Loss of dopamine in Parkinson's disease is hypothesized to impede movement by inducing hypo- and hyperactivity in striatal spiny projection neurons (SPNs) of the direct (dSPNs) and indirect (iSPNs) pathways in the basal ganglia, respectively. The opposite imbalance might underlie hyperkinetic abnormalities, such as dyskinesia caused by treatment of Parkinson’s disease with the dopamine precursor l-DOPA. Here we monitored thousands of SPNs in behaving mice, before and after dopamine depletion and during l-DOPA-induced dyskinesia. Normally, intermingled clusters of dSPNs and iSPNs coactivated before movement. Dopamine depletion unbalanced SPN activity rates and disrupted the movement-encoding iSPN clusters. Matching their clinical efficacy, l-DOPA or agonism of the D2 dopamine receptor reversed these abnormalities more effectively than agonism of the D1 dopamine receptor. The opposite pathophysiology arose in l-DOPA-induced dyskinesia, during which iSPNs showed hypoactivity and dSPNs showed unclustered hyperactivity. Therefore, both the spatiotemporal profiles and rates of SPN activity appear crucial to striatal function, and next-generation treatments for basal ganglia disorders should target both facets of striatal activity.
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We appreciate support from HHMI, the Stanford CNC Program, Stanford Photonics Research Center, Pfizer and a GG Technologies gift fund; fellowships from Stanford (J.D.M., T.H.K.), the Helen Hay Whitney Foundation (J.D.M.), the US National Institutes of Health (J.G.P., J.B.D.), HHMI (B.A.), the US National Science Foundation (B.A.), the Bill & Melinda Gates Foundation (B.A.), and the Swiss National Science Foundation (B.F.G.). We thank L. Burns, L. Kitch, E. Hamel, J. Lecoq, M. Larkin, T. Fieblinger, S. Ganguli, A. Girasole, A. Graybiel, A. Kreitzer, R. Malenka and A. Nelson for technical assistance and discussion, Inscopix Inc. for technical support and upgrades, and B. Rossi for scientific illustration.Reviewer information
Nature thanks D. Surmeier, G. Stuber and the other anonymous reviewer(s) for their contribution to the peer review of this work.
Extended data figures and tables
Extended Data Fig. 1 Characterizations of striatal SPN Ca2+ activity patterns in live brain slices and recorded in behaving mice using a chronic microendoscopy preparation.
a, We performed whole-cell patch-clamp recordings of SPNs in acute brain slices, using dual epifluorescence and infrared Nomarski (IR-DIC) microscopy to guide the recordings. We selectively recorded from fluorescent dSPNs and iSPNs in brain slices from Drd1acre and Adora2acre mice that had been injected into the striatum with AAV2/9-CAG-FLEX-GCaMP6m-WPRE.SV40. The numerical aperture used for the fluorescence recordings was matched to that used for Ca2+ imaging studies in freely behaving mice (Methods). b, Illustrative traces (top) of neural membrane potential (Vm) showing the changes that result upon stepwise injections of electrical current (bottom). The traces exhibit typical waveforms for SPNs. c, To visualize Ca2+ transients evoked by different numbers and frequencies of action potentials in iSPNs and dSPNs in brain slice recordings, we elicited spiking with 1-nA pulses (1-ms duration; 1 to 10 pulses, delivered at 5, 10, 20, 50 and 100 Hz). Top, an example of a Vm trace during 1–10 pulses injected at 10 Hz. Middle, example traces of current pulse injections delivered at 10 Hz. Bottom, a representative trace of somatic Ca2+ transients in response to the same 10-Hz current injections. d, Example Ca2+ activity traces for each current injection pattern tested in brain slices. As expected, electrical stimulation at higher frequencies evoked larger amplitude Ca2+ transients, with more sharply rising Ca2+ waveforms than those evoked at lower stimulation frequencies. Arrows mark current injections. e, f, Mean ± s.e.m. values for Ca2+ transient amplitudes (e) and area under the Ca2+ transient waveform (AUC; f) as a function of the number of action potentials evoked, for dSPNs and iSPNs in brain slices. Values for each cell are normalized to those evoked at the highest stimulation intensity (10 action potentials, 100 Hz). Ca2+ event amplitudes rose linearly with the number of action potentials (R2 > 0.99 for 5–20 Hz; R2 > 0.97 for all frequencies). There were no significant differences in event amplitude or AUC between dSPNs and iSPNs, at any stimulus intensity. n = 9 dSPNs and 8 iSPNs; two-way, mixed-design ANOVA. Exact P values can be found in the Supplementary Information for all extended data figures. g, h, Mean ± s.e.m. values for half-rise (g) and half-decay (h) times (t1/2), measured for the Ca2+ events evoked in dSPNs and iSPNs in brain slices, plotted as a function of the number of action potentials. Consistent with their more prolonged stimulus durations, lower stimulation frequencies yielded greater increases in the transient rise time. Ca2+ transient decay times were nearly independent of action potential frequency or number. i, Mean ± s.e.m. values of the AUC of stimulus-evoked Ca2+ events in dSPNs and iSPNs in brain slices, under control conditions or perfused with SKF81297 (1 μM) or quinpirole (10 μM), respectively. Neither drug significantly affected somatic Ca2+ event AUCs in either SPN type, regardless of stimulus intensity. n = 6 dSPNs and 6 iSPNs; two-way, repeated-measures ANOVA. The individual data points are plotted alongside the mean values. j, Two example time-lapse fluorescence image series, acquired over the course of experiments in a Drd1acre mouse (top) and an Adora2acre mouse (bottom). Scale bars are 125 μm and apply uniformly to all panels within each row. Insets show example Ca2+ transients in the absence and presence of dopamine receptor agonist SKF81297 or quinpirole. Scale bars are uniformly sized for all insets. k, Surgical implantation of the microendoscope did not affect the ability of mice to improve their motor performance on the accelerating rotarod assay, as shown by their increased latencies to fall off the rod, which parallel the performance improvements of control mice without an implanted microendoscope. P = 0.8; two-way, repeated-measures ANOVA; n = 13 control and 20 implanted mice. Inset, Microendoscope implantation did not alter levels of spontaneous movement in an open field arena. P = 0.7; n = 5 control and 6 implanted mice; Wilcoxon rank-sum test. Data points from individual mice are shown as open circles. l–n, Box-and-whisker plots of the rates (l), amplitudes (m) and full-width at half-maximum (FWHM) durations (n) of Ca2+ events observed in live normal (untreated) mice in individual dSPNs and iSPNs, before (Pre-lesion) and after (Post 14-d) dopaminergic lesions, as the mice were resting (left) or moving (right). In resting mice, Ca2+ event rates decreased in dSPNs and increased in iSPNs after the lesion (l) as characterized in Fig. 3. When the mice were moving, Ca2+ event rates in iSPNs were similar before and >14 days after the lesion, whereas the rates in dSPNs were depressed after the lesion. Each box-and-whisker plot is based on n = 3,325–3,703 dSPNs or iSPNs, from 12 Drd1acre and 13 Adora2acre mice, respectively, tracked before or 14 days after the 6-OHDA lesion. Horizontal lines denote median values, boxes cover the middle two quartiles and whiskers span 1.5× the interquartile range. Data denoted as ‘Pre-lesion’ were taken on day −5. Data denoted as ‘Post 14-d’ were taken on day 14.
