Acta Neuropathologica

Progressive supranuclear palsy (PSP) is a heterogeneous neurodegenerative disease characterised by the accumulation of misfolded 4-repeat tau within neurones and glial cells. There is limited longitudinal data on pathologically confirmed PSP patients with phenotypes other than classical Richardsons syndrome (RS), and the pathomechanisms responsible for the broad variability in clinical phenotype and progression are not well understood. An unresolved question in this context is whether distinct spatiotemporal patterns of tau pathology propagation exist within the clinicopathological spectrum of PSP. We identified 241 consecutive, pathologically confirmed patients with PSP from the Queen Square Brain Bank for Neurological Disorders (2010-2022). Phenotyping was performed based on clinical features present within the first 3 years from symptom onset according to the Movement Disorder Society (MDS) criteria, and specific clinical features and disease milestones were recorded. Genotyping was performed using Illumina NeuroBooster and NeuroChip arrays and MAPT haplotype, APOE genotype, TRIM11 rs564309, and SLC2A13 rs2242367 single nucleotide polymorphism status were collated from imputed data. Tissue sections from eight brain regions, mounted on glass slides, were immunostained for hyperphosphorylated tau and digitised using whole-slide scanning. Forty-one anatomical regions of interest were manually segmented, and total tau pathology burden was quantified using an automated, machine learning-based algorithm. The associations between survival and both clinicogenetic features and regional tau pathology burden were modelled using Cox regression and generalised linear models, respectively, and the Subtype and Stage Inference (SuStaIn) algorithm was used to identify subgroups with distinct progression patterns. We have identified: 1) several clinical predictors of survival in PSP and the relationship between regional tau pathology burden and survival; 2) novel anatomical reference standards for the expected distribution of tau pathology across MDS-defined PSP phenotypes, emphasising region-specific white matter involvement in patients with corticobasal syndrome and speech/language variants; 3) associations linking biological sex, MAPT haplotype, and TDP-43 co-pathology to clinical phenotype and regional tau pathology burden; 4) patterns of covariance in regional tau pathology implicating inter-regional connectivity in tau spreading; and 5) three distinct spatiotemporal patterns of tau pathology progression: one characterised by initial involvement of subcortical grey matter followed by rostral spread to frontal white matter and other cortical regions, and two characterised by early, simultaneous involvement of subcortical grey matter and frontal white matter. Taken together, these results indicate that PSP clinicopathological heterogeneity is mediated by propagation of tau pathology along anatomically connected networks, and via cell- autonomous mechanisms influenced by sex, genetic factors and possibly co-pathology.

Ataxia-telangiectasia (A-T) is a rare genetic disease caused by mutations in the gene encoding the ATM (ataxia-telangiectasia mutated) protein. Although neuronal degeneration in the cerebellum remains the most prominent sign in A-T pathology, neuroimaging studies reveal myelin abnormalities as early comorbidities. We hypothesize that these myelin defects are the direct consequence of ATM deficiencies in the oligodendrocytes (OL) lineage. We examined samples from ten A-T brains in which the ATM mutations had been mapped by targeted genomic sequencing and from Atm-/- mice. In healthy human cerebellum, we confirmed the presence of ATM in white matter OLs. In A-T, a significant reduction in OL density was found along with a massive astrogliosis. This white matter pathology was recapitulated in Atm-/- mice in an age- and gene dose-dependent fashion. Activated ATM was found expressed both in the nucleus and cytoplasm of OL progenitor cells (OPC) and myelinating mature OL. Its presence in the OL lineage is associated with novel OL-specific functions of the ATM protein affecting all stages of the OL life cycle. Blockage of ATM activity with KU-60019 or inducing DNA damage induced with etoposide altered the cell cycle in self-renewing OPC and triggered ectopic cell cycle re-entry in mature OL in vitro. Further, the differentiation program of OPC is highly sensitive to DNA damage either induced directly or by blocking DNA repair. As much of the impact of ATM deficiency in OL is independent of neuronal loss, our findings have important implications for the complex neurological symptoms of human A-T. HIGHLIGHTSO_LIOligodendrocytes are highly vulnerable to DNA double strand breaks C_LIO_LIATM regulates cell cycle control and differentiation of oligodendrocytes C_LIO_LIMyelin-pathology in Ataxia Telangiectasia is likely the cell-autonomous consequence of ATM deficiency in oligodendrocytes C_LI

