Methods and protocols
Derivation and synthesis of human monoclonal antibodies
Derivation of human monoclonal antibodies was performed by isolation of B-cells from CSF of patients with autoimmune encephalitis, or the peripheral blood of a healthy donor. Antibody-coding genes, of both heavy and light chains of G-isotype immunoglobulins were purified from B-cell lysates and amplified by PCR, before insertion into bacterial plasmids. For the recombinant expression of monoclonal antibodies, paired heavy and light chain-coding plasmids were co-transfected into HEK293T cells and purified from cell culture supernatants, as previously described. In this study, human monoclonal antibodies #003–102 and 008–218, which binds to the GluN1 subunit of the NMDAR, was derived from patient with NMDAR encephalitis (antibody herein referred to as NMDAR mAb) and human monoclonal antibody #113–115 and 113–175, reactive to the α1β3-containing GABAaR, was derived from a patient with GABAaR encephalitis (antibody herein referred to as GABAaR mAb). Isotype-matched control antibody, mGo-53, was derived from blood of a healthy donor (antibody herein referred to as Control mAb). All human monoclonal antibodies used in this study were generated by the laboratory of Harald Prüss at Charité-Universitätsmedizin, Berlin, with all required informed consent from patients (Kreye et al,
2016; Kreye et al,
2021).
Primary hippocampal cell cultures
Hippocampal cultures were prepared from embryonic day 18 Sprague-Dawley rat pups. Animal procedures were conducted in accordance with the European Community guidelines (Directive 2010/63/EU) regulating animal research, and were approved by the local Bordeaux Ethics Committee (APAFIS#3420-2015112610591204). Briefly, hippocampi were dissected in ice-cold HBSS containing Penicillin-Streptomycin (PS) and HEPES. Hippocampi were incubated with trypsin-EDTA and dissociated by mechanical trituration. Cell suspension—containing neurons and glia—was diluted in 60-mm sterile Petri dishes containing pre-warmed Neurobasal culture medium supplemented with horse serum and poly-
l-lysine coated 18-mm coverslips, at a density of 250–275 × 10
3 cells per ml. Dishes were maintained at 37 °C in 5% CO
2 in a humidity-controlled incubator. For standard primary cultures, at 3 days in vitro (DIV), a full media exchange with serum-free Neurobasal/B-27 culture media was performed. Full media exchanges continued twice weekly until use. Coverslips were flipped onto astrocyte feeder layers, 3 h after plating, and maintained in this inverted configuration. At DIV 3, a full media exchange with serum-free Neurobasal/B-27 culture media, containing 5 μM cytosine arabinoside was performed to prevent astrocyte proliferation. Kaech and Banker (
2006) protocols were used for experiments in which astrocytic expression of target surface proteins could interfere with data collection or add extraneous noise to imaging of neuronal cells (Kaech and Banker,
2006).
Where indicated, exogenous transgenes were introduced to neuronal cultures between DIV7-8 with a calcium phosphate transfection protocol. Briefly, a TE buffer solution containing purified bacterial plasmid DNA and 0.2 M CaCl2 was added dropwise to an equal volume HEPES-based phosphate buffer to form fine plasmid-containing calcium phosphate precipitates. The mass of DNA used for all transfection conditions did not exceed 2 μg total DNA per coverslip. Depending on the experimental requirements, combinations of the following bacterial plasmids were used: pRcCMV-flag-rGrin1, pRcCMVaa-SEP-rGrin1, pRK5CMV-rGabrg2-SEP, pRK5CMV-HA-SEP-rGria1, pcDNA3.1CMV-dsRed-rHomer1c, pEGFP-N1-CMV-mVenus-rGphn, pcDNA3CMVHA-hDRD1(wt) and pcDNA3CMV-CFP-hDRD1(ΔT2). Coverslips were transferred to 12-well culture plates, containing pre-warmed Neurobasal culture medium supplemented with kynurenic acid, 50 µl of plasmid precipitate suspension was added to each well and incubated for 90 min. The remaining precipitate suspension was then washed, and coverslips were returned to culture dishes until imaging at DIV 12–14. Autoantibodies and/or pharmacological reagents were added to neuronal cultures by dilution into the cell culture media, during a full media exchange the day prior to imaging. High-affinity autoantibody samples (003–102 and 113–115) were diluted to a final concentration of 0.5 μg per ml of media; lower-affinity autoantibodies (008–218 and 113–175 were applied to a final concentration of 1.0 μg per ml. Where indicated, tetrodotoxin was applied to a final concentration of 20 nM, D-APV at 1 μM, bicuculline at 5 μM and casein kinase 1 (CK1) inhibitor, CKI7, at 100 μM.
