Connecting single-cell transcriptomes to projectomes in mouse visual cortex

The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.

Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species

Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have revealed substantial diversity of glial cells, particularly astrocytes. To better understand glial cell types and their roles in neurobiology, we built a new suite of adeno-associated viral (AAV)-based genetic tools to enable genetic access to astrocytes and oligodendrocytes. These oligodendrocyte and astrocyte enhancer-AAVs are highly specific (usually > 95% cell type specificity) with variable expression levels, and our astrocyte enhancer-AAVs show multiple distinct expression patterns reflecting the spatial distribution of astrocyte cell types. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs.

Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas

Biological aging can be defined as a gradual loss of homeostasis across various aspects of molecular and cellular function. Aging is a complex and dynamic process which influences distinct cell types in a myriad of ways. The cellular architecture of the mammalian brain is heterogeneous and diverse, making it challenging to identify precise areas and cell types of the brain that are more susceptible to aging than others. Here, we present a high-resolution single-cell RNA sequencing dataset containing ~1.2 million high-quality single-cell transcriptomic profiles of brain cells from young adult and aged mice across both sexes, including areas spanning the forebrain, midbrain, and hindbrain. We find age-associated gene expression signatures across nearly all 130+ neuronal and non-neuronal cell subclasses we identified. We detect the greatest gene expression changes in non-neuronal cell types, suggesting that different cell types in the brain vary in their susceptibility to aging. We identify specific, age-enriched clusters within specific glial, vascular, and immune cell types from both cortical and subcortical regions of the brain, and specific gene expression changes associated with cell senescence, inflammation, decrease in new myelination, and decreased vasculature integrity. We also identify genes with expression changes across multiple cell subclasses, pointing to certain mechanisms of aging that may occur across wide regions or broad cell types of the brain. Finally, we discover the greatest gene expression changes in cell types localized to the third ventricle of the hypothalamus, including tanycytes, ependymal cells, and Tbx3+ neurons found in the arcuate nucleus that are part of the neuronal circuits regulating food intake and energy homeostasis. These findings suggest that the area surrounding the third ventricle in the hypothalamus may be a hub for aging in the mouse brain. Overall, we reveal a dynamic landscape of cell-type-specific transcriptomic changes in the brain associated with normal aging that will serve as a foundation for the investigation of functional changes in the aging process and the interaction of aging and diseases.

Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas

The classic view that neural populations in sensory cortices preferentially encode responses to incoming stimuli has been strongly challenged by recent experimental studies. Despite the fact that a large fraction of variance of visual responses in rodents can be attributed to behavioral state and movements, trial-history, and salience, the effects of contextual modulations and expectations on sensory-evoked responses in visual and association areas remain elusive. Here, we present a comprehensive experimental and theoretical study showing that hierarchically connected visual and association areas differentially encode the temporal context and expectation of naturalistic visual stimuli, consistent with the theory of hierarchical predictive coding. We measured neural responses to expected and unexpected sequences of natural scenes in the primary visual cortex (V1), the posterior medial higher order visual area (PM), and retrosplenial cortex (RSP) using 2-photon imaging in behaving mice collected through the Allen Institute Mindscope's OpenScope program. We found that information about image identity in neural population activity depended on the temporal context of transitions preceding each scene, and decreased along the hierarchy. Furthermore, our analyses revealed that the conjunctive encoding of temporal context and image identity was modulated by expectations of sequential events. In V1 and PM, we found enhanced and specific responses to unexpected oddball images, signaling stimulus-specific expectation violation. In contrast, in RSP the population response to oddball presentation recapitulated the missing expected image rather than the oddball image. These differential responses along the hierarchy are consistent with classic theories of hierarchical predictive coding whereby higher areas encode predictions and lower areas encode deviations from expectation. We further found evidence for drift in visual responses on the timescale of minutes. Although activity drift was present in all areas, population responses in V1 and PM, but not in RSP, maintained stable encoding of visual information and representational geometry. Instead we found that RSP drift was independent of stimulus information, suggesting a role in generating an internal model of the environment in the temporal domain. Overall, our results establish temporal context and expectation as substantial encoding dimensions in the visual cortex subject to fast representational drift and suggest that hierarchically connected areas instantiate a predictive coding mechanism.