BackgroundChitotriosidase (Chit-1) and chitinase-3-like protein 1 (CHI3L1) protein levels are increased in the cerebrospinal fluid (CSF) of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimers disease (AD). Few studies have examined the spatial expression of chitinase expressing cells with respect to neuropathologic hallmarks of disease. MethodsRNA-sequencing was used to examine Chit-1 and CHI3L1 gene expression in the spinal cord and motor cortex. Immunohistochemistry was used to characterize the distribution of Chit-1 and CHI3L1 expressing cells in ALS, C9-ALS, FTLD, AD, and non-neurologic disease controls. Immunofluorescence confocal microscopy was used to correlate distribution of Chit-1 and CHI3L1 expressing cells to TDP pathology. ResultsChit-1 gene expression was increased in the spinal cord, and CHI3L1 expression was increased in both the spinal cord and motor cortex of sALS and C9-ALS patients when compared to controls. Highest levels of Chit-1+ glia were in cortical regions that contain hallmark neuropathology for each neurodegenerative disease. CHI3L1+ glia were only significantly increased in sALS. Neither Chit-1+ nor CHI3L1+ glia were in close proximity to pTDP containing neurons in the motor cortex gray matter; however, there was a significant co-localization of glial pTDP with Chit-1 and CHI3L1 in the motor cortex white matter. ConclusionsChit-1 and CHI3L1 expressing cells were most abundant in the white matter of cortical regions affected by each neurodegenerative disease and the spinal cord. Chit-1 or CHI3L1 expressing cells in the white matter also contained phosphorylated TDP-43. We also observed correlations between levels of Chit-1 or CHI3L1 expressing cells in the white matter to disease duration. KEY MESSAGESO_ST_ABSWhat is already known on this topicC_ST_ABSPrior studies identified elevated levels of Chit-1 and CHI3L1 proteins in the CSF of various neurodegenerative conditions, though few studies examined levels of Chit-1 and CHI3L1 expressing cells both spatially and in relation to disease pathology. What this study addsWe performed an extensive spatial characterization of Chit-1 and CHI3L1 protein levels across multiple regions and neurodegenerative conditions. This study also correlates Chit-1 and CHI3L1 expression to TDP pathology and other clinical parameters of disease duration. How this study might affect research, practice or policyOur findings indicate that the majority of Chit-1 and CHI3L1 expressing glia are located in the cortical subpial layer and the white matter, suggesting a role for chitinases in modulating neuroinflammatory mechanisms or reparative/regenerative responses in the white matter of ALS and other neurodegenerative diseases. This study suggests new therapeutic opportunities for targeting chitinase expressing cells in neurodegenerative diseases.

BackgroundThe 2021 WHO classification of central nervous system tumors includes multiple molecular markers and patterns that are recommended for routine diagnostic use in addition to histology. Sequencing infrastructures for complete molecular profiling require considerable investment, while batching samples for sequencing and methylation profiling can delay turnaround time. We introduce RAPID-CNS2, a nanopore adaptive sequencing pipeline that enables comprehensive mutational, methylation and copy number profiling of CNS tumours with a single, cost-effective sequencing assay. It can be run for single samples and offers highly flexible target selection that can be personalized per case with no additional library preparation. MethodsUtilizing ReadFish, a toolkit enabling targeted nanopore sequencing without the need for library enrichment, we sequenced DNA from 22 diffuse glioma samples on a MinION device. Target regions comprised our Heidelberg brain tumor NGS panel and pre-selected CpG sites for methylation classification using an adapted random forest classifier. Pathognomonic alterations, copy number profiles, and methylation classes were called using a custom bioinformatics pipeline. The resulting data were compared to their corresponding standard NGS panel sequencing and EPIC methylation array results. ResultsComplete concordance with the EPIC array was found for copy number profiles. The vast majority (94%) of pathognomonic mutations were congruent with standard NGS panel-seq data. MGMT promoter status was correctly identified in all samples. Methylation families from the random forest classifier were detected with 96% congruence. Among the alterations decisive for rendering a WHO 2021 classification-compatible integrated diagnosis, 97% of the alterations were consistent over the entire cohort (completely congruent in 19/22 cases and sufficient for unequivocal diagnosis in all 22 samples). ConclusionsRAPID-CNS2 provides a swift and highly flexible alternative to conventional NGS and array-based methods for SNV/InDel analysis, detection of copy number alterations, target gene methylation analysis (e.g. MGMT) and methylation-based classification. The turnaround time of [~]5 days for this proof-of-concept study can be further shortened to < 24h by optimizing target sizes and enabling real-time computational analysis. Expected advances in nanopore sequencing and analysis hardware make the prospect of integrative molecular diagnosis in an intra-operative setting a feasible prospect in future. This low-capital approach would be cost-efficient for low throughput settings or in locations with less sophisticated laboratory infrastructure, and invaluable in cases requiring immediate diagnoses.

