RNA-programmable cell-type monitoring and manipulation in the human cortex with CellREADR

Abstract

Reliable and systematic access to diverse cell types is necessary for understanding the organization, function, and pathophysiology of human neural circuits. Methods for targeting human neural populations are scarce and currently center on identifying transcriptional enhancers and engineering viral capsids. Here, we demonstrate the utility of cell access through RNA sensing by endogenous adenosine deaminase acting on RNA (ADAR) (CellREADR), a programmable RNA sensor-effector technology that couples cellular RNA sensing to effector protein translation, for accessing, monitoring, and manipulating specific neuron types in the human cortex ex vivo. We design CellREADRs to target two subpopulations-calretinin (CALB2) GABAergic interneurons and forkhead box protein P2 (FOXP2) glutamatergic projection neurons-and then validate targeting specificity using histological, electrophysiological, and transcriptomic methods. CellREADR expression of channelrhodopsin and GCamp enables the manipulation and monitoring of these populations in live cortical microcircuits. By demonstrating specific, reliable, and programmable experimental access to human neuronal subpopulations, our results highlight CellREADR's potential for studying neural circuits and treating brain disorders.

Keywords: CP: Molecular biology; CP: Neuroscience; PatchSeq; RNA sensor; calcium imaging; cellular access; cortex; excitatory neuron; human neuroscience; interneuron; optogenetics; organotypic slice culture.

Figure 1.. Deploying CellREADR to target RNA-defined cell types in ex vivo human cortex

(A) Human organotypic slice model. The human neocortex (middle and inferior temporal gyri; left) was sectioned at 350 μm and cultured on semi-permeable membranes for up to 16 days in vitro (DIV; right). CellREADR AAV vectors were applied to slices on DIV0. Orientation: A, anterior; D, dorsal; P, posterior; V, ventral. (B) Schematic of CellREADR design. In the single-virus design (left), binding of the sensor to the target initiates ADAR-mediated editing of a stop codon to express the downstream effector (mNeon). The binary system (right) uses a CellREADR virus (top right) to drive expression of tTA2 (Tet-advanced transactivator). A reporter virus, conditionally expressing a selected effector molecule (e.g., mNeon, ChIEF, or GCamp7f) under the control of the Tet-responsive element (TRE), is co-applied. (C) CellREADR targeting of diverse neuronal populations. Binary CellREADRs (mNeonGreen) designed against somatostatin (SST), Unc-5 netrin receptor B (UNC5B), parvalbumin (PVALB), forkhead box protein P2 (FOXP2), and calretinin (CALB2) were applied to the neocortex of at least 3 donors. Slices were immunostained for mNeon at DIV7. The CellREADR binary system drove robust expression of mNeon in differing lamina and in cells of various morphologies. Magnified images are indicated by dashed red boxes; throughout, pia and white matter (WM) are illustrated with dotted lines. Scale bars: 200 μm (large image) and 50 μm (magnified image). (D) Histological analysis of binary FOXP2 and CALB2 CellREADR targeting. CellREADR mNeon distribution (green, left) and protein expression of target (purple, middle) are depicted at DIV7. Fluorescence intensity profiles at far left reveal the depth distribution of cells targeted by CellREADR. Dashed boxes indicate areas depicted in (F). Scale bars: 200 μm. (E) Localization of CellREADR-targeted cells. CellREADR mNeon fluorescence intensity profiles measured across the depth of the cortex (0% = pial surface, 100% = WM boundary) averaged from 6 slices (tissues from 3 donors). The solid line shows the mean; the shaded area shows the SEM. FOXP2-mNeon was relatively uniform throughout cortical layers, while CALB2-mNeon was more restricted to outer layers. (F) Immunohistochemical characterization of CellREADR specificity. Representative images showing colocalization of CellREADR-mNeon with the corresponding target. Scale bars: 50 μm. (G) Quantification of CellREADR specificities as measured by immunostaining. Each point denotes the specificity of labeling measured from an individual donor’s tissue (FOXP2, n = 5 donors; binary CALB2, n = 7; singular CALB2, n = 3). Horizontal bars indicate mean specificity values for each CellREADR. Throughout the figures, data are presented as mean ± SEM. (H) Benchmarking CellREADR efficiency with a human interneuron enhancer virus DLX2.0-YFP. CALB2 CellREADR and DLX2.0-YFP viruses (rAAV2-retro) were applied to slices cut sequentially from the same neocortical tissue specimen. Tissue was immunostained at DIV7 against mNeon or YFP. Slice boundaries are indicated by the solid white line, and the WM is demarcated by a dashed white line; boxes mark the inset images on the bottom. Scale bars: 1 mm (top images) and 200 μm (bottom images). (I) Localization of DLX2.0-YFP expression. Representative image illustrating the efficiency and distribution of labeling achieved with a DLX2.0-YFP virus (left), with fluorescence intensity profile (right; averages from 3 donors) illustrating the distribution of labeled cells. Compared to CALB2 CellREADR labeling (D and H), DLX2.0-YFP⁺ cells were less concentrated in the outer cortex. Scale bar: 250 μm. (J) DLX2.0-YFP targeting of the CALB2 population. Quantification of colocalization of DLX2.0-YFP expression and CALB2 measured by immunostaining (images not shown); note the inter-subject variability in the targeting of CALB2 cells (n = 7 donors). (K) Efficiency of binary and singular CALB2 CellREADRs compared to DLX2.0-YFP enhancer virus. Quantification of cells labeled at DIV7 per unit area (binary CALB2, n = 6 donors; singular CALB2, n = 3; DLX2.0-YFP, n = 3). Note that although the CellREADRs were designed to target only CALB2 interneurons rather than multiple interneuron subclasses, they labeled more cells than the DLX2.0 virus (one-way ANOVA with Tukey’s post hoc).