Survey of spiking in the mouse visual system reveals functional hierarchy

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically¹. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory²-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas³. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.

An anatomic transcriptional atlas of human glioblastoma

Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.

Comprehensive cellular-resolution atlas of the adult human brain

Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion‐weighted imaging (DWI), and 1,356 large‐format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto‐ and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

A comprehensive transcriptional map of primate brain development

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Hemorrhagic cystitis after allogeneic hematopoietic cell transplantation: risk factors, graft source and survival

Although hemorrhagic cystitis (HC) is a common complication of allogeneic hematopoietic cell transplantation (alloHCT), its risk factors and effects on survival are not well known. We evaluated HC in a large cohort (n=1321, 2003-2012) receiving alloHCT from all graft sources, including umbilical cord blood (UCB). We compared HC patients with non-HC (control) patients and examined clinical variables at HC onset and resolution. Of these 1321 patients, 219 (16.6%) developed HC at a median of 22 days after alloHCT. BK viruria was detected in 90% of 109 tested HC patients. Median duration of HC was 27 days. At the time of HC diagnosis, acute GVHD, fever, severe thrombocytopenia and steroid use were more frequent than at the time of HC resolution. In univariate analysis, male sex, age <20 years, myeloablative conditioning with cyclophosphamide and acute GVHD were associated with HC. In multivariate analysis, HC was significantly more common in males and HLA-mismatched UCB graft recipients. Severe grade HC (grade III-IV) was associated with increased treatment-related mortality but not with overall survival at 1 year. HC remains hazardous and therefore better prophylaxis, and early interventions to limit its severity are still needed.

Transcriptional landscape of the prenatal human brain

The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and postmitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in frontal lobe. Finally, many neurodevelopmental disorder and human evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

An anatomically comprehensive atlas of the adult human brain transcriptome

Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ∼900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography-the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function.

Motor impairment as a predictor of functional recovery and guide to rehabilitation treatment after stroke

OBJECTIVE

This study tests three hypotheses relevant for the efficient use of rehabilitation services after stroke: (a) the severity of initial motor impairment after stroke predicts discharge motor impairment and self-care mobility scores; (b) identification of those unlikely to show improvement in motor impairment can focus rehabilitzation efforts on use of compensatory techniques and assist devices; and (c) improvement in self-care mobility scores without change in motor impairment, balance, or cognition is a quantitative estimate of the value of teaching compensatory techniques and use of assist devices.

METHODS

We studied 171 sequential patients previously independent in the community who were admitted for inpatient rehabilitation within 17 +/- 12 SD days of an initial, unilateral, hemispheric, ischemic stroke. Impairment was assessed using the Fugl-Meyer upper limb motor (ULM), lower limb motor (LLM), and upper plus lower limb total motor (TM) subscores. Disability was assessed using the Functional Independence Measure (FIM), FIM self-care (FIMS), FIM mobility (FIMM), and FIM self-care plus FIM mobility (FIMSM) subscores. Spearman correlation coefficients tested strength of association between dependent and independent variables, stepwise linear regression tested the effects of clinically relevant co-variables, and positive and negative predictive values (PPV, NPV) assessed the clinical relevance of outcome-prediction models.

RESULTS

The highest correlations observed were between admission TM scores and the following discharge scores: TM (R = 0.92; p < 0.01), ULM (R = 0.91; p < 0.01), LLM (R = 0.82; p < 0.01), FIMSM (R = 0.67; p < 0.01), FIMM (R = 0.67; p < 0.001), FIM (R = 0.58; p < 0.0001). An admission TM score in the lowest quartile had a PPV of 0.74 for a discharge ULM score in the lowest quartile. An admission TM score in the highest quartile had a PPV of 0.86 for a discharge ULM score in the highest quartile. Similar but weaker PPVs were seen for admission TM scores and discharge LLM scores. Patients without significant change in TM scores (< or = 2 points) had a 17 +/- 9 SD improvement in FIMSM scores.