Extended Data Fig. 2 The spatial coordination index is a metric of the extent to which the activated neurons at an individual time point are spatially clustered.
a, Outline of the algorithm (Methods) used to compute the SCI at individual time points in the fluorescence Ca2+ movies. For each time point in a ΔF(t)/F0 movie, we created an image of all cells that were coactive within 1 s of each other. A schematic of an example image (left) has a mixture of active (red) and inactive (white) cells. We computed the set of distances between all pairs of active cells in the image (middle). We then compared these values to the set of pairwise distances between active neurons in shuffled versions of the data from the same image, in which the identities of all the individual cells were randomly permuted while maintaining the same set of cell centroid locations. The shuffled dataset as a whole comprised 1,000 different random shuffles. We compared the cumulative probability distribution function (CDF) of all pairwise distances between active cells in the real image, to that for the shuffled data (right). We then tested two hypotheses, that the activated cells in the real image were either more spatially clustered than expected from a random pattern of activation, or less spatially clustered than expected from random activation. To test these two hypotheses, we performed a pair of one-sided Kolmogorov–Smirnov tests, comparing the real CDF values to those of the shuffled data. We determined the SCI by selecting the smaller of the two P values from these two tests, taking its logarithm, and assigning the sign of the index according to whether the CDF of the real data showed greater (positive sign) or less (negative sign) spatial clustering than the CDF of the shuffled data. b, Depictions of three images with different SCI values. The left image has an SCI >0, due to its many neighbouring coactive cells. The middle image has an SCI near zero, implying the activation pattern is consistent with that of a random distribution. The right frame has an SCI <0, indicating the active cells are further apart than generally expected of random activity. c, Examples of three image frames of different SCI values, from an actual Ca2+ movie acquired in a Drd1acre mouse. Active cells are shown enlarged and shaded white, whereas inactive cells are shaded grey. On the left is an image with multiple neighbouring coactive neurons and a high SCI. The middle image has a modest but positive SCI. The right image has a negative SCI, indicating that the activated cells are further apart than expected given a random pattern of activation. d, Distributions of pairwise distances between all pairs of active dSPNs for the three corresponding image frames shown in c. The distributions for the real data are shown in red, whereas those for the shuffled datasets are shown in grey. e, Mean time-dependent cross-correlation functions between mouse speed and the SCI of Ca2+ activity in dSPNs (left) and iSPNs (right). Cross-correlation values are shown normalized to their values for abscissa values of ±4 s (Methods). We computed the SCI from Ca2+ event traces to which we applied forward-smoothing, using one of five different filter values (coloured curves; Methods). Error bars are omitted for clarity in e, but are comparable to those shown in f. The centre-of-mass of the cross-correlation functions occurred at positive time lags (around 12–60 ms), indicating that rises in spatially coordinated Ca2+ activity preceded increases in mouse speed (P < 0.06 for both genotypes and all filter time constants; Wilcoxon signed-rank test), but there were no significant differences across the two mouse lines (P > 0.05 for all filter time constants; Wilcoxon rank-sum test; n = 37 cross-correlation functions from 16 Drd1acre mice and n = 52 from 21 Adora2acre mice). f, Mean cross-correlation functions between mouse speed and the SCI of Ca2+ activity in dSPNs and iSPNs computed from Ca2+ event rasters forward-smoothed with a 1,000-ms time constant. Shading indicates s.e.m. e, f, Values taken from n = 16 Drd1acre mice and n = 21 Adora2acre mice, aggregated over the 1-h recordings on day −5 and the 30-min recordings performed on days −4 to −1 after saline vehicle injection but before drug administration.
Extended Data Fig. 3 Different types of movements recruit distinct but overlapping populations of spatially proximal dSPNs and iSPNs.