A homozygous variant in IVNS1ABP was identified in three siblings, displaying progeroid features with severe neuropathy. By generating isogenic induced pluripotent stem cells (iPSCs) from the patients fibroblasts and differentiating the iPSCs into neural progenitor cells (NPCs), we found that mutant IVNS1ABP fibroblasts, iPSCs, and NPCs exhibited disrupted cytokinesis, DNA damage and cellular senescence. Correspondingly, cerebral organoids displayed premature differentiation of NPCs to neurons. Molecular profiling as well as biochemical and cellular analysis revealed altered binding of mutant IVNS1ABP to actin /actin-associated proteins and dysregulated actin dynamics during cytokinesis. Taken together, we propose that mutant IVNS1ABP dysregulates actin polymerization and organization which is at least partly responsible for the cellular senescence phenotypes in this progeroid neuropathy syndrome.

Biochemical analysis of human brain tissue is typically done by homogenizing whole pieces of brain and separately characterizing the proteins, RNA, DNA, and other macromolecules within. While this has been sufficient to identify substantial changes, there is little ability to identify small changes or alterations that may occur in subsets of cells. To effectively investigate the biochemistry of disease in the brain, with its different cell types, we must first separate the cells and study them as phenotypically defined populations or even as individuals. In this project, we developed a new method for the generation of whole-cell-dissociated-suspensions (WCDS) in fresh human brain tissue that could be shared as a resource with scientists to study single human cells or populations. Characterization of WCDS was done in paraffin-embedded sections stained with H&E, and by phenotyping with antibodies using immunohistochemistry and fluorescence-activated cell sorting (FACS). Additionally, we compared extracted RNA from WCDS with RNA from adjacent intact cortical tissue, using RT-qPCR for cell-type-specific RNA for the same markers as well as whole transcriptome sequencing. More than 11,626 gene transcripts were successfully sequenced and classified using an external database either as being mainly expressed in neurons, astrocytes, microglia, oligodendrocytes, endothelial cells, or mixed (in two or more cell types). This demonstrates that we are currently capable of producing WCDS with a full representation of different brain cell types combined with RNA quality suitable for use in biochemical analysis.

ObjectiveBrain branks preserve extensive material relevant to neurodegenerative disease research. As these collections age, tissue becomes archival, raising the question of whether long-term fixed and stored human brain tissue remains suitable for contemporary immunohistochemical analyses. Materials and MethodsForty-one autopsy brains collected between 1946 to 1980 were examined. For each case, midbrain and hippocampus were available both as original paraffin-embedded blocks and as tissue stored long term in fixative. New paraffin blocks were prepared from the long-term fixated tissue. Sections from original and newly prepared blocks were immunohistochemically stained for -synuclein, hyperphosphorylated tau and amyloid-{beta}. Immunoreactivity was assessed using semi-quantitative scoring. ResultsOriginal blocks consistently showed good staining intensity and morphological preservation for each protein pathology. Newly prepared blocks showed slightly lower semi-quantitative scores for Lewy-related pathology, without statistically significant differences, except for astrocytic -synuclein in the substantia nigra in cases from the 1960s. Tau pathology displayed modestly reduced labelling, particularly of the neuropil threads and neurofibrillary tangles, most evident in cases from the 1950s. Amyloid-{beta}-positive senile plaques showed similar or slightly higher scores in newly prepared blocks, with no significant differences across regions. ConclusionHuman brain tissue preserved as paraffin-embedded blocks or stored in fixative for up to 78 years remains suitable for immunohistochemical analyses. Adequate-to-good detection of aggregated of -synuclein, hyperphosphorylated tau and amyloid-{beta} is achievable, indicating preserved pathological hallmarks of Lewy Body Disease and Alzheimers Disease in archival tissue.

