Mitochondrial oxidative phosphorylation (OxPhos) powers brain activity1,2, and mitochondrial defects are linked to neurodegenerative and neuropsychiatric disorders3,4, underscoring the need to define the brain's molecular energetic landscape5-10. To bridge the cognitive neuroscience and cell biology scale gap, we developed a physical voxelization approach to partition a frozen human coronal hemisphere section into 703 voxels comparable to neuroimaging resolution (3×3×3 mm). In each cortical and subcortical brain voxel, we profiled mitochondrial phenotypes including OxPhos enzyme activities, mitochondrial DNA and volume density, and mitochondria-specific respiratory capacity. We show that the human brain contains a diversity of mitochondrial phenotypes driven by both topology and cell types. Compared to white matter, grey matter contains >50% more mitochondria. We show that the more abundant grey matter mitochondria also are biochemically optimized for energy transformation, particularly among recently evolved cortical brain regions. Scaling these data to the whole brain, we created a backward linear regression model integrating several neuroimaging modalities11, thereby generating a brain-wide map of mitochondrial distribution and specialization that predicts mitochondrial characteristics in an independent brain region of the same donor brain. This new approach and the resulting MitoBrainMap of mitochondrial phenotypes provide a foundation for exploring the molecular energetic landscape that enables normal brain functions, relating it to neuroimaging data, and defining the subcellular basis for regionalized brain processes relevant to neuropsychiatric and neurodegenerative disorders.

Abstract To investigate the presence of a neurogenic niche in human adult hippocampus and the molecular basis of smaller dentate gyrus (DG) in Major Depressive Disorder (MDD), we applied single-nucleus RNA (snRNA- seq) and accessible chromatin sequencing (snATAC-seq), together with spatial RNA sequencing (Visium, 10x Genomics). We assayed the hippocampus proper from 9 neurotypical (age 40 ± 12 yrs.) and 7 untreated MDD (age 48 ± 10 yrs.) males (2-3 biological replicates). A subsample (3 MDDs; 3 neurotypicals) were used for Visium (2 biological replicates, 12 capture areas total). Samples had RIN ³ 7 (7.9 ± 0.4). Libraries were sequenced (NovaSeq 6000 Sequencer, Illumina) to 62,000 reads/cell for RNA libraries, 33,000 reads/cell for ATAC libraries, and 67,000 reads/spot for Visium libraries (total 41,878 spots). RNA and ATAC data were preprocessed using Seurat, Signac, and DoubletFinder, batch effects removed using Harmony. Multimodal data for 293,236 cells were integrated using Weighted Nearest Neighbor analysis in Seurat, cell types annotated using canonical gene expression, enriched genes identified by a Wilcoxon rank-sum test (Bonferroni-adjusted p-value), and prediction scores from integration with spatial data implemented with TransferData function in Seurat. Gene ontology (GO) terms were generated using clusterProfiler (FDR-adjusted q-value). Differentially expressed genes (DEGs) in MDDs vs. neurotypicals, were identified using a mixed linear model implemented in limma with a pseudobulk approach, we aggregated count matrix across sample and cluster, and used a random effect to control for multiple samples/donor and fixed effects for age, PMI, and batch. We identified hippocampus canonical cell types: granule neurons (GN), non-granule excitatory neurons (ExN), inhibitory neurons (InN), astrocytes, oligodendrocytes, microglia, vasculature, ciliated epithelial cells, choroid plexus, Cajal-Retzius, and oligodendrocyte progenitor cells (OPc). We discovered: a neural progenitor cell cluster (NPC) enriched for EGFR (p = 1.68E-35), BMPR1B (p = 1.25E-31), NOTCH2 (p = 4.43E-11), and DLL3 (p = 4.48E-21), with top GO terms ‘nervous system development’ (q=2.11E-05) and ‘cell fate commitment’ (q = 2.11E-05); and immature granule neurons (ImN) enriched for PROX1, DCX, CALB2 (p <2.23E-308), that expressed GAD1 (p <2.23E-308),with GO terms ‘neuron axonogenesis’ (q = 9.11E-05), ‘excitatory synapse assembly’ (q = 0.004), and ‘ephrin receptor signaling pathway’ (q = 0.024). ATAC showed NPC and ImN had increased chromatin accessibility of ASCL1, involved in neuronal commitment (p = 0.00013) and differentiation (p <2.23E-308). Visium confirmed the expected anatomical location of canonical cell clusters, and mapped NPCs and ImNs to the DG region. In MDD vs. neurotypicals, DEGs included: upregulated interferon inducible genes (IFI44, IFI6, IFIT1, etc.) in GN, ExN, InN, ImN, astrocyte, microglia, choroid plexus, OPC (p <0.01), and downregulated transthyretin (TTR), which transports thyroid hormone, in GN, ExN, InN, astrocyte, microglia, vasculature, and ciliated epithelial cells (p <4.06E-05). This first single cell and spatial multiome study of human adult hippocampus reveals a neurogenic niche and supports a role of neuroinflammation in MDD. GAD1 expression in ImN explains their known inhibition of mature GNs. Molecular landscape of DEGs in MDD cell population points to druggable targets for MDD. References 1.Ayhan, F., Kulkarni, A., Berto, S., et al. (2021). Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans. Neuron 109, 2091-2105.e2096. 10.1016/j.neuron.2021.05.003. 2.Franjic, D., Skarica, M., Ma, S., et al. (2022). Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells. Neuron 110, 452-469 e414. 10.1016/j.neuron.2021.10.036. 3.Wang, W., Wang, M., Yang, et al. (2022). Transcriptome dynamics of hippocampal neurogenesis in macaques across the lifespan and aged humans. Cell Res 32, 729-743. 10.1038/s41422-022-00678-y. 4.Zhou, Y., Su, Y., Li, S., et al. (2022). Molecular landscapes of human hippocampal immature neurons across lifespan. Nature 607, 527-533. 10.1038/s41586-022-04912-w. 5.Boldrini, M., Galfalvy, H., Dwork, A.J., et al. (2019). Resilience Is Associated With Larger Dentate Gyrus, While Suicide Decedents With Major Depressive Disorder Have Fewer Granule Neurons. Biol Psychiatry 85, 850-862. 10.1016/j.biopsych.2018.12.022.6. 6.Bergen, V., Lange, M., Peidli, S., Wolf, F.A., and Theis, F.J. (2020). Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology, 1-7. 10.1038/s41587-020- 0591-3.