CONCLUSIONS

Admission motor impairment scores (a) predict discharge impairment and activities of daily living mobility functional outcome; and (b) guide treatment toward improving motor impairment versus use of compensatory techniques and assistive devices. The use of compensatory techniques and assistive devices, without change in motor impairment, is associated with a 17 +/- 9 SD improvement in FIMSM score.

Mechanism of the immune response to human factor VIII in murine hemophilia A

Mice genetically deficient in factor VII (fVIII) are a model of hemophilia A. As a first step to reproduce in this mouse model what occurs over time in hemophilia A patients treated with human fVIII (hfVIII), we have investigated the time course and the characteristics of their immune response to hfVIII, after multiple intravenous injections. Anti-hfVIII antibodies appeared after four to five injections. They were IgG1 and to a lesser extent IgG2, indicating that they were induced by both Th2 and Th1 cells. Inhibitors appeared after six injections. CD4+ enriched splenocytes from hfVIII-treated mice proliferated in response to fVIII and secreted IL-10: in a few mice they secreted also IFN-gamma and in one mouse IL-4, but never IL-2. A hfVIII-specific T cell line derived from hfVIII-treated mice secreted both IL-4 and IFN-gamma, suggesting that it included both Th1 and Th2 cells. CD4+ enriched splenocytes of hfIII-treated mice recognized all hfVIII domains. Thus, hemophilic mice develop an immune response to hfVIII administered intravenously similar to that of hemophilia A patients. Their anti-hfVIII antibodies can be inhibitors and belong to IgG subclasses homologous to those of inhibitors in hemophilic patients; their anti-hfVIII CD4+ cells recognize a complex repertoire and both Th1 and Th2 cytokines, and especially IL-10, may drive the antibody synthesis.

Initial Functional Independence Measure Score and Interval Post Stroke Help Assess Outcome, Length of Hospitalization, and Quality of Care

Objective:

This study tests the hypothesis that the rehabilitation hospital admission functional Independence Measure (FIM) score and interval post stroke can be used to define clinically relevant functional recovery goals, estimate length of stay, and compare quality of care.

Background:

The effects of time from stroke to rehabilitation unit admission on admission and discharge FIM scores, length of rehabilitation stay, and change in FIM score/day have not yet been reported.

Methods:

Analysis was based on prospectively collected data from patients admitted to an inpatient stroke rehabilitation unit with FIM scores ≤ 90 and an initial, unilateral, hemispheric, thrombotic, or embolic stroke who were fully independent without the use of an assistive device before their stroke. Patients with severe (admission FIM < 54) and moderate (admission FIM 54–90) stroke deficits were divided into cohorts based on interval from stroke to rehabilitation hospital admission: 0–2, 2–4, and 4–6 weeks.

Results:

Over a 17-month interval, 87 patients met selection criteria. Significant improvements were seen in total FIM scores for all. For those with moderate stroke, all three time cohorts reached a FIM score of 102 ± 2 SEM after 35 ± 2 days on the rehabilitation unit. Patients admitted within 2 weeks of a severe stroke reached a plateau FIM score of 72 ± 6 after 43 ± 3 days on the rehabilitation unit compared with the 2–4 week group (FIM = 57 ± 5 after 53 ± 4 days) and the 4–6 week group (FIM = 54 ± 10 after 40 ± 6 days). Complications increased with severity of stroke and delay in rehabilitation hospital transfer.

Conclusions:

Admission FIM score and interval from stroke to rehabilitation hospital admission can be used to set FIM outcome goals, predict length of rehabilitation hospitalization needed to meet those goals, and compare quality of care across institutions with different referral patterns. Our results provide a benchmark against which to compare less intense or shorter duration inpatient treatment options.

Medical and neurological complications during inpatient stroke rehabilitation

BACKGROUND AND PURPOSE

We sought to assess the type, frequency, and clinical predictors of neuromedical complications occurring during inpatient rehabilitation after stroke.

METHODS

One hundred consecutive patient records were reviewed. All medical and neurological complications requiring a physician's order for further evaluation or treatment were recorded.

