A transcriptomic axis predicts state modulation of cortical interneurons.

Transcriptomics has revealed that cortical inhibitory neurons exhibit a great diversity of fine molecular subtypes1-6, but it is not known whether these subtypes have correspondingly diverse patterns of activity in the living brain. Here we show that inhibitory subtypes in primary visual cortex (V1) have diverse correlates with brain state, which are organized by a single factor: position along the main axis of transcriptomic variation. We combined in vivo two-photon calcium imaging of mouse V1 with a transcriptomic method to identify mRNA for 72 selected genes in ex vivo slices. We classified inhibitory neurons imaged in layers 1-3 into a three-level hierarchy of 5 subclasses, 11 types and 35 subtypes using previously defined transcriptomic clusters3. Responses to visual stimuli differed significantly only between subclasses, with cells in the Sncg subclass uniformly suppressed, and cells in the other subclasses predominantly excited. Modulation by brain state differed at all hierarchical levels but could be largely predicted from the first transcriptomic principal component, which also predicted correlations with simultaneously recorded cells. Inhibitory subtypes that fired more in resting, oscillatory brain states had a smaller fraction of their axonal projections in layer 1, narrower spikes, lower input resistance and weaker adaptation as determined in vitro7, and expressed more inhibitory cholinergic receptors. Subtypes that fired more during arousal had the opposite properties. Thus, a simple principle may largely explain how diverse inhibitory V1 subtypes shape state-dependent cortical processing.

Behavioral origin of sound-evoked activity in mouse visual cortex.

Sensory cortices can be affected by stimuli of multiple modalities and are thus increasingly thought to be multisensory. For instance, primary visual cortex (V1) is influenced not only by images but also by sounds. Here we show that the activity evoked by sounds in V1, measured with Neuropixels probes, is stereotyped across neurons and even across mice. It is independent of projections from auditory cortex and resembles activity evoked in the hippocampal formation, which receives little direct auditory input. Its low-dimensional nature starkly contrasts the high-dimensional code that V1 uses to represent images. Furthermore, this sound-evoked activity can be precisely predicted by small body movements that are elicited by each sound and are stereotyped across trials and mice. Thus, neural activity that is apparently multisensory may simply arise from low-dimensional signals associated with internal state and behavior.

Neural correlates of blood flow measured by ultrasound.

Functional ultrasound imaging (fUSI) is an appealing method for measuring blood flow and thus infer brain activity, but it relies on the physiology of neurovascular coupling and requires extensive signal processing. To establish to what degree fUSI trial-by-trial signals reflect neural activity, we performed simultaneous fUSI and neural recordings with Neuropixels probes in awake mice. fUSI signals strongly correlated with the slow (<0.3 Hz) fluctuations in the local firing rate and were closely predicted by the smoothed firing rate of local neurons, particularly putative inhibitory neurons. The optimal smoothing filter had a width of ∼3 s, matched the hemodynamic response function of awake mice, was invariant across mice and stimulus conditions, and was similar in the cortex and hippocampus. fUSI signals also matched neural firing spatially: firing rates were as highly correlated across hemispheres as fUSI signals. Thus, blood flow measured by ultrasound bears a simple and accurate relationship to neuronal firing.

Spatial modulation of visual responses arises in cortex with active navigation.

During navigation, the visual responses of neurons in mouse primary visual cortex (V1) are modulated by the animal's spatial position. Here we show that this spatial modulation is similarly present across multiple higher visual areas but negligible in the main thalamic pathway into V1. Similar to hippocampus, spatial modulation in visual cortex strengthens with experience and with active behavior. Active navigation in a familiar environment, therefore, enhances the spatial modulation of visual signals starting in the cortex.

Dopaminergic and Prefrontal Basis of Learning from Sensory Confidence and Reward Value.

Deciding between stimuli requires combining their learned value with one's sensory confidence. We trained mice in a visual task that probes this combination. Mouse choices reflected not only present confidence and past rewards but also past confidence. Their behavior conformed to a model that combines signal detection with reinforcement learning. In the model, the predicted value of the chosen option is the product of sensory confidence and learned value. We found precise correlates of this variable in the pre-outcome activity of midbrain dopamine neurons and of medial prefrontal cortical neurons. However, only the latter played a causal role: inactivating medial prefrontal cortex before outcome strengthened learning from the outcome. Dopamine neurons played a causal role only after outcome, when they encoded reward prediction errors graded by confidence, influencing subsequent choices. These results reveal neural signals that combine reward value with sensory confidence and guide subsequent learning.