Organotypic hippocampal slice culture
Hippocampal slice cultures were prepared from Sprague-Dawley rat pups at postnatal day 5. Hippocampi were dissected in ice-cold dissection solution composed of 0.5 mM CaCl2, 2.5 mM KCl, 0.7 mM KH2PO4, 2 mM MgCl2, 0.3 mM MgSO4, 50 mM NaCl, 0.9 mM Na2HPO4, 25 mM glucose, 2.7 mM NaHCO3, 175 mM sucrose and 2 mM HEPES (pH 7.4, 320 mOsm). After isolation, 350-μm thick transverse hippocampal slices were prepared using a McIlwain tissue chopper. Slices were rested in dissection solution at 4 °C for 30 min, before plating onto PTFE membrane sections (FHLC01300, Millipore, UK) placed on Millicell cell culture inserts (PICM03050, Millipore, UK) and cultured in six-well plates containing pre-warmed slice culture media. Slice culture media was composed of 50% BME, 25% HBSS, 25% horse serum and supplemented with 25 mM glucose and GlutaMAX™ supplement. Slice cultures were maintained at 35 °C with 5% CO2 in a humidity-controlled incubator. Full culture medium exchanges were performed the day after dissection, and then three times per week with pre-warmed slice culture medium, until electrophysiological recordings between DIV 12 and DIV 15. Where indicated, slice cultures were transfected using an adeno-associated viral strategy, to label inhibitory interneurons or to express a calcium reporter, GCaMPVI in excitatory neurons. Viral particles containing the plasmid pAAV-mDlx-GFP (purchased from AddGene, Plasmid #83900), or pAAVCaMKII-GCaMPVI, were applied directly onto hippocampal slices at DIV 1, during medium exchange. Hippocampal slices were exposed to viral particles until the subsequent medium exchange at DIV 4. Expression of soluble GFP was confirmed by immunofluorescence of sparsely localised cell bodies across hippocampal layers, between DIV 12 and DIV 15. In all cases, autoantibodies were applied to slice cultures the day before electrophysiological recordings, by dilution into the slice culture media. A 20 μl droplet of antibody-containing media was also applied directly onto the slice, above the membrane insert, to facilitate diffusion of autoantibodies into the cultured tissue.
Quantum dot single-particle tracking
Hippocampal primary neurons transfected with either GluN1-SEP or GABAaR-SEP and Homer1c-DsRed or Gephyrin-mCherry as a synaptic marker respectively, were incubated for 10 min at 37 °C with rabbit polyclonal antibodies against GFP subunit (1/10,000). Neurons were then washed and incubated for 10 min at 37 °C with quantum dots 655 goat F(ab)2 anti-rabbit (Invitrogen, 1/10,000). Quantum dots were detected by using a mercury lamp and appropriate excitation/emission filters. Images were obtained with an acquisition time of 50 ms with up to 1000 consecutive frames. Signals were detected using an EM-CCD camera (Quantem, Roper Scientific). Quantum dots were followed on randomly selected dendritic regions for up to 20 min. Quantum dot recording sessions were processed with the MetaMorph software (Universal Imaging Corp.). The instantaneous diffusion coefficient, D, was calculated for each trajectory, from linear fits of the first four points of the mean square-displacement versus time function using MSD(t) = 5r 2 4(t)=4Dt. The 2D trajectories of single molecules in the plane of focus were constructed by correlation analysis between consecutive images using a Vogel algorithm. The synaptic diffusion coefficient was calculated from GluN2-QD trajectories that were only present inside the synaptic area, defined by Gephyrin or Homer staining. The instantaneous diffusion coefficient is reported as the median 25–75% (interquartile range, IQR).