The PTPN11 gene was recently described as a novel lesional epilepsy gene by extensive exome-wide sequencing studies. However, germline mutations of PTPN11 and other RAS-/MAP-Kinase signaling pathway genes cause Noonan syndrome, a multisystem disorder characterized by abnormal facial features, developmental delay, and sporadically, also brain tumors. Herein, we performed a deep phenotype-genotype analysis of a comprehensive series of ganglioglioma (GG) with brain somatic alterations of the PTPN11 gene compared to GG with other common MAP-Kinase signaling pathway alterations. Seventy-two GG were submitted to whole exome sequencing and genotyping and 86 low grade epilepsy associated tumors (LEAT) to DNA-methylation analysis. Clinical data were retrieved from hospital files including postsurgical disease onset, age at surgery, brain localization, and seizure outcome. A comprehensive histopathology staining panel was available in all cases. We identified eight GG with PTPN11 alterations, copy number variant (CNV) gains of chromosome 12, and the commonality of additional CNV gains in FGFR4, RHEB, NF1, KRAS as well as BRAFV600E alterations. Histopathology revealed an atypical and complex glio-neuronal phenotype with subpial tumor spread and large, pleomorphic, and multinuclear cellular features. Only three out of eight patients with GG and PTPN11 alterations were free of disabling-seizures two years after surgery (38% Engel I). This was remarkably different from our series of GG with BRAFV600E mutations (85% Engel I). Our data point to a subgroup of GG with cellular atypia in glial and neuronal cell components, adverse postsurgical outcome, and genetically characterized by PTPN11 and other Noonan syndrome-related alterations of the RAS-/MAP-Kinase signaling pathway. These findings need prospective validation in clinical practice as they argue for an adapted WHO grading system in developmental, glio-neuronal tumors associated with early-onset focal epilepsy. These findings also open avenues for targeted medical treatment.

Pigmented paraganglioid carcinoid tumors (PPCT) of the lung are a rare, underrecognized, and poorly characterized morphologic variant of pulmonary neuroendocrine tumors (NETs). While these tumors are usually diagnosed as typical carcinoid (TC) tumors, PPCT may represent a diagnostic challenge due to the histologic resemblance with extra-adrenal paraganglioma (PG). In this study, we aimed to comprehensively characterize the histomorphologic, immunophenotypic, and transcriptomic profiles of PPCT in comparison to TC and PG using spatially resolved transcriptomic analysis. Using a tissue microarray (TMA) composed of 38 tumors, including 20 TC, 16 PG, and 2 PPCT, we performed immunohistochemical (IHC) and digital spatial transcriptomic (GeoMx(R) DSP) profiling. The TMA included two punches and two regions of interest (ROIs) per case. Cellular transcriptomes were selected based on epithelial (PanCK+), sustentacular (S100+), and immune (CD45+) compartments. By IHC, PPCT retained neuroendocrine markers (synaptophysin, INSM1, chromogranin A) but showed decreased or absent pancytokeratin cocktail expression and increased number of sustentacular cells highlighted by strong expression of S100 and SOX-10, similar to PG. Expression of AE1/AE3 and CK8/18 confirmed their epithelial origin and helped distinguish them from PG. The transcriptome of PPCT clustered with that of TC but displayed distinct expression patterns in a small subset of genes. Although the sustentacular and immune compartments showed limited divergence, the epithelial compartment showed differentially expressed genes in PPCT including FABP5, MLPH, GPNMB, and SOX1, which indicate upregulation of melanocytic and neural crest markers. Gene set enrichment analysis (GSEA) revealed significant upregulation of pathways related to inflammation (e.g., TLR4-TRAF6-TAK1), PTEN trafficking, and inositol phosphate metabolism. PPCT show increased melanocytic pathway expression, which may explain the morphologic resemblance to PG.