Major depressive disorder (MDD) is a leading cause of disability worldwide. Risk for MDD is heritable, and the genetic structure of founder populations enables investigation of rare susceptibility alleles with large effect. In an extended Old Order Mennonite family cohort, we identified a rare missense variant in GPR156 (c.1599G>T, p.Glu533Asp) associated with a two-fold increase in the relative risk of MDD. GPR156 is an orphan G protein-coupled receptor localized in the medial habenula, a region implicated in mood regulation. Insertion of a human sequence containing c.1599G>T into the murine Gpr156 locus induced medial habenula hyperactivity and abnormal stress-related behaviors. This work reveals a human variant that is associated with depression, implicates GPR156 as a target for mood regulation, and introduces informative murine models for investigating the pathophysiology and treatment of affective disorders.

Introduction: Previous studies have shown an association between vascular disease and Alzheimer’s disease, but there are few studies have considered a relationship between brain arterial remodeling and biomarkers of Alzheimer's disease. Our study aims to find the association between specific arterial characteristics in brain arterial remodeling and Alzheimer's pathology. Method: We analyzed 132 brain autopsy cases from the Brain Arterial Remodeling Study (BARS), a collection of brains from multiple brain banks in the United States and abroad. Brain sections were obtained systematically by each brain bank, and the anatomical location was harmonized across the banks. The brain slides were stained with LH&E to measure the lumen and wall thickness of the pial, CSF-floating small arteries, parenchymal arteries, and arterioles. Then lumen area, wall thickness, lumen-to-wall ratio (LWR), and wall proportion (which serves as a measure of vessel stenosis) were calculated. We used immunohistochemistry to stain for beta-amyloid, phospho-tau, and Iba1, a measure of microglia. Each stained slide was processed automatically using Visiopharm (version 2021.12) by color thresholding and pattern detection to quantify the number of amyloid plaques and microglial (Iba1+ cells) per 100 µm 2 and the percentage of tissue area stained positive by phospho-tau, and the number of microglial cells per 100 µm 2 . Results: Overall, a thicker arterial wall was associated with a greater area of tau staining and a lower lumen-to-wall ratio (suggestive of inward remodeling) was associated with a higher number of microglial cells (table 1). There was a statistical interaction between measures of arterial remodeling by anatomical location (pial vs. parenchymal, P<0.01) and amyloid measures. Stratifying by arterial anatomical location, however, demonstrated that parenchymal arteries with large lumen (B=0.12 ±0.03 per µm 2 , P<0.001) and thicker arterial wall (B=1.10 ± 0.18 per µm 2 , P<0.001) had a higher number of amyloid plaques per 100 µm 2 . Conclusion: Brain arteries immediately supplying the brain and their parenchymal offsprings related to measures of tau phosphorylation and neuroinflammation. Parenchymal arteries and arterioles that are dilated proportional to their wall thickness also relate to a greater load of amyloid deposition. Further investigation is needed to clarify these relationships.