Spontaneous behaviors drive multidimensional, brainwide activity.

Neuronal populations in sensory cortex produce variable responses to sensory stimuli and exhibit intricate spontaneous activity even without external sensory input. Cortical variability and spontaneous activity have been variously proposed to represent random noise, recall of prior experience, or encoding of ongoing behavioral and cognitive variables. Recording more than 10,000 neurons in mouse visual cortex, we observed that spontaneous activity reliably encoded a high-dimensional latent state, which was partially related to the mouse's ongoing behavior and was represented not just in visual cortex but also across the forebrain. Sensory inputs did not interrupt this ongoing signal but added onto it a representation of external stimuli in orthogonal dimensions. Thus, visual cortical population activity, despite its apparently noisy structure, reliably encodes an orthogonal fusion of sensory and multidimensional behavioral information.

Synthesis and biological activity of azido analogues of 5,6-dimethylxanthenone-4-acetic acid for use in photoaffinity labeling.

5,6-Dimethylxanthenone-4-acetic acid (1) is scheduled for phase III clinical trials as a vascular disrupting agent. However, its biochemical receptor(s) have yet to be identified. In this report, the synthesis of azido analogues of 1 that could be used for photoaffinity labeling of proteins as an approach toward identifying its molecular targets is described. While 5-azidoxanthenone-4-acetic acid (2) and 5-azido-6-methylxantheone-4-acetic acid (3) were found to have biological activities similar to that of 1, 6-azido-5-methylxanthenone-4-acetic acid (4) was unstable and could not be evaluated. Both azido compounds 2 and 3 activated NF-kappaB, induced the production of tumor necrosis factor in cultured mouse splenocytes, and induced hemorrhagic necrosis of colon 38 tumors in mice. Photoreaction of lysates from spleen cells with tritiated 2 resulted in two radiolabeled protein bands at 50 and 14 kDa that could be competitively inhibited with cold 1 and cold 2. The azido compounds 2 and 3 exhibit all the requirements for use in photoaffinity labeling of potential receptor(s) for 1.

High-Yield Methods for Accurate Two-Alternative Visual Psychophysics in Head-Fixed Mice.

Research in neuroscience increasingly relies on the mouse, a mammalian species that affords unparalleled genetic tractability and brain atlases. Here, we introduce high-yield methods for probing mouse visual decisions. Mice are head-fixed, facilitating repeatable visual stimulation, eye tracking, and brain access. They turn a steering wheel to make two alternative choices, forced or unforced. Learning is rapid thanks to intuitive coupling of stimuli to wheel position. The mouse decisions deliver high-quality psychometric curves for detection and discrimination and conform to the predictions of a simple probabilistic observer model. The task is readily paired with two-photon imaging of cortical activity. Optogenetic inactivation reveals that the task requires mice to use their visual cortex. Mice are motivated to perform the task by fluid reward or optogenetic stimulation of dopamine neurons. This stimulation elicits a larger number of trials and faster learning. These methods provide a platform to accurately probe mouse vision and its neural basis.

A comparison of the ability of DMXAA and xanthenone analogues to activate NF-kappaB in murine and human cell lines.

