluated HFO OR and event-triggered modulation index (MI) to quantify R (100-250 Hz) and FR (250-600 Hz) coupling strength with different SWA passbands (0.5-1, 1-2, 2-3, 3-4, and 4-8 Hz). We used HFO phasor transform and circular statistics to evaluate phase coupling angle distributions. RESULTS: We identified 15 children with ES with pre-treatment EEG recorded at 2000 Hz. Thirteen out of 15 patients had HFOs and were included for analysis. There were six treatment responders and seven nonresponders three months after treatment initiation. Responders and nonresponders were similar in age (6.1 vs 7.2 mo), ES diagnosis duration (0.7 vs 2.6 mo), and HFO OR (R: 1.07 vs 2.30/min, FR: 0.43 vs 1.96/min). No differences between responders and nonresponders were seen in HFO MI at different SWA. Coupling of R and FR to 2-3 Hz SWA demonstrated increased incidence rate ratio in nonresponders relative to responders at distinct phase coupling angle distributions. CONCLUSIONS: This study demonstrates the feasibility of interictal scalp R and FR detection and quantification of scalp R and FR coupling to SWA in ES. SIGNIFICANCE: HFO phase coupling with SWA may be useful as a marker of potential treatment refractoriness in patients with ES.

Scalp EEG interictal high frequency oscillations as an objective biomarker of infantile spasms.

OBJECTIVE: To investigate the diagnostic utility of high frequency oscillations (HFOs) via scalp electroencephalogram (EEG) in infantile spasms. METHODS: We retrospectively analyzed interictal slow-wave sleep EEGs sampled at 2,000 Hz recorded from 30 consecutive patients who were suspected of having infantile spasms. We measured the rate of HFOs (80-500 Hz) and the strength of the cross-frequency coupling between HFOs and slow-wave activity (SWA) at 3-4 Hz and 0.5-1 Hz as quantified with modulation indices (MIs). RESULTS: Twenty-three patients (77%) exhibited active spasms during the overnight EEG recording. Although the HFOs were detected in all children, increased HFO rate and MIs correlated with the presence of active spasms (p < 0.001 by HFO rate; p < 0.01 by MIs at 3-4 Hz; p = 0.02 by MIs at 0.5-1 Hz). The presence of active spasms was predicted by the logistic regression models incorporating HFO-related metrics (AUC: 0.80-0.98) better than that incorporating hypsarrhythmia (AUC: 0.61). The predictive performance of the best model remained favorable (87.5% accuracy) after a cross-validation procedure. CONCLUSIONS: Increased rate of HFOs and coupling between HFOs and SWA are associated with active epileptic spasms. SIGNIFICANCE: Scalp-recorded HFOs may serve as an objective EEG biomarker for active epileptic spasms.

Prospective observational study: Fast ripple localization delineates the epileptogenic zone.

OBJECTIVE: To investigate spatial correlation between interictal HFOs and neuroimaging abnormalities, and to determine if complete removal of prospectively identified interictal HFOs correlates with post-surgical seizure-freedom. METHODS: Interictal fast ripples (FRs: 250-500 Hz) in 19 consecutive children with pharmacoresistant focal epilepsy who underwent extra-operative electrocorticography (ECoG) recording were prospectively analyzed. The interictal FRs were sampled at 2000 Hz and were visually identified during 10 min of slow wave sleep. Interictal FRs, MRI and FDG-PET were delineated on patient-specific reconstructed three-dimensional brain MRI. RESULTS: Interictal FRs were observed in all patients except one. Thirteen out of 18 patients (72%) exhibited FRs beyond the extent of neuroimaging abnormalities. Fifteen of 19 children underwent resective surgery, and survival analysis with log-rank test demonstrated that complete resection of cortical sites showing interictal FRs correlated with longer post-operative seizure-freedom (p < 0.01). Complete resection of seizure onset zones (SOZ) also correlated with longer post-operative seizure-freedom (p = 0.01), yet complete resection of neuroimaging abnormalities did not (p = 0.43). CONCLUSIONS: Prospective visual analysis of interictal FRs was feasible, and it seemed to accurately localize epileptogenic zones. SIGNIFICANCE: Topological extent of epileptogenic region may exceed what is discernible by multimodal neuroimaging.

Interrater reliability in visual identification of interictal high-frequency oscillations on electrocorticography and scalp EEG.