a, To study and compare movements of different types made by freely moving mice, we used custom software to extract from the behavioural videos the intervals from −4 to 4 s surrounding the onset of each movement bout. Using this software, we manually labelled each bout as an instance of forward locomotion, a left or right turn, grooming or upward rearing. If the mouse made multiple types of movement within an individual bout, we labelled the bout according to the first movement type exhibited, as only the interval from −1 to 2 s relative to motion onset was used in subsequent analyses of the accompanying neural Ca2+ activity. b, The fraction (mean ± s.e.m.) of SPNs that exhibited Ca2+ activity, relative to the baseline periods immediately preceding each movement type. Relative to baseline (dashed line), there was a significant increase in the fraction of dSPNs and iSPNs activated for all movement types except grooming. **P < 5 × 10−3 and ***P < 5 × 10−8 for dSPNs; ##P < 10−4 and ###P < 10−10 for iSPNs; Wilcoxon signed-rank test. Data in b and c are from n = 492 forward movements, 657 right turns, 810 left turns, 732 grooming and 204 rearing bouts from 17 Drd1acre mice, and n = 790 forward, 785 right turns, 1,015 left turns, 792 grooming and 164 rearing bouts from 21 Adora2acre mice. c, Rates (mean ± s.e.m.) of Ca2+ events in dSPNs and iSPNs, plotted as a function of time relative to the onsets of different types of movements. Event rates are shown normalized to the values of −2 to −1 s before motion onset and rose significantly above baseline values during all types of movement in both cell types. P < 10−6 for both cell types and all movement types; Wilcoxon signed-rank test. d, Mean values of the neural ensemble similarity computed for the sets of dSPNs and iSPNs that were active during pairs of bouts of either the same (on-diagonal) or different (off-diagonal) types of movements (Methods). For all movement types, the similarities of the cell ensembles that were active on different bouts of the same movement type were significantly greater than those of the ensembles that were active during the baseline periods before each bout. #P < 0.05; Kolmogorov–Smirnov test, corrected for multiple comparisons using a Benjamini–Hochberg procedure with a false-discovery rate of 0.05. Off-diagonal asterisks indicate that the neural ensembles that were active during bouts of two different movement types were significantly less similar to each other than the ensembles activated on different bouts of the same movement type, for both of the two movement types under consideration. *P < 0.05; Kolmogorov–Smirnov test, corrected for multiple comparisons using a Benjamini–Hochberg procedure with a false-discovery rate of 0.05. e, The cumulative distribution functions show the range of ensemble similarity values for the dSPN and iSPN ensembles that were activated on two bouts of the same movement type or on two bouts of different movement types (as described in d). For both iSPNs and dSPNs, ensemble similarity values were significantly lower for two bouts of different movement types than for two different bouts of the same movement type. P < 0.01; Kolmogorov–Smirnov test. f, Mean pairwise distances between the individual dSPNs or iSPNs activated on bouts of two different movement types. We normalized the values by comparing the mean weighted distance between the cells that were active during the two movement types to the same quantity determined under the null hypothesis that the spatial probability distributions of active cells on the two movement types were the same. For the latter determination, we created shuffled datasets in which we randomly permuted the firing rate of each cell between the two movement types, and we averaged the results over twenty-five different shuffled datasets. We normalized each distance value by taking the actual mean value, subtracting the mean value determined under the null hypothesis, and then dividing this difference by the standard deviation of the distance across the twenty-five shuffled datasets (Methods). Asterisks indicate that the mean pairwise distance was significantly greater than that expected by chance, indicating that the two movement types activated spatially distinguishable cell ensembles. *P < 0.05; Wilcoxon signed-rank test, corrected for multiple comparisons using a Benjamini–Hochberg procedure with a false-discovery rate of 0.05. Plots in d–f are based on n = 102 and n = 126 comparisons between bouts of the same movement type, and 255 and 315 comparisons of bouts of different movement types, in Drd1acre and Adora2acre mice, respectively. Values are from n = 17 Drd1acre mice and n = 21 Adora2acre mice, aggregated over the 1-h recordings on day −5 and the 30-min recordings performed on days −4 to −1 after saline vehicle injection but before drug administration.
Extended Data Fig. 4 Simultaneous recordings of dSPNs and iSPNs show that the two cell types encode movement with indistinguishable spatiotemporal patterns of activation.
a, To image dSPN and iSPN Ca2+ activity concurrently, we prepared mice that expressed GCaMP6m in both cell types but tdTomato only in dSPNs (Methods). Mice were head-fixed on a running wheel beneath the objective lens of a two-photon microscope. A piezoelectric actuator moved the axial position of the objective to allow volumetric imaging across four planes at different depths of the tissue (15-μm axial spacing). The mice were free to run or rest on the wheel (Supplementary Video 3). We tracked the motion of the wheel using a rotary encoder (500 encoder pulses per revolution) that provided a read-out of the instantaneous locomotor speed. We computed the mean speed of the mouse at a time-resolution matching that of the two-photon volume acquisition rate (6 Hz, or 166 ms per time bin). We identified periods of movement by marking all time bins in the mean speed trace with values >0.2 cm s−1. To identify instances of motion onset, we selected all time bins for which speeds were <0.2 cm s−1 for at least 1 s in the immediately prior time bins, and >0.2 cm s−1 for at least 1 s in the immediately subsequent time bins. To identify instances of motion offset, we used the opposite criterion. b, Histological section of dorsomedial striatum expressing tdTomato (red) in Drd1acre positive cells and immunostained for GFP (green) to visualize GCaMP6m expression. Closed arrowheads point to three example dSPNs that expressed both GCaMP6m and tdTomato. Open arrowheads point to three putative iSPNs that expressed GCaMP6m but not tdTomato. Scale bar, 50 μm. c, Representative cell maps from each of the four imaging planes in an example mouse with 118 detected dSPNs (blue) and 183 detected iSPNs (red). Scale bars, 100 μm. d, Representative traces of Ca2+ activity from 10 dSPNs (blue) and 10 iSPNs (red) from the same mouse as in c. Grey shading here and in e, g, h denotes periods classified as movement on the running wheel. e, Locomotor speed on the running wheel (top) and Ca2+ activity traces of individual dSPNs (middle) and iSPNs (bottom), during part of an imaging session in an example mouse. Note the clear correlation between locomotion and Ca2+ activity in both cell types. f, Mean cumulative distribution functions of Ca2+ event rates in dSPNs (n = 699) and iSPNs (n = 1020) were nearly identical, during periods of rest (left) and running (right). g, Mean Ca2+ event rates in dSPNs and iSPNs as a function of mouse locomotor speed. Events rates are shown normalized to their mean levels when the mice were resting (speed <0.2 cm s−1). Grey shading denotes speeds at which we classified the mouse as moving (>0.2 cm s−1). h, Mean locomotor speed (bottom) and the fraction of SPNs that are activated (top), plotted as a function of time relative to motion onset (left) and offset (right). We determined the onset time of neural activity as the time at which the mean percentage of active cells was ≥3 s.d. of the percentage of active cells during the baseline periods of −3 to −1 s relative to motion onset. Using this criterion, dSPNs and iSPNs respectively activated −666 ± 97 ms and −733 ± 51 ms before motion onset (mean ± s.e.m; n = 5 mice; Methods), which were statistically indistinguishable. P = 0.9; Wilcoxon