Glioblastoma is a highly malignant brain tumor in which maximal safe resection is associated with improved survival, yet the oncological benefit of resection varies by molecular subtype. Recent work has shown that DNA methylation-defined subtypes, particularly receptor tyrosine kinase (RTK) I and II, benefit from complete CE (contrast-enriched) resection compared to mesenchymal tumors, highlighting the need for pre- or intraoperative tools that guide resection based on tumor biology. Here, we present iSTAMP (intraoperative Spatially-informed Tumor Architecture Mapping and Profiling) a real-time, label-free molecular classification framework using stimulated Raman scattering microscopy and graph-based deep learning to predict glioblastoma epigenetic subtypes intraoperatively (within 5-7 minutes). Across 1,295 intraoperative tissue samples from 236 patients profiled with EPIC methylation arrays, our graph attention network achieved high predictive performance for all major subtypes (AUC range 0.88-0.99), with spatially stable predictions across tumor regions. RTK subtypes, but not mesenchymal tumors, showed significant survival benefit from GTR (HR = 0.42, p = 6.1 x10-6). Explainable AI methods revealed subtype-specific histopathological features, including necrosis and macrophage infiltration in mesenchymal tumors versus glio-fibrillary matrix or axon-rich regions in RTK tumors. Spatial transcriptomic validation confirmed cellular correlates with defined subtype specific SRH features. These findings support the integration of Raman-based molecular diagnostics into intraoperative workflows to guide biologically informed surgical strategies in glioblastoma.

BackgroundPathogenic mitochondrial (mt)DNA variants cause neuromuscular disease with highly variable severity and phenotypic presentation, the reason for which is poorly understood. Cells are thought to tolerate the presence of pathogenic mtDNA variants up to a threshold proportion with little or no functional consequence, developing significant respiratory complex defects above this threshold. We developed a robust method to identify deficient muscle fibres, applied it to biopsies from 17 patients carrying the common m.3243A>G variant and examined the relationship between respiratory deficiency and m.3243A>G level in hundreds of single skeletal muscle fibres. We hypothesised that single-cell between-patient differences may explain the vast clinical heterogeneity of mtDNA disease. ResultsImmunohistochemical measurements of respiratory complexes I and IV and unsupervised machine learning identified muscle fibres with respiratory deficiency; the pattern of deficiency and proportion of deficient fibres (range 0-64%) varies between patients. Tissue homogenate m.3243A>G level is a poor surrogate for the broad and complex distributions of m.3243A>G level in single cells from individual patients. Estimated thresholds do not differ between patients, but sections with narrow m.3243A>G distributions have a lower proportion of deficient fibres. ConclusionsInter-individual differences in respiratory complex deficiency in muscle fibres from patients with m.3243A>G are more complex than previously thought and may be driven by differential segregation and expansion of mtDNA molecules. Our quantitative observations could constrain the range of feasible mechanisms responsible for phenotypic diversity in mitochondrial disease.

Understanding how diffuse mild traumatic brain injuries can provoke common and persistent post-concussive symptoms (PCS), such as impaired sleep, is crucial to prevent and treat chronic disability and neurodegeneration. We mapped the spatially-resolved single cell landscape of diffuse mTBI pathology in a mouse model of blast exposure; identifying brainstem injuries predictive of later PCS. Repeated mTBI was necessary to establish chronic microglial activation and phagocytosis of myelin in the pontine reticular formation; where IL33 release by oligodendrocytes predicted microgliopathy. In postmortem brainstem tissues from patients with traumatic brain injury, chronic microglial activation and myelin phagocytosis was evident up to 20 years after diffuse mTBI caused by blast. In living patients with chronic blast mTBI, myelin injury in pontine projections mediated sleep disturbance and other PCS, with a dose dependent effect of mTBI number on sleep disturbance severity. These results support a mechanism for diffuse mTBIs to cause delayed persistent PCS.