Figure 2.. PatchSeq validation of CALB2 CellREADR targeting

(A) Reference gene expression profiles of human MTG interneurons described in a prior study. CALB2 expression is largely restricted to VIP subclass interneurons, indicating that the CALB2 READR should primarily target VIP interneurons. Of the 19 CALB2 READR-targeted cells studied by PatchSeq, all but 1 cell mapped to the VIP subclass (transcriptomic types of the 19 cells are listed at right; the number indicates count of cells) according to the classification scheme adapted from Tasic et al. and Hodge et al. (B) Expression of selected genes in CALB2 READR cells. CALB2 transcripts were detected in all but 1 cell, which was mapped onto the SST subclass. READR-targeted cells rarely expressed canonical markers of interneuron subclasses other than VIP (e.g., LAMP5, SST, and PVALB). Interestingly, 5 of the 6 cells that mapped to the PAX6 SYT6 type expressed the SLC17A7 (vesicular glutamate transporter 1), which is expressed widely across human MTG glutamatergic populations (Figure S2A); these cells also expressed the GABAergic marker GAD1. (C) PatchSeq electrophysiological measures of CALB2 READR-targeted neurons. Input-output curves illustrate the variation in rheobase, gain, and maximum firing frequency across the sampled population. The interrelationship between gene expression and physiological properties is further illustrated in Figure S3. (D) Variation in electrophysiological properties across and within interneuron transcriptomic types. Membrane responses to depolarizing and hyperpolarizing currents from cells mapped to the same transcriptomic types. Cells mapped to the PAX6 SYT6 type exhibited variation in the frequency and accommodation of action potential firing and exhibited varying responses to hyperpolarization. Scale bars: 20 mV, 200 ms. (E) Morphologies of CALB2 READR-targeted cells from the PatchSeq subset. Laminar positions of reconstructed neurons are illustrated at the top. Blue circles indicate somata (not to scale), and profiles indicate the vertical and horizontal densities of dendrites (black) and axons (red). Cortical depth is indicated on the left vertical axis; average layer boundaries are shown on the right vertical axis. Complete cell tracings are shown at the bottom. Figure S6 shows morphologies of additional CALB2- and FOXP2-targeted cells. The morphology of READR-targeted interneurons was also compared to those targeted previously using a distinct method (Figure S7). Scale bars: 200 μm.

Figure 3.. CALB2- and FOXP2-targeted neurons exhibit distinct physiological profiles and spontaneous activities