rank-sum test. i, Mean locomotor speed as a function of time relative to the occurrences of Ca2+ events in dSPNs and iSPNs. For each cell, we normalized these traces to the mean speed 20 s before Ca2+ excitation, then averaged the traces across all cells of each type and all mice. j, Mean pairwise coactivity (Methods) for dSPN–dSPN, iSPN–iSPN and dSPN–iSPN cell pairs, computed as a function of the distances between the pairs of cells, normalized to coactivity values in temporally shuffled datasets (1,000 distinct shuffles) in which time-correlated activity patterns were scrambled. Cyan shading indicates proximal (20–100 μm) cell pairs. Data are from periods of movement on the running wheel. k, Pairwise coactivity values (mean ± s.e.m.) were significantly greater for proximal cell pairs than those in temporally shuffled datasets (*P < 0.05; Wilcoxon rank-sum test; n = 5 mice), and did not depend on the SPN types. n.s. denotes P > 0.05; Wilcoxon rank-sum test. Data points from individual mice are shown as open circles. l, We created GLMs to make time-dependent predictions of mouse locomotor speed based on the ΔF(t)/F0 activity traces of the cells determined by two-photon Ca2+ imaging. We used the GLM libraries in MATLAB (Mathworks), using a Gaussian noise model and taking the identity function as the linking function. We used 70% of the time bins in the set of ΔF(t)/F0 traces for training the GLM, and 30% for testing it. To study the accuracy of the speed predictions as a function of the number of cells (n) included in the GLM, for each value of n, we randomly chose n cells from the total available, constructed the GLM and computed the Pearson’s correlation coefficient between the actual and predicted speed traces. For each n value, we repeated this procedure with 10 different randomly chosen subsets of cells and then computed the mean correlation coefficient of the real and predicted speeds across the 10 different sub-samplings. In an example mouse, traces of the actual running speed (grey) were well fit by models based on the activity of either dSPNs (blue) or iSPNs (red). m, Mean Pearson correlation coefficients for an example mouse between the actual and predicted running speeds, for GLMs based on either dSPNs or iSPNs (10 sets of randomly chosen cells for each abscissa value, out of 301 total cells). Inset shows the correlation coefficients (mean ± s.e.m.) from n = 5 mice, computed using either 115 dPSNs or 115 iSPNs from each mouse. Data points from individual mice are shown as open circles and were statistically indistinguishable across the two cell types. P = 0.13; Wilcoxon signed-rank test. f–j, Colour shading denotes s.e.m. for n = 5 Drd1acre × Ai14 mice.
Extended Data Fig. 5 6-OHDA injections rapidly ablate SNc dopamine neurons and disrupt motor behaviour without impairing the fidelity of Ca2+ event detection.
a, Example coronal brain section from an experimental mouse, immunostained for GCaMP6m (anti-GFP, green) and tyrosine hydroxylase (anti-TH, red). DAPI was used to stain the nuclei (blue). White lines demarcate the position of the implanted microendoscope, and the boundaries of nearby brain areas. AcbC, accumbens core; Cg, cingulate cortex; CPu, caudate/putamen; IC, insular cortex; M1 and M2, motor cortices; Pir, piriform cortex; S1 and S2, somatosensory cortices. Labels are adapted from an anatomical atlas of the mouse brain38. Scale bar, 1 mm. b, Representative midbrain coronal sections acquired 1 day after unilateral infusions of saline (top) or 6-OHDA (middle), or >14 days after 6-OHDA infusion (bottom), and then immunostained for tyrosine hydroxylase (red). DAPI was used to stain the nuclei (blue). Dopamine cell bodies are absent in the SNc of mice that received 6-OHDA, at both 1 and >14 days after 6-OHDA infusion. Scale bar, 500 μm. c, 24 h after infusions into SNc of 6-OHDA but not of saline, mice exhibited disrupted patterns of spontaneous locomotion in an open field arena. P = 4 × 10−3 for 6-OHDA and P = 0.8 for saline; n = 7 saline-treated and 14 6-OHDA-treated mice; Wilcoxon signed-rank test for comparisons to the pre-lesion behaviour of each mice. d, The median fluorescence intensity across the entire imaging field (normalized to pre-lesion values on day −5 for each mouse and then averaged across mice) decreased significantly after 6-OHDA lesions in mice of both genotypes. P < 10−7 comparing median fluorescence intensities (normalized to pre-lesion means) averaged across 5 days before versus 5 days after lesion; Wilcoxon rank-sum test. However, fluorescence intensities stabilized 15–17 days after the 6-OHDA lesion, and there were no further significant changes over time in either mouse line. P > 0.05; n = 5 Drd1acre and 7 Adora2acre mice; Spearman correlation. Error bars indicate s.e.m. for 5 Drd1acre and 7 Adora2acre mice. e, The number of active SPNs (mean ± s.e.m.) detected in total on each day of the study, normalized to the mean value (dashed horizontal line) detected before 6-OHDA infusion (days shaded grey). On days on which mice received drug treatments (Fig. 1a), the data shown here are from the initial portions of the recording sessions before drug administration. The number of active cells was stable across the study, except for a single pairwise difference in the number of active iSPNs. Friedman ANOVA; n = 5 Drd1acre and n = 7 Adora2acre mice; P > 0.05 for Drd1acre and P = 0.01 for Adora2acre; P = 5 × 10−4 for post hoc test comparing the number of iSPNs detected 1 day before the lesion and 15 days after the lesion; Fisher’s least significant difference test with a Holm–Bonferroni correction for multiple comparisons. f, Cumulative distributions of peak ΔF/F values for Ca2+ events from individual dSPNs (top) and iSPNs (bottom), before and after 6-OHDA lesion. After the lesion, Ca2+ event amplitudes were significantly greater in dSPNs (3.7 ± 0.02% (pre-lesion) versus 6.0 ± 0.03% (14 days after)), but smaller in iSPNs (4.4 ± 0.02% (pre-lesion) versus 4.0 ± 0.02% (14 days after)). Data are mean ± s.e.m.; P < 10−10 for both SPN types; Wilcoxon rank-sum test. Data in f and g are from n = 3,332–3,734 dSPNs or iSPNs, from before (day −5) or 14 days (day 14) after 6-OHDA lesion, in n = 12 Drd1acre mice and 13 Adora2acre mice, respectively. g, Cumulative distributions of the signal detection fidelity (d′) of Ca2+ events in individual dSPNs (top) and iSPNs (bottom), before and after 6-OHDA lesion. Owing to the decrease in background fluorescence intensity, Ca2+ events in dSPNs became easier to detect after 6-OHDA lesion, as quantified by the increase in d′ values for dSPNs. d′ = 17 ± 0.1 (mean ± s.e.m.; pre-lesion) versus 29 ± 0.2 (14 days after). The changes in d′ values for iSPNs were smaller in magnitude (d′ = 22 ± 0.1 (pre-lesion) versus 19 ± 0.1 (14 days after)), while keeping the optical conditions for Ca2+ event detection extremely favourable. Crucially, all changes in Ca2+ event detection fidelity values were opposite to those observed for Ca2+ event rates in the two cell types (Fig. 3), and thus cannot account for the event rate changes. h, d′ values for Ca2+ events from individual dSPNs (left) and iSPNs (right), before and after 6-OHDA lesions, and after drug treatments in mice following 6-OHDA lesion. d′ values increased after 6-OHDA lesions and decreased after the drug treatments in dSPNs. By contrast, d′ values decreased after 6-OHDA lesions and increased after drug treatment in iSPNs. ***P < 10−10 for all conditions in both genotypes; Wilcoxon rank-sum test; values are from n = 1,770–2,027 dSPNs from 5 Drd1acre mice and n = 1,719–2,393 iSPNs from 6 Adora2acre mice, recorded before (day −5) and after 6-OHDA lesion (day 14), or after the lesion and quinpirole (day 16), SKF81297 (day 18) and l-DOPA (day 20) treatments. As in g, these changes in d′ have an opposite sign to the changes in Ca2+ event rates (Fig. 4), and thus cannot account for the latter effects. Throughout the study, d′ values remained extremely high, in that a d′ value >16 corresponds mathematically to a mean rate of <10−10 errors in Ca2+ event detection per hour. This nearly vanishing predicted error rate is unattainable experimentally over many hours of recording but underscores the highly favourable conditions for Ca2+ imaging.