High-frequency oscillations (HFOs), including ripples (Rs) and fast ripples (FRs), are promising biomarkers of epileptogenesis, but their clinical utility is limited by the lack of a standardized approach to identification. We set out to determine whether electroencephalographers experienced in HFO analysis can reliably identify and quantify interictal HFOs. Two blinded raters independently reviewed 10 intraoperative electrocorticography (ECoG) samples from epilepsy surgery cases, and 10 scalp EEG samples from epilepsy monitoring unit evaluations. HFOs were visually marked using bandpass filters (R, 80-250 Hz; FR, 250-500 Hz) with a sampling frequency of 2,000 Hz. There was agreement as to the presence or absence of epileptiform discharges (EDs), Rs, and FRs, in 17, 18, and 18 cases, respectively. Interrater reliability (IRR) was favorable with κ = 0.70, 0.80, and 0.80, respectively, and similar for ECoG and scalp electroencephalography (EEG). Furthermore, interclass correlation for rates of Rs (0.99, 95% confidence interval [CI] 0.96-0.99) and FRs (0.77, 95% CI 0.41-0.91) were superior in comparison to EDs (0.37, 95% CI -0.60 to 0.75). Our data suggest that HFO identification and quantification are reliable among experienced electroencephalographers. Our findings support the reliability of utilizing HFO data in both research and clinical arenas.

Automated Detection of High Frequency Oscillations in Human Scalp Electroencephalogram.

High frequency oscillations (HFOs) > 80 Hz are a promising biomarker of epileptic tissue. Recent evidence has shown that spontaneous HFOs can be recorded from the scalp, but detection of these electrographic events remains a challenge. Here, we modified a simple automatic detector, used originally for intracranial EEG (iEEG) recordings, to detect ripples and fast ripples in scalp EEG. We analyzed scalp EEG recordings of seven subjects and validated our detector and artifact rejection algorithm via visual review. Of the candidate events marked by the detector, 40% and 60% were confirmed to be ripples and fast ripples, respectively, by human visual review, making this algorithm suitable for supervised detection. Detected HFOs occurred at a rate of <1/min in most channels, and the average duration was 47 and 24 ms for ripples and fast ripples, respectively. The simplicity of the algorithm, with only a single parameter, enables the consistent application of automatic detection across recording modalities, and it could therefore be a tool for the assessment and localization of epileptic activity.

Visual and semi-automatic non-invasive detection of interictal fast ripples: A potential biomarker of epilepsy in children with tuberous sclerosis complex.

OBJECTIVES: We aim to establish that interictal fast ripples (FR; 250-500 Hz) are detectable on scalp EEG, and to investigate their association to epilepsy. METHODS: Scalp EEG recordings of a subset of children with tuberous sclerosis complex (TSC)-associated epilepsy from two large multicenter observational TSC studies were analyzed and compared to control children without epilepsy or any other brain-based diagnoses. FR were identified both by human visual review and compared with semi-automated review utilizing a deep learning-based FR detector. RESULTS: Seven out of 7 children with TSC-associated epilepsy had scalp FR compared to 0 out of 4 children in the control group (p = 0.003). The automatic detector has a sensitivity of 98% and false positive rate with average of 11.2 false positives per minute. CONCLUSIONS: Non-invasive detection of interictal scalp FR was feasible, by both visual and semi-automatic detection. Interictal scalp FR occurred exclusively in children with TSC-associated epilepsy and were absent in controls without epilepsy. The proposed detector achieves high sensitivity of FR detection; however, expert review of the results to reduce false positives is advised. SIGNIFICANCE: Interictal FR are detectable on scalp EEG and may potentially serve as a biomarker of epilepsy in children with TSC.

Toxoplasmic encephalitis during mycophenolate mofetil immunotherapy of neuromuscular disease.

OBJECTIVE: To show that immunotherapy with medications such mycophenolate mofetil (MMF) can cause serious complications in patients with neuromuscular disorders. METHODS: Two patients with neuromuscular disorders on immunotherapy with long-term MMF who developed toxoplasmic encephalitis (TE) were included in this case series. RESULTS: One patient with myasthenia gravis and one patient with inflammatory myopathy on immunotherapy with long-term MMF developed severe TE. Diagnosis was based on clinical presentation, MRI brain imaging characteristics, and CSF PCR positivity for Toxoplasma gondii. Both patients were treated with pyrimethamine, sulfadiazine, and leucovorin for 2 months without clinical improvement, and both died. CONCLUSIONS: Immunotherapy with medications such as MMF can cause devastating TE in non-HIV patients with neuromuscular disorders. Early consideration and recognition of this complication is important to possibly prevent unfavorable outcomes. The utility of screening and prophylaxis against toxoplasmosis in individuals with neuroimmunologic disorders and other autoimmune disorders who receive immunosuppressive therapy requires future study.

The Oldest Case of Decapitation in the New World (Lapa do Santo, East-Central Brazil).

We present here evidence for an early Holocene case of decapitation in the New World (Burial 26), found in the rock shelter of Lapa do Santo in 2007. Lapa do Santo is an archaeological site located in the Lagoa Santa karst in east-central Brazil with evidence of human occupation dating as far back as 11.7-12.7 cal kyBP (95.4% interval). An ultra-filtered AMS age determination on a fragment of the sphenoid provided an age range of 9.1-9.4 cal kyBP (95.4% interval) for Burial 26. The interment was composed of an articulated cranium, mandible and first six cervical vertebrae. Cut marks with a v-shaped profile were observed in the mandible and sixth cervical vertebra. The right hand was amputated and laid over the left side of the face with distal phalanges pointing to the chin and the left hand was amputated and laid over the right side of the face with distal phalanges pointing to the forehead. Strontium analysis comparing Burial 26's isotopic signature to other specimens from Lapa do Santo suggests this was a local member of the group. Therefore, we suggest a ritualized decapitation instead of trophy-taking, testifying for the sophistication of mortuary rituals among hunter-gatherers in the Americas during the early Archaic period. In the apparent absence of wealth goods or elaborated architecture, Lapa do Santo's inhabitants seemed to use the human body to express their cosmological principles regarding death.