(A) Passive membrane properties of cells targeted by CALB2 (n = 60 cells) and FOXP2 (n = 43 cells) CellREADRs. Membrane capacitance and input resistance, but not hyperpolarizing sag ratio or resting membrane potential, differed between the two populations. Black bars indicate mean and SEM (Mann-Whitney U-test for non-normal distributions, t test for normal distributions). (B) Active properties of cells targeted by CALB2 (n = 60) and FOXP2 (n = 43) CellREADRs. Firing responses in response to current injections, with frequency plotted against current step. Insets show action potentials (APs) elicited by current injections at 2× rheobase; these examples were selected to represent the mean input-output curves for each cell type (black). The rheobase, gain, max firing frequency, and the coefficient of variation of the AP inter-spike interval all differed statistically between CALB2- and FOXP2-targeted populations (Mann-Whitney U-test or t test). Cross-correlations between all physiological properties are presented in Figure S5. (C) AP properties of cells targeted by CALB2 (n = 60) and FOXP2 (n = 43) CellREADRs. APs were elicited with a 2 ms current step. AP properties from different stimulation regimes are presented in Figure S4. AP half-width was measured at 50% of peak voltage and was found to be smaller in CALB2-targeted cells. AP height and threshold did not vary between target cell groups. The fast afterhyperpolarization (fAHP) following the AP was larger in CALB2-targeted cells. APs were aligned on their rising phase to compare waveforms between target cell groups (bottom). Group means are illustrated by black lines. CALB2-targeted cells exhibited a shorter AP duration and a smaller afterdepolarization than FOXP2-targeted cells (Mann-Whitney U-test or t test). Scales bars: 20 mV, 2 ms (left); 20 mV, 2 ms (middle); and 5 mV, 20 ms (right). (D) Subthreshold synaptic activity and suprathreshold firing were observed in targeted cells. Excitatory and inhibitory postsynaptic potentials (EPSPs and IPSPs, respectively) were detected in both CALB2- and FOXP2-targeted populations. Representative traces demonstrating EPSPs and IPSPs in cells of both populations are shown. Scale bars: 1 mV, 200 ms. (E) Recorded cells exhibited spontaneous firing from their resting potentials. Examples of spontaneous firing activity observed in CALB2- (red, n = 3 cells) and FOXP2- (blue, n = 3) targeted cells are illustrated, with average firing frequencies (observed over a 3 min period) indicated at right. Scale bars: 20 mV, 1,000 ms. (F) CALB2-targeted cells (n = 66 cells) were more likely than FOXP2-targeted cells (n = 50) to exhibit spontaneous firing (chi-squared test). (G) Spontaneous activity, measured as the frequency of spontaneous AP firing, differed between CALB2- and FOXP2-targeted populations (Mann-Whitney U test). (H) Traces demonstrating spontaneous AP firing from CALB2- (red) and FOXP2- (blue) targeted cells in either baseline conditions (left) or in the presence of glutamatergic blockers (right). Scale bars: 20 mV, 1,000 ms. (I) Glutamatergic blockers (CNQX/AP-5) reduced spontaneous firing frequency in most cells (CALB2, n = 6 cells; FOXP2, n = 2) but did not eliminate firing in every cell.

Figure 4.

Cell-type-specific optical manipulation of human neurons with CellREADR (A) CellREADR expression of an optogenetic effector, ChIEF, enables optogenetic control of AP firing in CALB2- but not FOXP2-targeted cells. CALB2-ChIEF neurons fired in response to 100 ms, 642 nm light pulses (left) or trains of 2 ms pulses (6/6 cells fired APs in response to both stimuli, with some failures in the train). Light stimuli depolarized FOXP2-ChIEF but did not drive AP firing (0/10 cells fired in response to stimuli; gray traces, individual trials from a single cells; black traces, averages). Scale bars: 20 mV, 20 ms, 50 ms. (B) Representative targeting scheme for optical interrogation of CALB2 synaptic connectivity. Putative postsynaptic cells were labeled with a DLX2.0-YFP virus (top left, green). A binary CellREADR vector driving CALB2-ChIEF-tdTomato was used to activate presynaptic cells (top right, red). During optical stimulation of the ChIEF-tdTomato⁺ population, patch-clamp recordings were made from YFP⁺/ChIEF-tdTomato⁻ cells; at the end of recordings, biocytin-filled patched cells were recovered (bottom right, purple, biocytin-streptavidin [SAV]). Scale bar: 50 μm. (C) Postsynaptic currents elicited by CALB2-ChIEF activation. Voltage-clamp recordings (average of 10 trials) made from a DLX2.0-YFP⁺/ChIEF-tdTomato⁻ neurons during optical stimulation of the CALB2-ChIEF population (left). Stimulation elicited optical postsynaptic currents (oPSCs) at the glutamate reversal potential (V_rev(Glu)) but not at the GABA reversal potential (V_rev(GABA)). Bicuculline was applied to verify that the observed oIPSCs were GABAergic. In DLX2.0-YFP⁺/ChIEF-tdTomato⁻ cells, oPSCs were never observed at V_rev(GABA). Averaged traces were recorded from a hSyn-mCherry⁺ pyramidal neuron during optical stimulation of the CALB2-ChIEF population (right). In this example, oPSCs were detected at V_rev(GABA) but not V_rev(Glu), indicating that the cell received glutamatergic inputs. These inputs were not blocked by bicuculline. No cell exhibited oPSCs at both V_rev(GABA) and V_rev(Glu). Scale bars: 0.2 pA, 50 ms (left) and 2 pA, 50 ms (right). (D) Failure rate of optically triggered synaptic currents. To illustrate trial-to-trial variability in oPSC responses, 10 trials from a DLX2.0-YFP⁺/ChIEF-tdTomato⁻ cell are shown at V_rev(Glu). The first light pulse had a failure rate of 10% (1/10), while the fourth light pulse had a failure rate of 40% (4/10; averaged response, black). Scale bar: 2 pA, 50 ms. (E) Waveforms of optically evoked postsynaptic responses. Optical PSCs measured at V_rev(Glu) from DLX2.0-YFP⁺/ChIEF-tdTomato⁻ interneurons and hSyn-mCherry⁺ pyramidal neurons were aligned to the light pulse and overlaid (left). All oPSCs were normalized to the peak current (right). The monophasic rise time and small jitter relative to the 2 ms light stimulus indicate that PSCs were monosynaptic events directly triggered by the optical pulse (averaged response, black). Scale bars: 2 pA, 10 ms (left) and 0.2 pA, 5 ms (right). (F) Quantification of postsynaptic responses to CALB2-ChIEF activation. When recordings were made from DLX2.0-YFP⁺/CALB2-ChIEF⁻ interneurons, oIPSCs were observed in 6/16 cells (37.5%), and oEPSCs were not detected. Recordings were also made from hSyn-tdTomato⁺ pyramidal neurons during CALB2-ChIEF activation. oIPSCs were detected in 3/14 cells (21.4%), and oEPSCs were detected in 2/14 cells (14.3%).