Immunocytochemistry, imaging and analysis
Surface transfected GluN1-Flag, GluA1-SEP or γ2-GABAaR-SEP were specifically stained in live neurons using rabbit polyclonal antibodies against Flag (1/200, Sigma Aldrich, F2555, 15 min 37 °C) or against GFP (1/500, Thermo Fischer, A6455, 15 min 37 °C). Neurons were then fixed with 4% paraformaldehyde for 15 min. After blocking with 1% BSA for 1 h, neurons were incubated with secondary antibody Goat anti-rabbit Alexa 488 antibodies (Invitrogen, A11008, 1/1000, 1 h) for GluN1-Flag and GluA1-SEP or Donkey anti-rabbit Alexa 568 antibodies (Invitrogen, A10042, 1/1000, 1 h) for GABAaR-SEP. Neurons were washed, mounted and preparations were kept at 4 °C until observation using a spinning disk microscope Nikon Ni-E with spinning Yokogawa X1. Activation of astrocytes and microglial cells was investigated by immunostaining for GFAP or Iba1, respectively. Following incubation of organotypic hippocampal cultures with either NMDAR mAb, or antibody-free culture media, slices were briefly washed before fixation in 4% paraformaldehyde 4% sucrose PBS solution for 30 min at room temperature. Following fixation, slices were washed and aldehydic fluorescence was quenched with 50 mM ammonium chloride for 30 min. Slices were then washed again and submerged in permeabilization solution (0.5% Triton X-100 in PBS) and maintained overnight at 4 °C. Slices were washed before blocking with a 20% BSA PBS solution at 4 °C until the following day. Slices were then immunostained by submersion in 5% BSA PBS solution containing either rabbit antiGFAP (Abcam AB278054) or rabbit anti-Iba1 (WAKO 019-19741) at 1:1000 at 4 °C until the following day. Slices were then washed in 5% BSA PBS solution 4 times, over 2 h, at room temperature and under agitation. Secondary antibody (goat anti-rabbit alexafluor-488, Thermo Fisher A11008) was then added to 5% BSA PBS solution and slices were incubated at room temperature for 4 h, with agitation. Finally, slices were washed four times in PBS, over 2 h, before mounting in Vectashield anti-fade mounting medium, containing DAPI as a counterstain. A 200 µm spacer was added between the slide and cover glass to prevent compression and deformation of slices. Slices were kept at 4 °C until imaging. To quantify the level of GFAP and Iba1 expression and microglial and astrocytic cell morphology in organotypic slices, 20-µm thick zstacks were taken from the CA1 hippocampal subfield and maximum intensity projections were generated. A uniform threshold was applied across all projection images to identify the relative ratio of Iba1+ or GFAP+ pixels per stack projection, with the expectation that an increased activation of microglia or astrocytes will result in an increased expression of these intracellular proteins, and thus an increased positive-pixel ratio. Immunostainings of endogenous gephyrin were carried out with the following protocols: Following 24-h incubation with experimental autoantibodies, hippocampal cultures were washed, fixed and quenched previously as described. Cultures were then permeabilized in 0.1% Triton X-100 PBS solution for 15 min at room temperature. Coverslips were then washed in PBS and blocked as described before, and subsequently incubated with either mouse anti-gephyrin (Synaptic Systems 147 111), at 1:1000 for 2 h at room temperature, to label gephyrin scaffolds independent of phosphorylation status; or alternatively with phospho-specific mouse anti-gephyrin (Synaptic Systems 147 011), under the same protocols, to label gephyrin scaffolds phosphorylated at S270. Coverslips were then washed and labelled with goat anti-mouse alexafluor-488 (Thermo Fisher A11001), for 1 h at room temperature before washing and mounting and storage as described above.
