Human tissue
Post-mortem brain tissue (motor cortices) from MS patients and non-neurological controls were provided by a UK prospective donor scheme with full ethical approval from the UK Multiple Sclerosis Society Tissue Bank (MREC/02/2/39) and from the MRC-Edinburgh Brain Bank (16/ES/0084). MS diagnosis was confirmed by neuropathological means by F. Roncaroli (Imperial College London) and Prof. Colin Smith (Centre for Clinical Brain Sciences, Centre for Comparative Pathology, Edinburgh) and clinical history was provided by R. Nicholas (Imperial College London) and Prof. Colin Smith. Tables 1 and 2 include details on samples used for histological analysis and array tomography, respectively (Online Resource Table 1,2). Table 3 gives a detailed list of the tissue samples used for each individual analysis (Online Resource Table 3). For histological analysis, tissue blocks of 2 cm × 2 cm × 1 cm were collected, fixed, dehydrated and embedded in paraffin blocks. 4 μm sequential sections were cut and stored at room temperature. Grey matter MS lesions were identified using anti-Proteolipid Protein (PLP) immunostaining (Online Resource Fig. 1a, b). The samples chosen had obviously myelinated and demyelinated areas on the same section. MS demyelinated areas refer to areas with distinct lesions in the upper cortical layers and MS myelinated to normal appearing myelinated cortical layers. For array tomography, 1cm3 motor cortex blocks were collected upon autopsy and further dissected in 1 mm x 1 mm x 5 mm array tomography samples before processing. The mean age for all samples is 63.75 years (control) and 62.70 years (MS), subdivided into paraffin samples: 77.60 years (control) and: 58.78 years (MS) and AT samples: 49.90 years (control) and 67.40 years (MS). Overall, 23 male and 30 female samples were used (controls: 15 male and 5 female samples, MS: 8 male and 25 female samples). Each sample was assessed by a neuropathologist and no signs of confounding neurodegenerative diseases were seen in any sample.
Animals
Mice were housed and used according to the standard UK Home Office regulations, under project license PADF15B79. PSD95-eGFP animals were a gift from S.G.N.Grant (Centre for Clinical Brain Sciences, University of Edinburgh) [50]. 8–10-week-old male mice were used for all experiments.
Array tomography (AT)
Dissected tissue blocks were processed as previously described [25]. Briefly, small tissue blocks containing all 6 cortical layers were fixed for 2–3 h in 4% PFA, 2.5% sucrose in 0.01 M PBS and washed in 3.5% sucrose, 50 mM glycine in 0.01 mM PBS at 4 °C overnight. AT samples were then dehydrated in graded series of ethanol for 5 min each, followed by 5-min incubation with 50:50 ethanol 100% LRWhite (London Resin Medium grade, Agar scientific) and 100% LRWhite alone. Samples were then left overnight at 4 °C in LRWhite for complete infiltration, transferred to gelatin capsules filled with cold LRWhite and polymerized at 52 °C overnight. Tissue was sectioned into ribbons of 70 nm serial sections (30–40 sections/ribbon) with an ultramicrotome (Leica Ultracut) using a Ultra Jumbo Diamond Knife 35° (Diatome) and mounted in gelatin covered coverslips that were allowed to air dry before immunohistochemistry.
LPC-induced cortical demyelinating lesion in cortex
In 8–10-week-old C57BL/6 or PSD95-eGFP anesthetized male mice; a craniotomy was made above the left motor cortex. Briefly, using a 0.6 mm dental drill tip and low drilling speed we thinned the skull above the M1 and M2 areas (2 mm Ø) avoiding brain overheating. When the skull was adequately thinned saline application allows for the removal of the cranial top avoiding damage to the underlying brain tissue. Macroporous, poly(ethylene glycol) (PEG) based cylindrical scaffolds (cryogel) were synthesized as previously reported [14] to dimensions 2 mm Ø × 0.5 mm depth and loaded with either PBS (control) or 10 mg/mL L-α-Lysophosphatidylcholine (LPC, L4129, Sigma-Aldrich) and placed onto the exposed cortical surface. The skin was subsequently sutured back over the cryogel and the animals were left to recover. The release properties of LPC from the 2 mm Ø × 0.5 mm cryogel showed successful release of 80% of the total LPC amount within 48hrs and 100% by 120hrs (Online Resource Fig. 5). Two time points were chosen for the present study (2 and 3 weeks post-surgery), characterized by the presence of focal demyelination in the superficial layers of the motor cortex. Mice were subsequently perfused with 4% PFA (Sigma-Aldrich), the brain tissue was harvested, cryoprotected in 30% sucrose, frozen in 2-methyl-butane (Sigma-Aldrich) and stored at − 80 °C.