Light sheet fluorescence microscopy (LSFM) is a widely used imaging technique for living and large cleared samples. However, high-performance LSFM systems are often prohibitively expensive and not easily scalable for high-throughput applications. Here, we introduce a cost-effective, scalable, and versatile high-resolution imaging framework, called projected Light Sheet Microscopy (pLSM), which repurposes readily available off-the-shelf consumer-grade components and an over-the-network control architecture to achieve high-resolution imaging of living and cleared samples. We extensively characterize the pLSM framework and showcase its capabilities through high-resolution, multi-color imaging and quantitative analysis of mouse and post-mortem human brain samples cleared using various techniques. Moreover, we show the applicability of pLSM for high-throughput molecular phenotyping of human induced pluripotent cells (iPSC)-derived brain and vessel organoids. Additionally, we utilized pLSM for comprehensive live imaging of bacterial pellicle biofilms at the air-liquid interface, uncovering their intricate layered architecture and diverse cellular dynamics across different depths. Overall, the pLSM framework has the potential to further democratize LSFM by making high-resolution light sheet microscopy more accessible and scalable.

Accumulating evidence points to altered immune response in suicide, which implicates malfunction of blood-brain barrier that we investigate in the present study through transcriptional profiling of the human Neurovascular unit (NVU).

Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to the severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with the presence of suicidal ideation were found within 18 co-expressed modules (p < 0.05), as well as in 3 co-expressed modules associated with suicidal ideation severity (p < 0.05, not explained by severity of depression). Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified and investigated using RNA-seq data from postmortem brain that revealed gene expression differences with moderate effect sizes in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity are associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.

Background: Infectious diseases can contribute to substance abuse. Here, a fatal case of borreliosis and substance abuse is reported. This patient had a history of multiple tick bites and increasing multisystem symptoms, yet diagnosis and treatment were delayed. He experimented with multiple substances including phencyclidine (PCP), an N-methyl-d-aspartate (NMDA) receptor antagonist that opposes NMDA agonism caused by Borrelia infection. During PCP withdrawal, he committed one homicide, two assaults, and suicide. Methods: Brain tissue was obtained from autopsy and stained for microglial activation and quinolinic acid (QA). Immunoflouresence (IFA) and fluorescence in situ hybridization (FISH) were used to identify the presence of pathogens in autopsy tissue. Results: Autopsy tissue evaluation demonstrated Borrelia in the pancreas by IFA and heart by IFA and FISH. Activated microglia and QA were found in the brain, indicating neuroinflammation. It is postulated that PCP withdrawal may exacerbate symptoms produced by Borrelia-induced biochemical imbalances in the brain. This combination may have greatly increased his acute homicidal and suicidal risk. Patient databases also demonstrated the risk of homicide or suicide in patients diagnosed with borreliosis and confirmed multiple symptoms in these patients, including chronic pain, anxiety, and anhedonia. Conclusions: Late-stage borreliosis is associated with multiple symptoms that may contribute to an increased risk of substance abuse and addictive disorders. More effective diagnosis and treatment of borreliosis, and attention to substance abuse potential may help reduce associated morbidity and mortality in patients with borreliosis, particularly in endemic areas.

Abstract Suicide rates have increased steadily world-wide over the past two decades, constituting a serious public health crisis that creates a significant burden to affected families and the society as a whole. Suicidal behavior involves a multi-factorial etiology, including psychological, social and biological factors. Since the molecular neural mechanisms of suicide remain largely uncharacterized, we examined transcriptional- and methylation profiles of postmortem brain tissue from subjects who died from suicide as well as their neurotypical healthy controls. We analyzed temporal pole tissue from 61 subjects, free from antidepressant and antipsychotic medication, using whole genome RNA-sequencing and DNA-methylation profiling using an array that targets over 850,000 CpG sites. Expression of , a key regulator of inflammation and neuroprotection, was significantly downregulated in the suicide-decedent group. Moreover, we identified a total of 40 differentially methylated regions in the suicide decedent group, mapping to seven genes with inflammatory function. There was a significant association between DNA methylation and expression in the control group that was absent in the suicide decedent group, confirming its dysregulation. expression was significantly associated with the expression of multiple inflammatory factors in the brain tissue. Overall, gene sets and pathways closely linked to inflammation were significantly upregulated, while specific pathways linked to neuronal development were suppressed in the suicide decedent group. Excitotoxicity as well as suppressed oligodendrocyte function were also implicated in the suicide decedents. In summary, we have identified central nervous system inflammatory mechanisms that may be active during suicidal behavior, along with oligodendrocyte dysfunction and altered glutamate neurotransmission. In these processes, NPAS4 might be a master regulator, warranting further studies to validate its role as a potential biomarker or therapeutic target in suicidality.

Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context1-5. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly concordant tissue features were identified by either spatial epigenome or spatial transcriptome we also observed distinct patterns, suggesting their differential roles in defining cell states. Linking epigenome to transcriptome pixel by pixel allows the uncovering of new insights in spatial epigenetic priming, differentiation and gene regulation within the tissue architecture. These technologies are of great interest in life science and biomedical research.

Abstract Background The hypothalamic-pituitary-adrenal (HPA) axis is a major stress response system, and excessive HPA responses can impact major depressive disorder and suicide. We examined relationships between reported early-life adversity (ELA), recent-life stress (RLS), suicide, and corticotropin-releasing hormone (CRH), CRH binding protein, FK506-binding protein (FKBP5), glucocorticoid receptor (GR), and brain-derived neurotrophic factor (BDNF) in postmortem human prefrontal cortex (BA9), and anterior cingulate cortex (BA24). Methods Thirteen quadruplets, matched for sex, age, and postmortem interval and consisting of suicide decedents and healthy controls, were divided equally into those with and without ELA. ELA, RLS, and psychiatric diagnoses were determined by psychological autopsy. Protein levels were determined by western blots. Results There were no suicide- or ELA-related differences in CRH, CRH binding protein, GR, or FKBP5 in BA9 or BA24 and no interaction between suicide and ELA (P > .05). For BDNF, there was an interaction between suicide and ELA in BA24; suicides without ELA had less BDNF than controls without ELA, and controls with ELA had less BDNF than controls without ELA. CRH in BA9 and FKBP5 in anterior cingulate cortex correlated negatively with RLS. Least Absolute Shrinkage and Selection Operator logistic regression with cross-validation found combining BDNF, GR, and FKBP5 BA24 levels predicted suicide, but ELA did not contribute. A calculated “suicide risk score” using these measures had 71% sensitivity and 71% specificity. Conclusion A dysregulated HPA axis is related to suicide but not with ELA. RLS was related to select HPA axis proteins in specific brain regions. BDNF appears to be dysregulated in a region-specific way with ELA and suicide.

OBJECTIVE:Postmortem examination of the essential tremor cerebellum has revealed a variety of pathological changes centered in and around Purkinje cells. Studies have predominantly focused on cerebellar neuronal connections. Bergmann glial morphology has not yet been studied in essential tremor. Among their many roles, Bergmann glia in the cerebellar cortex ensheath Purkinje cell synapses and provide neuroprotection. Specifically, the complex radial processes and lateral appendages of Bergmann glia are structural domains that modulate Purkinje cell synaptic transmission. In this study, we investigate whether Bergmann glia morphology is altered in the essential tremor cerebellum. METHODS:We applied the Golgi-Kopsch method and used computerized three-dimensional cell reconstruction to visualize Bergmann glia in the postmortem cerebellum of 34 cases and 17 controls. We quantified morphology of terminal structures (number of terminations and lateral appendage density) and morphology of radial processes (total process length, branch length, branch order, and branch volume) in each glial cell. We quantified number of branches and volume as well. RESULTS:Essential tremor cases had a 31.9% decrease in process terminations and a 35.7% decrease in lateral appendage density in Bergmann glia. Total process length and branch length did not differ between essential tremor cases and controls. We found also a reduction in number of secondary and tertiary branches and tertiary branches volume. INTERPRETATION:These findings suggest that Bergmann glia in essential tremor cases have more alterations in their terminal structures, with a relative preservation of radial processes, and highlight a potential role for these astrocytes in the disease pathophysiology.

Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with presence and severity of suicidal ideation were found within 18 and 3 co-expressed modules respectively (p < 0.05), not explained by severity of depression. Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified, and tested using RNA-seq data from postmortem brain that revealed gene expression differences in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity is associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.

Converging Evidence Shows Associations between Inflammation in suicide, which We Will Investigate Using Omics Approaches.