RESULTS

Complications were urinary tract infection (44 cases), depression (33), musculoskeletal pain (31), urinary retention (25), falls (25), fungal dermatitis (24), hypotension (19), diabetes mellitus (16), hypertension (15), and other neuromedical problem (194). The mean +/- SD numbers of medical and neurological complications per patient were 3.6 +/- 2 and 0.6 +/- 0.8, respectively. Complications were independently related to both the severity of functional disability as judged by Barthel score (r = -.42, P < .001) and length of rehabilitation hospital stay (r = .54, P < .001). Cardiac complications were predicted by New York Heart Association class 3 or 4 symptomatology on admission (P < .05). The age, sex, interval from stroke to rehabilitation hospital admission, and ischemic versus hemorrhagic etiology of the stroke were unrelated to the number of complications observed. Thirteen patients required transfer back to an acute-care hospital, one of whom died within 24 hours of transfer. There were no deaths on the rehabilitation unit.

CONCLUSIONS

We have defined the type and frequency of neuromedical complications during inpatient rehabilitation after stroke. Their frequency varies with the severity of stroke, cardiovascular comorbidity, and length of stay.

Videofluoroscopic evidence of aspiration predicts pneumonia and death but not dehydration following stroke

In order to assess the risk of pneumonia, dehydration, and death associated with videofluoroscopic evidence of aspiration following stroke, the clinical records of 26 patients with aspiration and 33 randomly selected, case-matched, dysphagic controls without videofluoroscopic evidence of aspiration were reviewed. The videofluoroscopic modified barium swallow technique included 5 ml-thin and thick liquid barium, 5 ml barium pudding, and 1/4 cookie coated with barium, plus additional 20 and 30 ml of thin liquid barium. Patients were assessed a mean of 2 +/- 1 SD months poststroke and were followed for a mean of 16 +/- 8 SD months poststroke. The odds ratio for developing pneumonia was 7.6 times greater for those who aspirated any amount of barium irrespective of its consistency (p = 0.05). The odds ratio for developing pneumonia was 5.6 times greater for those who aspirated thickened liquids or more solid consistencies compared with those who did not aspirate, or who aspirated thin liquids only (p = 0.06). Dehydration was unrelated to the presence or absence of aspiration. The odds ratio for death was 9.2 times greater for those aspirating thickened liquids or more solid consistencies compared with those who did not aspirate or who aspirated thin liquids only (p = 0.01). Aspiration documented by modified videofluoroscopic barium swallow technique is associated with a significant increase in risk of pneumonia and death but not dehydration following stroke.

Depression in patients referred to a dementia clinic. A three-year prospective study

Of 225 patients referred to a dementia clinic, depression occurred in 31 (70%) of 44 patients not thought to be demented, six (24%) of 25 with cognitive impairment not severe enough to warrant the label dementia, and 24 (15%) of 156 with various forms of dementia, including 19 (19%) of 99 with Alzheimer-type dementia. Follow-up over three years has shown that 16 (57%) of 28 of the depressed, nondemented patients went on to develop frank dementia. Thirteen of these 16 had some sign, often subtle, of organic neurologic disease. Depressed elderly patients with any of the following are at high risk to develop dementia: evidence of cerebrovascular, extrapyramidal, or spinocerebellar disease; a modified Hachinski ischemic score of 4 or greater; a Mental Status Questionnaire score under 8; a dementia behavior score of 7 or higher; or confusion on low doses of tricyclic antidepressants. Dementing illnesses can present as depression with relatively little cognitive impairment.

The dexamethasone suppression test. An indicator of depression in stroke but not a predictor of rehabilitation outcome

The dexamethasone suppression test (DST) result was found to be abnormal in 49% of patients who were an average of seven weeks post stroke. The DST response correlated with depressive symptoms as measured by both the Zung and modified Hamilton Depression scales. The specificity of the DST for clinically diagnosed depression reached 87% for the 8 AM cortisol determination, with a corresponding sensitivity of 47%. It was not related to the patient's final level of self-care function as measured by the Barthel score, need for nursing home placement following discharge, or duration of rehabilitation needed to achieve maximum benefit. Abnormal responses were more prevalent in cerebral hemisphere than in brain-stem or cerebellar strokes. The more extensive the stroke the more likely the possibility of an abnormal DST response. The DST response is stable, with test-retest replicability being 84% at two weeks and 74% at seven weeks.