Functional kinase assay
Kinase activity profiling was analysed by using a microarray assay containing 144 (STK) or 196 (PTK) phosphosites immobilised on a porous ceramic membrane, each of these phosphosites encoded in 13 amino acid long peptides which derived from literature or computational predictions with the phosphorylation of these phosphosites is then used to predict one or multiple upstream kinases (Protein tyrosine kinases for the PTK PamChip® and Serine threonine kinases for the STK PamChip®). In brief, STK or PTK microarrays were exposed to lysated neurones treated with NMDAR, GABAaR or control mAb for 24 h, following the manufacturer’s protocol. Fluorescently labelled anti-phospho-antibodies were used to detect the phosphorylation activity of kinases present in the sample. Images of each array were taken at several exposure times by a camera in the Pamgene workstation. Images are later used by the BioNavigator® software for image quantification, quality control, statistical analysis, visualisation and interpretation.
Electrophysiology
Spontaneous excitatory and inhibitory postsynaptic currents (sEPSC and sIPSC, respectively) were recorded using a whole-cell patch-clamp technique in voltage-clamp configuration. In summary, hippocampal slice cultures were transferred to the chamber of an upright microscope, containing 34 °C carbogen-bubbled extracellular solution composed of 126 mM NaCl, 3.5 mM KCl, 2 mM CaCl2, 1.3 mM MgCl2, 1.2 mM NaH2PO4, 25 mM NaHCO3 and 12.1 mM glucose (pH 7.4, 310 mOsm), perfused at approximately 2 ml per min. Neurons in the pyramidal cell layer of the CA1 hippocampal subfield were visualised using infrared differential interference contrast imaging. Patch pipettes for voltage-clamp recordings were filled with intracellular solution composed of 130 mM CsMeS, 20 mM HEPES, 0.2 mM EGTA, 5 mM QX-314·Cl, 2 mM NaCl, 4 mM Mg-ATP and 0.4 mM Na-GTP (pH 7.3, 290 mOsm). Pipette resistance ranged from 4–6 MΩ. After achieving a whole-cell configuration, AMPA receptor-mediated sEPSCs were recorded while clamping the membrane potential at −70 mV. After 10 min of sEPSC recording, cells were then clamped at 0 mV to record 10 min of GABAa receptor-mediated sIPSCs. Traces were recorded using a Multiclamp 700B amplifier and a Digidata 1550B interface controlled by Clampex 10.7 (Molecular Devices). Series resistance was monitored throughout the experiment by a brief voltage step of −5 mV at 30 s intervals. Data were discarded if series resistance was found to vary by more than 20% during the recording session. Traces were analysed using Clampfit software, in which synaptic events were detecting using an automated template search protocol. To permit correct characterisation of synaptic event amplitudes and kinetic parameters, extracted events were manually inspected for adherence to inclusion criteria. Specifically, events were discarded in instances where two synaptic events were found to be superimposed, where events occurred during a series resistance test or when peak amplitude failed to exceed 2 standard deviations of the baseline. Amplitudes of all detected events are displayed as cumulative frequency distributions, and for quantification, mean event amplitudes were calculated for each cell recorded (Control mAb: n = 25 cells; NMDAR mAb: n = 9 cells & GABAaR mAb: n = 15 cells). Error bars represent the standard error of the mean.
Quantification of tonic GABAergic currents was performed by the same recording configuration described above for GABAa receptor-mediated inhibitory currents, with the modification that tetrodotoxin was added to the extracellular recording solution, to a final concentration of 2 μM. After 5 min recording of a stable baseline period, bicuculline was washed into the recording solution, at a concentration of 5 μM. The amplitude of tonic GABAergic currents was estimated by recording the mean baseline before addition of bicuculline and subtracting the measured baseline after addition and 5-min wash-in of the drug. Control Experiments without BCC wash-in were used to ensure that baselines did not significantly drift during a 15-min recording period, by generating a “predicted” baseline based on linear regression fitting of the first 5 min of recording and comparing to the experimentally measured value (Fig.
EV2I).