Figure 5.. Cell-type-specific monitoring of population activity with CellREADR

(A) Correlation between AP firing and GCamp7f signals. APs (black) were elicited by current injections in single cells expressing either CALB2-GCamp7f (n = 4 cells) or FOXP2-GCamp7f (n = 4). Calcium transients (green) were concurrently imaged at the cell soma and proximal dendrite. Traces show 6 APs and the resultant GCaMP signal measured from a CALB2-GCamp7f cell (top left, current injection represented by gray box; top inset shows the voltage trace at an expanded timescale). The relationship between the baseline-subtracted change in fluorescence and AP firing (right) was established by varying the current injection, counting APs, and making a linear fit of ΔF/F versus AP counts (CALB2: R² = 0.84; FOXP2: R² = 0.93). Scale bars: 20 mV, 100 ms (inset) and 20 mV, 2,000 ms. (B) Calcium imaging detects subthreshold events as well as APs. Recording of a CALB2-GCaMP7f demonstrating three evoked APs (black trace, at gray box) followed by a spontaneous subthreshold depolarization and then a single spontaneous AP. The calcium transient for these three events (green) is depicted; the rise times for each event were as follows: Tau_3AP = 390 ms, Tau_{Depolarization} = 1,760 ms, and Tau_1AP = 202 ms. Scale bars: 20 mV, 100 ms (inset) and 20 mV, 2,000 ms. (C) Maximum projection of CALB2-GCamp7f (left, red) and FOXP2-GCamp7f (right, blue) neurons measured in baseline conditions. Background-subtracted fluorescent profiles of somata were collected from 90 s video stacks (red and blue traces). CellREADR typically labeled 10–50 cells within a field of view. Scale bars: 50 μm, 20 s. (D) Color maps depicting population calcium signal dynamics. Calcium signals from slices labeled with CALB2-GCamp7f (left, red; n = 6 slices) or FOXP2-GCamp7f (right, blue n = 7) cells are represented by a color map (intensity scale at bottom; each map represents a recording performed on a single slice; slices are from 4 donors). Spontaneous activity levels varied between slices. Calcium signals from selected individual cells are depicted to the right of the color maps; most transients were small-amplitude, fast-rising events, similar to the transients produced by APs in (A). Large-amplitude, slow-rising transients (marked with asterisks) similar to the subthreshold events in (B) were also observed. Scale bars: 20 s (population maps) and 10 s (individual traces). (E) Correlated calcium events in slice populations. The correlation of cellular CALB2-GCaMP7f (n = 6 slices) or FOXP2-GCaMP7f (n = 7) calcium signals was measured within each slice and then compared between groups (CALB2- and FOXP2-targeted populations). Calcium signals were more strongly correlated in the FOXP2-targeted population (unpaired t test). (F) Calcium signal responses to nicotinic acetylcholine receptor activation. Nicotine (300 μM) was applied to a subset of slices following imaging baseline activity. Each image represents a region of interest (ROI) in a single slice labeled with either CALB2-GCaMP7f (left, red; n = 3 slices) or FOXP2-GCaMP7f (right, blue; n = 3). Scale bar: 20 s. (G) Nicotine application did not change the proportion of active cells within the labeled populations (CALB2, p = 0.08; FOXP2, p = 0.999; Fisher’s exact test). However, nicotine application increased the area of measured calcium events, normalized to baseline in CALB2-targeted cells (two-way ANOVA with Fisher’s least significant difference [LSD] post hoc). The dashed line on both graphs represents unity.