Extended Data Fig. 6 Lesion of dopamine neurons altered Ca2+ event rates in dSPNs and iSPNs during spontaneous open field exploration and forced movement on the rotarod.
a, b, Cumulative probability distributions of Ca2+ event rates in dSPNs (left) and iSPNs (right) while mice were resting (a) or in locomotion (b) before the lesion of dopamine neurons, 1 day after the lesion (day 1), and >14 day after the lesion (day 14). Ca2+ event rates in dSPNs were depressed at both time points after the lesion, during rest and locomotion. Ca2+ event rates in iSPNs were elevated at both time points after the lesion when mice were resting. However, when the mice were moving, iSPN activity rates were elevated at 1 day but not >14 days after the lesion, compared to values from before the lesion. The distributions of Ca2+ event rates in dSPNs in resting mice were nearly identical at 1 and >14 days, making it hard to visually distinguish the two plots. Data are from 12 Drd1acre mice and 13 Adora2acre mice. The Drd1acre mice yielded a total of 2,554–3,732 activated dSPNs during movement and rest, across the different days of the study, whereas the Adora2acre mice yielded 3,209–3,702 iSPNs. All comparisons within each SPN type between Ca2+ event rates from before the lesion to those 1 d and 14 d after the lesion were significant. P < 10−3; Wilcoxon rank-sum test. c, Cumulative distribution functions of Ca2+ event rates in individual dSPNs and iSPNs as mice walked on the rotarod. At 1 day after dopamine depletion (day 1), Ca2+ event rates were reduced in dSPNs and increased in iSPNs. At >14 days after dopamine depletion (day 14), Ca2+ event rates were still reduced in dSPNs but in iSPNs were at or even slightly below normal values. Data pre-lesion and >14 days after dopamine depletion are based on 5 Drd1acre mice and 7 Adora2acre mice; however, 1 day after dopamine depletion only 2 Drd1acre mice and 3 Adora2acre mice could perform the rotarod assay without falling off, precluding determinations of Ca2+ event rates from the other mice on that day. All comparisons within each SPN type between Ca2+ event rates from before the lesion to those 1 and >14 days after the lesion were highly significant (P < 10−10; Wilcoxon rank-sum test), except for the comparison of iSPN activity rates from before the lesion to those >14 days after (P = 5 × 10−3; Wilcoxon rank-sum test). d, Rates of Ca2+ events (mean ± s.e.m.) as mice walked on the rotarod, normalized to the corresponding values from before dopamine depletion. dSPN activation rates were substantially reduced at both time points after the lesion. iSPN event rates were substantially increased 1 day after the lesion (day 1), but had returned to near baseline levels by 14 days after the lesion (day 14), mirroring the effects of dopamine depletion on dSPN and iSPN activity during spontaneous movement (see Fig. 3f). **P < 5 × 10−3 and ***P < 5 × 10−7; Wilcoxon rank-sum test. Owing to the large numbers of Ca2+ events across thousands of SPNs that contributed to these calculations, the slight depression of Ca2+ event rates in iSPNs at 14 days after the lesion was statistically significant. e, The extent of pairwise coactivation of dSPNs (left) and iSPNs (right) during the rotarod assay, as a function of the pairwise distance between cells, before dopamine depletion, at 1 and >14 days after dopamine depletion. Values are normalized to those attained from shuffled datasets in which the times of the Ca2+ events of each cell were randomized (Methods). The spatial clustering of activity in proximal iSPN pairs (20–100 μm apart) was significantly reduced 14 days after the lesion, relative to values from beforehand. P < 10−16; Wilcoxon rank-sum test; n = 7 Adora2acre mice. Shaded areas denote s.e.m. Data and statistical tests in c–e are from 1,930, 712 and 1,672 dSPNs and 1,731, 853 and 1,607 iSPNs that were active during the rotarod assay pre-lesion, 1 (day 1), and 14 (day 14) days after the lesion, respectively.
Extended Data Fig. 7 In healthy mice, D1R or D2R antagonists affect SPN activity similarly to an acute (but not chronic) loss of dopamine neurons, whereas dopamine receptor agonists have divergent effects from those observed in dopamine-depleted mice.