DMXAA (5,6-dimethylxanthenone-4-acetic acid), the most potent of a series of xanthenone (XAA) analogues developed in this laboratory, is currently undergoing combination clinical trials as an antivascular agent for cancer treatment. XAAs have a complex mode of action, and in vitro assays that are predictive of in vivo antitumor activity have been difficult to develop. In this study, we have utilized a series including XAA, DMXAA, and mono-substituted XAA derivatives to determine firstly whether in vitro NF-kappaB activation of mouse cell lines predicts for the in vivo antitumor potential of this class of agents, and secondly whether the relative activity of these analogues is similar in murine and human cell lines. Electromobility shift assays were used to measure NF-kappaB activation in murine HECPP endothelial and 70Z/3 pre-B cells, and in human HPLNEC.B3 endothelial and Raji B-lymphoma cells. A significant correlation was obtained between NF-kappaB activation in HECPP cells by a series of XAA analogues at 100 microg/ml (r = 0.78, p = 0.008) and at 300 microg/ml (r = 0.75, p = 0.01) and the amount of hemorrhagic necrosis induced in Colon 38 tumors. Different structure-activity relationships were observed in human and murine cell lines. 8-MeXAA, which was inactive in HECPP and 70Z/3 murine cell lines, showed similar NF-kappaB activation to DMXAA in human HPLNEC.B3 cells and Raji B-lymphoma cells. These results suggest that the receptor protein(s) in human cells that mediate the human response may have a lower stringency to that for murine cells. We also noted differences in the dose-response relationships for NF-kappaB activation between lymphoid and endothelial lines that were species independent. With increasing concentrations of DMXAA, NF-kappaB activation in both murine and human lymphoid lines showed a reproducible fluctuation, while in endothelial lines, the intensity of NF-kappaB activation was relatively constant above a threshold concentration. The results demonstrate interspecies differences in the NF-kappaB response to XAA analogues, and may also reflect the complex nature of NF-kappaB regulation.

Induction of tumour necrosis factor and interferon-gamma in cultured murine splenocytes by the antivascular agent DMXAA and its metabolites.

The induction of haemorrhagic necrosis by 5,6-dimethylxanthenone-4-acetic acid (DMXAA) in transplantable murine tumours depends on the in situ synthesis of cytokines, particularly tumour necrosis factor (TNF). Since the in vivo action of DMXAA would be greatly clarified by the development of an in vitro model, we investigated whether DMXAA could induce cytokines in cultured murine splenocytes. DMXAA alone induced low amounts of TNF with an optimal concentration of 10 microg/mL and an optimal time of 4 hr. When combined with low concentrations of lipopolysaccharide, deactivated-lipopolysaccharide (dLPS) or phorbol-12-myristate-13-acetate that did not elicit TNF production alone, synergistic TNF production was obtained. DMXAA also induced interferon-gamma at an optimal dose of 300 microg/mL, but the addition of dLPS had no further effect. Decreasing culture pH, although not changing the optimal concentrations for stimulation, increased both TNF and interferon-gamma production in response to DMXAA. The major DMXAA metabolites, DMXAA-glucuronide and 6-hydroxy-5-methylxanthenone-4-acetic acid, did not induce either cytokine alone, in combination with dLPS or at low pH. The results indicate that DMXAA rather than a metabolite is responsible for cytokine induction and suggest that the microenvironment of the tumour may be responsible for the observed selective induction of cytokines in tumour tissue.

Neutrophil influx and chemokine production during the early phases of the antitumor response to the vascular disrupting agent DMXAA (ASA404).

5,6-Dimethylxanthenone-4-acetic acid (DMXAA) acts through tumor vascular disruption and cytokine production and is the first of its class to enter phase 3 trials. We characterized leukocytes and cytokines in murine Colon 38 tumors before and after DMXAA treatment. Tumor mass declined 50% 24 hours after DMXAA administration, but the leukocyte count per gram of tumor increased threefold owing to a large influx of Ly6G(+)CD11b(+)F4/80(-) cells with the morphology of neutrophils. However, B and T lymphocytes, natural killer cells, and macrophages in the tumor all decreased in numbers. Seven chemokines were substantially induced in the tumor, spleen, and serum 4 hours after DMXAA administration. Using cultured spleen cell subpopulations, CD11b(+) cells (largely monocytes and macrophages) were shown to be the primary producers of tumor necrosis factor alpha, interleukin 6 (IL-6), and macrophage inflammatory 1alpha (MIP-1alpha). CD49b(+) natural killer cells produced IP-10, whereas CD45R(+) B lymphocytes produced regulated upon activation normal T cell express sequence. T lymphocytes were not major producers of cytokines in the response to DMXAA. Murine peripheral blood leukocytes (PBLs) produced a similar panel of cytokines in culture to that detected in mouse serum after DMXAA treatment. Cytokines in human PBL cultures were subsequently measured with the aim of identifying potential serum markers of the human response to DMXAA. IP-10 (P < .001), monocyte chemoattractant protein 1 (P < .001), and sCD40L (P < .01) were decreased, whereas IL-8 (P < .001) and MIP-1alpha (P = .03) were increased in DMXAA-treated compared with untreated PBL cultures from a group of 12 donors.