Telomeres, the repetitive DNA elements at chromosome ends, are pivotal for maintenance of genome integrity. Previous studies from our group and others have highlighted the translational potential of tissue-based telomere length measurements to address the clinical challenge of improving diagnosis, individualized risk stratification, and accurate prognostication of different diseases. Here, we describe a high-throughput method that quantitates cell type-specific telomere lengths at a single cell level in archival tissues from patient cohorts for research on prognosis. This approach is based on telomere-specific fluorescence in situ hybridization (FISH) combined with multiplex immunostaining for cell type-specific antibodies, followed by semi-automated slide scanning and multi-channel acquisition of fluorescent images using the TissueFAXS Plus microscopy workstation and TissueQuest software (TissueGnostics). Here, we demonstrate that this method is sufficiently robust and reproducible to detect biologically significant differences in telomere lengths in archived tissues either on whole slides or sampled across tissue microarrays, which is essential when assessing prognosis in large patient cohorts.

BackgroundThe Myeloid differentiation primary response gene (MYD88) mutation in primary central nervous system lymphomas (PCNSL) may be associated with unfavourable prognosis, however the evidence remains limited. We aimed to comprehensively characterise PCNSLs by integration of clinicopathological, molecular, treatment and survival data. MethodsWe retrospectively identified and validated 57 consecutive patients with PCNSLs according to the 2017 WHO classification of lymphoid neoplasms over a 13-year period. Formalin-fixed paraffin-embedded tumour samples underwent real-time allele-specific polymerase chain reaction assay to detect MYD88 mutation. We used multivariable Cox regression for survival analysis including age, treatment, and MYD88 as covariates. We searched the literature for studies reporting demographics, treatment, MYD88 and survival of PCNSL patients, and incorporated individual-patient data into our analyses. ResultsThe median age was 66 years and 56% were women. All 57 patients had non-germinal PCNSL and the majority (81%) received either single or combined therapies. There were 46 deaths observed over the median follow-up of 10 months. MYD88 mutation status was available in 41 patients of which 36 (88%) were mutated. There was an association between MYD88 mutation and better survival in the multivariable model (hazard ratio [HR] 0.34; 95% confidence interval [CI] 0.12-0.95; p=0.039) but not in a univariable model. After incorporating additional 18 patients from the literature, this association was reproducible (HR 0.31, 95% CI 0.13-0.77, p=0.012). ConclusionsAdjusting for confounders, MYD88 mutation is associated with better survival. While further validation is warranted, identification of MYD88 mutation can identify patients who may benefit from novel targeted therapies. Key pointsO_LIMYD88 mutation is common in PCNSLs. C_LIO_LIMYD88 mutation in PCNSLs is associated with better survival after adjusting for age at diagnosis and treatment. C_LIO_LIIdentification of MYD88 mutation in PCNSLs can identify patients who may benefit from novel targeted therapies and enhance survival. C_LI Importance of the studyPCNSLs are rare and associated with lower survival than their systemic counterparts. The emergence of new molecular targets in PCNSLs, such as mutations in the MYD88 gene, offers hope for more effective therapeutics. Few studies have investigated the association between MYD88 mutation and survival. These studies, however, are limited by inconsistent inclusion of clinical variables and suboptimal analytic approach, such as overfitting model or incomplete adjustment for important confounders. Our study integrates treatment, molecular and survival data for 57 patients diagnosed with PCNSL. We demonstrate that without adequate adjustment for confounders such as age at diagnosis and treatment, MYD88 mutation does not affect survival. However, a multivariable survival model including these variables shows MYD88 mutation to be associated with better survival. While further validation of this association is warranted, our findings suggest that identification of MYD88 mutation can identify patients who may benefit from novel targeted therapies and enhance survival.

Mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) is a recently discovered histopathological lesion entity. Approximately half of affected individuals carry a pathogenic brain mosaicism in the X-linked SLC35A2 gene, and all suffer from epilepsy. In this work, we extended the search for genetic alterations of MOGHE by investigating sex chromosome copy number alterations in 29 brain tissue samples from 19 males and 10 females with histopathologically confirmed MOGHE. Twenty individuals carried pathogenic SLC35A2 variants, while no genetic alteration was identified in nine individuals using targeted deep panel sequencing. Interestingly, DNA methylation-derived copy number variation (CNV) plots revealed significant gains of the Y chromosome in 16/19 males (84.2%) and in 5/10 females (50%). These findings were validated by chromogenic and fluorescent in situ hybridisation (ISH), PCR amplification of Y-specific sequences, and microscopic localisation of cells with Y-chromosomal gain in clusters of oligodendroglial hyperplasia. PCR and ISH demonstrated lesion-restricted Y-chromosome gains, absent in the overlying non-lesional neocortex. Together with pathogenic variants in the X-chromosomal SLC35A2 gene, Y-chromosomal sequences detected in phenotypic females and mosaic Y chromosome gains in males provide a genomic correlate for all cases of MOGHE. Based on SLC35A2 mutational status and Y-chromosome copy number changes, we stratified the cohort into three subgroups: SLC35A2-mutant without Y gain (SLC+/Y-, n = 8), SLC35A2-mutant with Y gain (SLC+/Y+, n = 12), and SLC35A2-wild type with Y gain (SLC-/Y+, n = 9). These genetically defined subgroups also differed in their clinical presentation, with individuals from group 2 having the earliest disease onset and the largest lesion volume on MRI. These findings expand the genetic spectrum of epileptogenic cortical malformations and highlight a potentially overlooked role of sex chromosome biology in this focal epilepsy.

BackgroundTau pathology is common in age-related neurodegenerative diseases. Tau pathology in primary age-related tauopathy (PART) and in Alzheimers disease (AD) has a similar biochemical structure and anatomic distribution, which is distinct from tau pathology in other diseases. However, the molecular changes associated with intraneuronal tau pathology in PART and AD, and whether these changes are similar in the two diseases, is largely unexplored. MethodsUsing GeoMx spatial transcriptomics, mRNA was quantified in CA1 pyramidal neurons with tau pathology and adjacent neurons without tau pathology in 6 cases of PART and 6 cases of AD, and compared to 4 control cases without pathology. Transcriptional changes were analyzed for differential gene expression and for coordinated patterns of gene expression associated with both disease state and intraneuronal tau pathology. ResultsSynaptic gene changes and two novel gene expression signatures associated with intraneuronal tau were identified in PART and AD. Overall, gene expression changes associated with intraneuronal tau pathology were similar in PART and AD. Synaptic gene expression was decreased overall in neurons in AD and PART compared to control cases. However, this decrease was largely driven by neurons lacking tau pathology. Synaptic gene expression was increased in tau-positive neurons compared to tau-negative neurons in disease. Two novel gene expression signatures associated with intraneuronal tau were identified by examining coordinated patterns of gene expression. Genes in the up-regulated expression pattern were enriched in calcium regulation and synaptic function pathways, specifically in synaptic exocytosis. These synaptic gene changes and intraneuronal tau expression signatures were confirmed in a published transcriptional dataset of cortical neurons with tau pathology in AD. ConclusionsPART and AD show similar transcriptional changes associated with intraneuronal tau pathology in CA1 pyramidal neurons, raising the possibility of a mechanistic relationship between the tau pathology in the two diseases. Intraneuronal tau pathology was also associated with increased expression of genes associated with synaptic function and calcium regulation compared to tau-negative disease neurons. The findings highlight the power of molecular analysis stratified by pathology in neurodegenerative disease and provide novel insight into common molecular pathways associated with intraneuronal tau in PART and AD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/23295440v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1b46a40org.highwire.dtl.DTLVardef@1ab9efcorg.highwire.dtl.DTLVardef@52cad7org.highwire.dtl.DTLVardef@182fffc_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com (License GLSO).

Retrotransposition has generated thousands of intronless gene copies in mammalian genomes, yet their contribution to brain development and evolution remains largely unexplored. Here we uncover a critical role for RBMX retrocopy in shaping neurodevelopment and modulating disease. Pathogenic variants in RBMX, an X-linked splicing regulator, cause intellectual disability, microcephaly, and cortical malformations. Through integrated human genetic, cellular, and mouse model studies, we show that RBMX pathogenic variants disrupt cortical development through both loss- and gain-of-function mechanisms. Surprisingly, despite severe phenotypes in humans, Rbmx-deficient mice display only mild cortical abnormalities, a discrepancy likely due to compensation by Rbmxl1, a retrocopy that arose independently in mice and humans. We demonstrate that RBMX and RBMXL1 share protein and RNA partners and act redundantly in brain development, with RBMXL1 buffering the impact of RBMX deficiency. These findings establish retrocopies as functional paralogs safeguarding neurodevelopment, and suggest that functional RBMX retrocopy could contribute to the robustness and evolutionary diversification of mammalian brain.