a–c, Example locomotor trajectories (15-min duration) of mice moving freely within a circular arena (a) and paired example traces of mouse locomotor speed and the mean rate of Ca2+ events in dSPNs (b) and iSPNs (c) after administration of saline vehicle or a selective antagonist of D1Rs (SCH23390, 0.2 mg kg−1) or D2Rs (raclopride, 1 mg kg−1). Both drugs reduced locomotion relative to vehicle. P = 10−4; Wilcoxon signed-rank test; n = 18 mice. d, e, Mean Ca2+ event rates in dSPNs (d) and iSPNs (e) as a function of locomotor speed, following administration of saline vehicle, a D1R- or D2R-selective antagonist (0.2 mg kg−1 SCH23390 or 1 mg kg−1 raclopride, respectively) (top) or a D1R- or D2R-selective agonist (1 mg kg−1 SKF81297 or 1 mg kg−1 quinpirole, respectively) (bottom). Rates are normalized to cell population means when mice were at rest (<0.5 cm s−1) after vehicle injection (Methods). Colour shading surrounding each curve denotes s.e.m. f, SPN Ca2+ event rates during rest and movement after treatment with a dopamine-receptor antagonist or agonist. The D1R antagonist (SCH23390) reduced dSPN but not iSPN activity. The D2R antagonist (raclopride) increased iSPN but not dSPN activity. Both agonists (quinpirole, SKF81297) reduced activity in both SPN types during rest and movement. *P < 0.05, **P < 5 × 10−3, ***P < 5 × 10−7; Wilcoxon signed-rank test comparing all drug conditions to saline vehicle injection; n = 14 speed bins per mouse in the resting state (<0.5 cm s−1) and 24 speed bins per mouse in the moving state (>0.5 cm s−1); n = 7 Drd1acre and 11 Adora2acre mice. g, h, Mean Ca2+ event rates in dSPNs (g) and iSPNs (h) relative to motion onset (left) and offset (right) following administration of saline vehicle, SCH23390 or raclopride (top), or SKF81297 or quinpirole (bottom). Traces are normalized to cell population means averaged over the time period from −2 to −1 s preceding motion onset. Raclopride increased dSPN (P = 6 × 10−11) and iSPN (P = 2 × 10−9) activation at motion onset. Wilcoxon rank-sum test; comparing 11 time bins for the interval of 0–2 s after motion onset to the baseline periods in each of the 7 Drd1acre and 11 Adora2acre mice. SCH23390 slightly altered dSPN (P = 0.02) but not iSPN activation (P = 0.4) at motion onset. In Drd1acre mice, there were n = 1,917 (vehicle), 134 (SCH23390) and 129 (raclopride) instances of motion onset, whereas in Adora2acre mice there were 2,798 (vehicle), 155 (SCH23390) and 233 (raclopride) such instances. Colour shading surrounding each curve denotes s.e.m. i, j, Coactivity of proximal (20–100 μm apart) dSPN (i) or iSPN (j) cell pairs during periods of movement, following administration of saline vehicle, SCH23390 or raclopride (top) or saline, SKF81297 or quinpirole (bottom). Coactivity values are plotted after subtraction of the coactivity values determined for temporally shuffled datasets under the same drug treatment conditions, and then normalized to the values attained for saline administration. Comparing measured values for each drug to those attained with saline; *P < 0.05, **P < 5 × 10−3 and ***P < 5 × 10−7; Wilcoxon signed-rank test; 8 spatial bins of cell–cell separation for each of the n = 7 Drd1acre and n = 11 Adora2acre mice. d–j, Data are based on the same 7 Drd1acre and 11 Adora2acre mice. Figure 1a shows the schedule of drug treatments. Data acquired in the 30-min Ca2+ imaging sessions after drug administration have been normalized for each mouse to the values determined on the same day during the 30-min Ca2+ imaging sessions occurring after saline vehicle administration but before drug treatment.
Extended Data Fig. 8 Dopamine depletion reduces the movement-type specificity of iSPN activity patterns.
a, Following dopamine depletion, we classified mouse movement bouts into different types, as in Extended Data Fig. 3. After 6-OHDA lesion, there were insufficient bouts of upward rearing to allow statistical analyses. b, Percentages of SPNs (mean ± s.e.m.) that exhibited Ca2+ activity, relative to the baseline periods (dashed line) immediately before each movement type, >14 days after 6-OHDA lesion. Compared to baseline periods, there was a significant increase in dSPN and iSPN activity for all movement types, except during grooming. *P < 0.05 and **P < 5 × 10−3 for dSPNs; #P < 0.05 and ##P < 5 × 10−3 for iSPNs; Wilcoxon signed-rank test. Data in b and c are based on 206 forward movements, 200 right turns, 290 left turns and 314 grooming bouts in 13 Drd1acre mice and 331 forward movements, 295 right turns, 194 left turns and 339 grooming bouts in 21 Adora2acre mice. c, Rates of Ca2+ events (mean ± s.e.m.) in dSPNs and iSPNs as a function of time relative to the onsets of different types of movements, >14 days after 6-OHDA lesion. Event rates are shown normalized to the values from −2 to −1 s before motion onset. As found when all movements were grouped together (Fig. 3g), the rates of iSPNs hardly increase at motion onset in parkinsonian mice. d, Mean values of the neural ensemble similarity computed for the sets of dSPNs and iSPNs that were active during pairs of bouts of either the same (on-diagonal) or different (off-diagonal) types of movements, in freely behaving mice >14 days after 6-OHDA lesion (Methods). For each pair of movement types, values are shown normalized to the corresponding value found in healthy mice before 6-OHDA lesion. Asterisks indicate a significant difference between the pre- and post-lesion values. *P < 0.05; Wilcoxon rank-sum test, corrected for multiple comparisons using a Benjamini–Hochberg procedure with a false-discovery rate of 0.05. e, Cumulative distribution functions showing the range of ensemble similarity values for the sets of dSPNs and iSPNs that activated on two bouts of different movement types. The similarity of the dSPN ensembles activated on different movement types decreased significantly after 6-OHDA, indicating that the representations of different movements became more distinct. P < 0.05; Kolmogorov–Smirnov test. By comparison, the iSPN ensembles activated on different types of movements became more similar after 6-OHDA lesion, consistent with a reduction in the selectivity of iSPN movement encoding. P < 0.05; Kolmogorov–Smirnov test. f, Mean pairwise distances between the individual dSPNs or iSPNs activated on bouts of two different movement types, in freely behaving mice >14 days after 6-OHDA lesion. We expressed the values as z scores, as described in Extended Data Fig. 3f. For each pair of movement types, we then normalized each z score by the corresponding value found in healthy mice before 6-OHDA lesion. g, Cumulative distribution functions showing the normalized distances between dSPNs (left) and iSPNs (right) (computed as in f) before and after 6-OHDA lesion, for bouts of different movement types. The mean pairwise distances between iSPNs, but not dSPNs, that activated on bouts of different movement types decreased significantly after 6-OHDA lesion, indicating that the iSPN cell ensembles active on the different movement types were less spatially distinguishable after 6-OHDA lesion. P = 0.02; Kolmogorov–Smirnov test. Plots in d–g are based on n = 102 and n = 126 comparisons between bouts of the same movement type, and 255 and 315 comparisons of bouts of different movement types, in 17 Drd1acre and 21 Adora2acre mice, respectively, before 6-OHDA lesion, and on n = 72 and n = 78 comparisons between bouts of the same movement type, and 180 and 195 comparisons of bouts of different movement types in 12 Drd1acre and 13 Adora2acre mice, respectively, >14 days after 6-OHDA lesion. The pre-lesion data are the same as in Extended Data Fig. 3. The data >14 days after the lesion are aggregated from the 1-h recordings on day 14 plus the 30-min recordings on day 20 that occurred after saline vehicle injection but before administration of 6 mg kg−1 l-DOPA (see Fig. 1a).