Characterisation of intrinsic cellular excitability of hippocampal pyramidal cells was performed using a whole-cell current-clamp approach. In these experiments, patch pipettes were filled with intracellular solution composed of 127 mM K-gluconate, 8 mM KCl, 10 mM HEPES, 15 mM phosphocreatine, 4 mM Mg-ATP and 0.3 mM Na-GTP. The recording paradigm consisted of 12 sweeps of 2 s duration. A 500 ms variable-amplitude current step was introduced between 250 and 750 ms on each sweep, outside the current step epoch, cells were injected with 0 pA of current. Current step amplitudes ran sequentially from hyperpolarising (−150 pA) to depolarising (400 pA), in 50 pA increments. Traces were recorded using a Multiclamp 700B amplifier and a Digidata 1550B interface controlled by Clampex 10.7 (Molecular Devices), and data were analysed using Clampfit. Input–output curves were generated by extracting the number of action potential discharges inside each applied depolarising current step. Action potentials were identified using a template search algorithm in Clampfit. Resting membrane potential was estimated in each recorded cell by measuring the mean membrane potential during the final 1 s of each sweep, such that measurement would not be affected by variable-amplitude current epochs. The threshold for action potential firing was calculated using the first observed action potential in each cell recording. The threshold was defined as the lowest mV value at which the action potential waveform exceeded 20 mV per millisecond. Rheobase was defined as the lowest amplitude of an applied current step, in which an action potential was elicited. Input resistance was calculated from each of the three hyperpolarising current steps (−150, −100, and −50 pA), using the equation (Input Resistance) = (Mean Baseline Voltage)/(Injected Current). Intrinsic properties of inhibitory interneurons were characterised as described above, in hippocampal slices infected with an AAV-inducing soluble cytoplasmic GFP expression under an interneuron-specific (mDlx) promoter (see slice culture methods above), where patched cells were identified as GFP-positive under 488 nm LED illumination. Spontaneous action potential firing frequencies were quantified using a cell-attached voltage-clamp configuration. For these experiments, patch pipettes were filled with 150 mM NaCl. After formation of a seal between the cell membrane and patch pipette, in the order of gigaohm resistance, the voltage clamp was set to a potential at which zero current was injected through the pipette. Traces were recorded using a Multiclamp 700B amplifier and a Digidata 1550B interface controlled by Clampex 10.7 (Molecular Devices), and data were analysed using Clampfit. Action potential spikes were extracted from trances using a template search algorithm.
Calcium imaging
Organotypic hippocampal cultures were virally transfected using an AAV, inducing the expression of calcium reporter, GCaMPVI, under the excitatory neuron-specific promotor for CaMKII. Transfection was performed as described above at DIV 1 (see organotypic hippocampal slice culture methods) after 24 h exposure to either Control, NMDAR or GABAaR mAb, the CA1 subfield of hippocampal slice cultures was imaged using a spinning disk confocal microscope (Nikon Ni-E with spinning Yokogawa X1), at a frame rate of approximately 3 Hz. Slice cultures were maintained in warmed (37 °C) BrainPhys neuronal culture media throughout the imaging procedure, where time-lapse recordings in a single Z-plane were acquired for 7 min. Acquired image stacks were then analysed using a set of custom-built scripts for ImageJ software. Briefly, somatic regions of interest (ROIs) were selected by creating a “virtual δF/F image stack”. Mean fluorescence intensity was then measured in each ROI across the 7 min recording interval, and fluorescence fluctuations were determined by creating δF/F traces, where δF = Mean fluorescence intensity at frame n; and F = mean fluorescence intensity of the prior five consecutive frames (n − 6 to n − 1 frames). Spikes were then identified by running a spike detection algorithm, which searched the δF/F trace for incidents where point values on the δF/F function exceeds three times the standard deviation of the full δF/F trace. Spike detections were manually inspected in a subset of ROIs in each recording to ensure adequate and equivalent detections across acquisitions.
Quantification and statistical analysis
Comparisons between groups were either performed with parametric statistical tests (Student’s t test, one-way ANOVA followed by post hoc test) or with non-parametric Mann–Whitney test (single quantum dots). Statistical tests and the number of samples are described in the figure legends. Significance levels were defined as *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001, ****P ≤ 0.0001.