The vastly spreading COVID-19 pneumonia is caused by SARS-CoV-2. Lymphopenia and cytokine levels are tightly associated with disease severity. However, virus-induced immune dysregulation at cellular and molecular levels remains largely undefined. Here, the leukocytes in the pleural effusion, sputum, and peripheral blood biopsies from severe and mild patients were analyzed at single-cell resolution. Drastic T cell hyperactivation accompanying elevated T cell exhaustion was observed, predominantly in pleural effusion. The mechanistic investigation identified a group of CD14+ monocytes and macrophages highly expressing CD163 and MRC1 in the biopsies from severe patients, suggesting M2 macrophage polarization. These M2-like cells exhibited up-regulated IL10, CCL18, APOE, CSF1 (M-CSF), and CCL2 signaling pathways. Further, SARS-CoV-2-specific T cells were observed in pleural effusion earlier than in peripheral blood. Together, our results suggest that severe SARS-CoV-2 infection causes immune dysregulation by inducing M2 polarization and subsequent T cell exhaustion. This study improves our understanding of COVID-19 pathogenesis.

Meningiomas are the most common primary brain tumors and, despite their benign reputation, often behave aggressively. Meningiomas are morphologically heterogeneous, yet the full significance of their histologic diversity is unclear. This is in large part because many features are not readily quantifiable by traditional observer-based light microscopy. Molecular testing improves prognostic stratification, but is not universally accessible. We therefore sought to determine whether an artificial intelligence (AI)-trained program could predict specific genomic and epigenomic patterns in meningiomas, and whether it could extract more prognostic information out of standard hematoxylin and eosin (H&E) histopathology than the current WHO classification. To do this, we developed Morphologic Set Enrichment (MSE), an interpretable computational pathology framework that quantifies statistical enrichment of morphologic patterns, cells, and tissue architecture from H&E whole-slide images. The MSE meningioma histology program was able to accurately predict DNA methylation subtypes and concurrent chromosome 1p/22q losses, in the process identifying specific morphologic patterns associated with key genomic and epigenomic alterations. It also added prognostic value independent of standard clinical and pathological variables. These results demonstrate that AI-based quantitative morphologic profiling can capture clinically and biologically relevant information that redefines risk stratification for meningiomas, incorporating histological information not included in existing grading schemes.

A subset of gliomas has DNA repair defects that lead to hypermutated genomes. While such tumors are resistant to alkylating chemotherapies, they may also express more mutant neoantigens on their cell surfaces, and thus be more responsive to immunotherapies. A fast, inexpensive method of screening for hypermutated gliomas would therefore be of great clinical value. Since immunohistochemistry (IHC) for the DNA mismatch repair (MMR) proteins Msh2, Msh6, Mlh1, and Pms2 is already used to screen for hypermutated colorectal cancers, we sought to determine whether that panel might have similar utility in gliomas. MMR IHC was scored in 100 WHO grade I-IV gliomas with known tumor mutation burdens (TMB), while blinded to TMB data. Eight of 100 cases showed loss of one or more MMR proteins by IHC, and all 8 were hypermutated. Among the remaining 94 gliomas with intact MMR IHC, only one was hypermutated; that tumor had an inactivating mutation in another DNA repair gene, ATM. Overall accuracy, sensitivity, and specificity were 99%, 89%, and 100%, respectively. The strongest correlates with hypermutation were prior TMZ treatment, MGMT promoter methylation, and IDH1 mutation. Among MMR-deficient hypermutated gliomas, 50% contained both MMR-lost and MMR-retained tumor cells. Together, these data suggest that MMR IHC could be a viable front-line screening test for gliomas in which immunotherapy is being considered. They also suggest that not all cells in a hypermutated glioma may actually be MMR-deficient, a finding that might need to be considered when treating such tumors with immunotherapies.