Extended Data Fig. 9 After unilateral lesion of SNc dopamine cells, l-DOPA and dopamine agonists induce a contralateral turning bias, and l-DOPA can also induce dyskinesia.
a–c, Time traces showing mean ± s.e.m. effects of different doses of l-DOPA, SKF81297 and quinpirole on the contralateral rotational bias of mice, scored in 20-min time bins, >14 days after unilateral 6-OHDA lesion. All drug doses had their maximal behavioural effects approximately 30 min after drug administration. All dose–time interactions differed significantly from vehicle treatment (P < 5 × 10−3), and the effects of l-DOPA and SKF81297 were dose-dependent (P < 5 × 10−3). Two-way, repeated-measures ANOVA. d, Time traces of the mean ± s.e.m. mouse rotational bias for the three different drugs in a–c, at doses of each drug that induce comparable levels of rotational bias during the time window used in our studies for Ca2+ imaging (shaded in grey), during which we assessed the effects of these drugs on dSPN and iSPN activity in parkinsonian mice (Fig. 4). e, Comparison of the net rotational bias in the first 40 min after administration of the three drugs at the same doses as in d. Note that, as assessed by their effects on turning behaviour, these three compounds were statistically indistinguishable at these doses. ‘ns’ denotes P > 0.2 for comparisons between drugs; n = 13 mice; Wilcoxon signed-rank test. However, all drugs had significant effects relative to vehicle treatment. **P < 5 × 10−3; Wilcoxon signed-rank test; n = 13 mice. f–i, Time traces showing how different dosages of l-DOPA affect the mean ± s.e.m. axial (f), orofacial (g), limb (h) and total (i) AIMS values, a behavioural measure of dyskinesia in preclinical models of Parkinson’s disease31. All three l-DOPA doses had significant effects compared to vehicle treatments (P < 0.02; two-way ANOVA) and differed significantly in their effects at the different dosages (P < 0.05). As in d, the grey shading in i denotes the time window used for Ca2+ imaging (Figs. 4, 5). j, l-DOPA increased the peak total AIMS values, in a dose-dependent manner, in the first 40-min after mice received the l-DOPA doses in f–i. *P < 0.05, **P < 5 × 10−3; Wilcoxon signed-rank test. Error bars in a–d and f–i indicate s.e.m. All data in a–j are from a distinct cohort of n = 13 freely moving mice not subject to the protocol of Fig. 1a.
Extended Data Fig. 10 SPNs encode specific movements via the activation of spatial clusters of cells consisting of both dSPNs and iSPNs.
a, Classical models of the basal ganglia, such as the rate model1,2, posit opposing roles for dSPNs and iSPNs in movement generation. A simple instantiation of these ideas (a ‘stop–go’ model11) predicts increased dSPN and decreased iSPN activity at movement initiation, and decreased dSPN and increased iSPN activity at movement termination. This is depicted here schematically in the traces of aggregate SPN Ca2+ activity in the model (middle), relative to motion onset and offset (top). However, in the actual data the activity of both SPN types increases at motion onset and decreases at motion offset (bottom). b, Other types of models are more compatible with the concurrent activation of both SPN types at motion onset. In ‘suppression–selection’ models15, dSPNs select a motor program, while iSPNs simultaneously suppress competing motor programs. In these models, specific subsets of dSPNs and iSPNs coactivate to select and suppress specific motor programs, respectively. Here we depict this idea using schematic traces of single-cell activity. dSPNs that encode either ‘type A’ or ‘type B’ movements activate selectively during one or the other type of movement (see top trace of movements in a). By contrast, iSPNs, which suppress competing movements such as those of ‘type C’ and ‘type D’, activate on both ‘type A’ and ‘type B’ movement bouts. A prediction of this model is that the cell populations encoding different types of movement are more similar (that is, less selective), and possibly more broadly distributed anatomically, for iSPNs than dSPNs. However, the actual data reported here show that the selectivity and spatial distributions of neural responses during movement are comparable in both SPN types (Fig. 2c–e and Extended Data Figs. 3d–f, 4j, k). c, More specifically, we found action-selective ensembles in both dSPNs and iSPNs (Extended Data Fig. 3). Unlike the suppression–selection model in b, our findings suggest that dSPNs and iSPNs coordinate to select motor programs, depicted here as traces of single-cell activity in which movement ‘type A’ and ‘type B’ encoding dSPNs and iSPNs activate selectively on bouts of movement types A and B, respectively (see top trace of movements in a). Furthermore, the dSPNs or iSPNs activated for one movement type were physically closer to each other than to SPNs activated for different movement types (Extended Data Fig. 3f). These analyses quantify what is visually apparent in the Ca2+ videos of striatal activity, which show that multiple, segregated clusters of coactive dSPNs or iSPNs activate at the onset of motion (Supplementary Videos 1, 2). Finally, using two-photon microscopy to image the simultaneous patterns of Ca2+ activity in dSPN and iSPN ensembles, we found that the coactivity of nearby dSPN–iSPN pairs was indistinguishable from that of pairs of the same SPN type (Extended Data Fig. 4). Combining these findings, our data show that different subsets of spatially intermingled dSPNs and iSPNs activate for distinct types of movement (for example, ‘type A’ and ‘type B’ movements, bottom depictions of ‘spatial distribution’).