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.

Understanding the peopling of the Americas remains an important and challenging question. Here, we present (14)C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.

Morphological affinities of Homo naledi with other Plio-Pleistocene hominins: a phenetic approach

ABSTRACT Recent fossil material found in Dinaledi Chamber, South Africa, was initially described as a new species of genus Homo, namely Homo naledi. The original study of this new material has pointed to a close proximity with Homo erectus. More recent investigations have, to some extent, confirmed this assignment. Here we present a phenetic analysis based on dentocranial metric variables through Principal Components Analysis and Cluster Analysis based on these fossils and other Plio-Pleistocene hominins. Our results concur that the Dinaledi fossil hominins pertain to genus Homo. However, in our case, their nearest neighbors are Homo habilis and Australopithecus sediba. We suggest that Homo naledi is in fact a South African version of Homo habilis, and not a new species. This can also be applied to Australopithecus sediba.

Rock art at the pleistocene/holocene boundary in Eastern South America.

BACKGROUND: Most investigations regarding the first americans have primarily focused on four themes: when the New World was settled by humans; where they came from; how many migrations or colonization pulses from elsewhere were involved in the process; and what kinds of subsistence patterns and material culture they developed during the first millennia of colonization. Little is known, however, about the symbolic world of the first humans who settled the New World, because artistic manifestations either as rock-art, ornaments, and portable art objects dated to the Pleistocene/Holocene transition are exceedingly rare in the Americas. METHODOLOGY/PRINCIPAL FINDINGS: Here we report a pecked anthropomorphic figure engraved in the bedrock of Lapa do Santo, an archaeological site located in Central Brazil. The horizontal projection of the radiocarbon ages obtained at the north profile suggests a minimum age of 9,370 ± 40 BP, (cal BP 10,700 to 10,500) for the petroglyph that is further supported by optically stimulated luminescence (OSL) dates from sediment in the same stratigraphic unit, located between two ages from 11.7 ± 0.8 ka BP to 9.9 ± 0.7 ka BP. CONCLUSIONS: These data allow us to suggest that the anthropomorphic figure is the oldest reliably dated figurative petroglyph ever found in the New World, indicating that cultural variability during the Pleistocene/Holocene boundary in South America was not restricted to stone tools and subsistence, but also encompassed the symbolic dimension.

Ube3a is required for experience-dependent maturation of the neocortex.

Experience-dependent maturation of neocortical circuits is required for normal sensory and cognitive abilities, which are distorted in neurodevelopmental disorders. We tested whether experience-dependent neocortical modifications require Ube3a, an E3 ubiquitin ligase whose dysregulation has been implicated in autism and Angelman syndrome. Using visual cortex as a model, we found that experience-dependent maturation of excitatory cortical circuits was severely impaired in Angelman syndrome model mice deficient in Ube3a. This developmental defect was associated with profound impairments in neocortical plasticity. Normal plasticity was preserved under conditions of sensory deprivation, but was rapidly lost by sensory experiences. The loss of neocortical plasticity is reversible, as late-onset visual deprivation restored normal synaptic plasticity. Furthermore, Ube3a-deficient mice lacked ocular dominance plasticity in vivo when challenged with monocular deprivation. We conclude that Ube3a is necessary for maintaining plasticity during experience-dependent neocortical development and suggest that the loss of neocortical plasticity contributes to deficits associated with Angelman syndrome.

Downregulation of NR3A-containing NMDARs is required for synapse maturation and memory consolidation.

NR3A is the only NMDA receptor (NMDAR) subunit that downregulates sharply prior to the onset of sensitive periods for plasticity, yet the functional importance of this transient expression remains unknown. To investigate whether removal/replacement of juvenile NR3A-containing NMDARs is involved in experience-driven synapse maturation, we used a reversible transgenic system that prolonged NR3A expression in the forebrain. We found that removal of NR3A is required to develop strong NMDAR currents, full expression of long-term synaptic plasticity, a mature synaptic organization characterized by more synapses and larger postsynaptic densities, and the ability to form long-term memories. Deficits associated with prolonged NR3A were reversible, as late-onset suppression of transgene expression rescued both synaptic and memory impairments. Our results suggest that NR3A behaves as a molecular brake to prevent the premature strengthening and stabilization of excitatory synapses and that NR3A removal might thereby initiate critical stages of synapse maturation during early postnatal neural development.