Extended Data Fig. 11 Implications for basal ganglia dysfunction in parkinsonian and dyskinetic states.
a–c, Schematic depictions of the spatial organization of SPN activity. Active cells are shown as filled circles. a, Prior to dopamine loss both dSPNs and iSPNs exhibit spatially clustered patterns of coactivation when mice are resting. Clusters of the two cell types are spatially overlapping (Extended Data Figs. 4, 10). During movement, both cell types undergo an increase in the number of active cells and extent to which activity is spatially clustered. b, After dopamine loss dSPN activity decreases in rate but remains spatially clustered in resting mice (Fig. 3e, j). Moreover, dSPNs still coactivate in a spatially clustered manner during movement initiation (Fig. 3g). The rate of iSPN activity is increased after dopamine depletion in resting mice (Fig. 3e). However, iSPNs are less responsive at the onset of and throughout movement, and their motion-related activity shows almost no spatial clustering (Fig. 3g–j). c, During l-DOPA-induced dyskinesia (LID), dSPNs are hyperactive, unresponsive to movement, and spatiotemporally decorrelated (Fig. 5c–h), much like iSPNs after dopamine loss. During LID, iSPNs are hypoactive but retain their movement-related activation and spatial clustering (Fig. 5c–h), much like dSPNs after dopamine depletion. d–f, Iconic depictions of the SPN activity patterns during normal, parkinsonian and dyskinetic states, and the implications for downstream basal ganglia function. Icons are inspired by those in previous work32. For each icon in the top row, the height of the rectangular pedestal represents the amplitude of spontaneous SPN activity in resting mice. The height and width of protrusions above the pedestals respectively denote the amplitude and spatial distribution of motion-related SPN activity. On the basis of the known excitatory and inhibitory projections between basal ganglia nuclei, the icons in subsequent rows show the predicted consequences for the downstream neural targets. In these icons, indentations into the rectangular pedestal denote inhibitions of neural activity during active movement. The globus pallidus pars externa (GPe) and the sub-thalamic nucleus (STN) are in the basal ganglia’s indirect pathway and receive signals from striatal iSPNs. In the direct pathway, dSPNs project directly to the globus pallidus pars interna and substantia nigra pars reticulata (GPi/SNr), where signals from the two basal ganglia pathways converge (purple icons). GPi/SNr activity influences motor program selection by modulating downstream thalamacortical neurons and brainstem motor nuclei (not depicted). d, Before dopamine depletion, GPi/SNr cells receive signals during movement from the direct and indirect pathways that should induce, respectively, spatially structured patterns of neural activation and inhibition in GPi/SNr. We hypothesize that the convergence and spatial patterning of these bidirectional modulations enhance the specificity of the disinhibitory signals transmitted from GPi/SNR (left purple icon). In this view, the spatially coordinated, joint modulation of activity in GPi/SNr by both dSPNs and iSPNs may be crucial for well-choreographed motor programs15. e, After dopamine depletion, spontaneous activity is reduced in dSPNs and increased in iSPNs. The rate model predicts that these changes in spontaneous activity lead to increases in spontaneous GPi/SNr activity (middle purple icon), tonically suppressing movement. Dopamine depletion also abolishes the spatially clustered, motion-related activation of iSPNs. This added deficit in motion-related iSPN activity is unaccounted for by the rate model and may upset the normal bidirectional spatial patterning of GPi/SNR output activity. This in turn may reduce the specificity of GPi/SNr inhibition, causing abnormal movement specification and motor coordination. f, During LID, spontaneous activity rises in dSPNs and declines in iSPNs. The rate model predicts that these changes should tonically drive movement by suppressing GPi/SNr activity (right purple icon). LID also disrupts the amplitude and spatial structure of motion-related dSPN activity. This decorrelated dSPN hyperactivity may disrupt the normally focused suppression of GPi/SNr activity during movement, resulting in increased but less specified movements.
This file contains a Supplementary Note, Supplementary Methods, Supplementary References and Supplementary Table 1
Locomotion evokes spatially clustered dSPN activity Synchronized videos of a D1-Cre mouse exploring an open field arena (left) and somatic Ca2+ activity (∆F/F) activity in the mouse’s striatal dSPNs (right). The mouse is initially at rest, during which the cells are relatively quiescent. As the mouse begins to actively explore the arena, the cells become more active, and their dynamics are visibly organized into anatomical clusters of co-active neurons. The video is played back at 2× real speed.Scale bars are 10 cm (black) and 150 μm (white).
Locomotion evokes spatially clustered iSPN activity Synchronized videos of an A2A-Cre mouse exploring an open field arena (left) and somatic Ca2+ activity (∆F/F) activity in the mouse’s striatal iSPNs (right). The mouse is initially at rest, during which the cells are relatively quiescent. As the mouse begins to actively explore the arena, the cells become more active, and their dynamics are visibly organized into anatomical clusters of co-active neurons. The video is played back at 2× real speed. Scale bars are 10 cm (black) and 150 μm (white).
Two-photon Ca2+ imaging of SPN activity patterns in an awake, head-fixed mouse Simultaneously acquired videos of a head-fixed mouse running on a wheel during two-photon fluorescence Ca2+ imaging (left), and the concurrent Ca2+-related changes in fluorescence intensity in SPNs (right). For each of four axial planes (15-μm spacing) in the brain, we represented Ca2+ signals as ΔF(x, y, t) /σ (x, y), where the normalization factor σ (x, y) is an estimate of each pixel’s baseline noise (Methods). The video shows the mean two-dimensional projection of the data acquired simultaneously at the four planes. When the mouse runs, there is a clear increase in the extent of spatially coordinated SPN Ca2+ activity as compared to when the mouse is at rest. The video is played back at 3× real speed. Scale bar is 100 μm.
A montage of representative videos of dSPN and iSPN Ca2+ activity in freely behaving mice in normal, parkinsonian and dsykinetic statesVideos of dSPN and iSPN Ca2+ activity in one representative D1-Cre mouse (top) and a representative A2A-Cre mouse (bottom), respectively, acquired using the miniature fluorescence microscope as the mice explored an open field arena. The first column (left) shows Ca2+ activity under normal conditions, in which the rates of dSPN and iSPN activity are balanced and both SPN types exhibit spatiotemporally coordinated activity. 14 days after the 6-OHDA lesion (middle), dSPNs are hypoactive, whereas iSPNs are hyperactive and have lost their spatiotemporal coordination. During L-DOPA-induced dyskinesia (right), iSPNs are hypoactive, whereas dSPNs are hyperactive and have lost their spatiotemporal coordination. The videos are played back at 4× real speed. Scale bar is 100 μm.