Immunohistochemistry
Human post-mortem brain tissue
Paraffin sections were rehydrated and microwaved for 15 min in Vector Unmasking Solution for antigen retrieval (H-3300, Vector). For chromogenic immunohistochemistry, endogenous peroxidase and alkaline phosphatase activities were blocked for 10 min with Bioxal solution (SP-6000, Vector). Sections were then blocked with 2.5% normal horse serum (S-2012, Vector) for 1 h at room temperature. Primary antibodies were incubated in antibody diluent solution (003,118, Thermo Fisher Scientific), overnight at 4 °C in a humidified chamber. The next day, horse peroxidase or alkaline phosphatase-conjugated secondary antibodies (Vector) were applied for 1 h at room temperature. Staining was developed with either DAB peroxidase substrate kit or alkaline phosphatase substrate kit (both from Vector) according to the manufacturer’s instructions.
For immunofluorescence, sections were incubated with Autofluorescent Eliminator Reagent (2160, MERCK-Millipore) for 1 min and briefly washed in 70% ethanol after antigen retrieval. The sections were subsequently incubated with Image-iT® FX Signal Enhancer (I36933, Thermo Fisher Scientific) for 30 min at room temperature, washed and blocked for 1 h with 10% normal horse serum, 0.3% Triton-X in PBS. Primary antibodies were diluted in antibody diluent solution (as above) and incubated overnight at 4 °C in a humidified chamber. The next day sections were incubated with Alexa Fluor secondary antibodies (Thermo Fischer Scientific, 1:1000) for 1 h at room temperature and counterstained with Hoechst for nuclear visualization. All slides were mounted using Mowiol mounting medium (475,904, MERCK- Millipore).
Array tomography
Dried ribbons were incubated in 50 mM glycine in 0.01 M PBS for 5 min, washed in 3.5% sucrose, 50 mM glycine in 0.01 mM PBS and blocked with 0.1% BSA, 0.05% Tween-20 in Tris Buffered Saline solution (TBS) for 30 min at room temperature. Primary antibodies were diluted in blocking solution (all antibodies 1:50 dilution) and placed on ribbons overnight at 4 °C. The following day ribbons were washed in TBS and incubated with secondary antibodies diluted in blocking solution with 0.01 mg/mL DAPI for 30 min at room temperature (all secondary antibodies diluted 1:100). Finally, ribbons were washed and mounted on microscope slides with Shandon Immunomount (Thermo Scientific).
Mouse tissue
10 μm thick cryosections were briefly washed in PBS and microwaved for 15 min in Vector Unmasking Solution for antigen retrieval (H-3300, Vector) before blocking with 10% normal horse serum, 0.3% Triton-X in 1xPBS for 1 h at room temperature. Primary antibodies were diluted in antibody diluent (003,118, Thermo Fisher Scientific) and sections were incubated overnight at 4 °C in a humidified chamber. The following day, cryosections were incubated with Alexa Fluor secondary antibodies (Thermo Fischer Scientific, 1:1000) for 1½ hrs at room temperature and counterstained with Hoechst for nuclear visualization. All slides were mounted using Mowiol mounting medium (475,904, MERCK- Millipore).
Image acquisition and analysis.
Human post-mortem tissue
Entire sections were imaged using the Zeiss AxioScan Slide scanner or the Vectra® Polaris™ Automated Quantitative Pathology Imaging System. All quantifications were performed using Zeiss Zen lite imaging software and QuPath open source software [2].
For cell density quantification 5–10 fields were chosen that included all cortical layers or L2/3 only, manually quantified and presented as cells/mm2 or cells/cm2. GM thickness was manually quantified by measuring the distance from the cortical surface to the lower edge of cortical layer six. At least 20 different measurements were obtained per section. Axonal measurements were obtained after double blinded quantification of SMI312-possitive axons as previously described [24]. Briefly, the relative axonal density crossing 100 μm line was measured from 10–20 different areas depending on the section size.
For synaptic density quantification, 5–6 stacks (184.58 μm × 184.58 μm each) from layer 2/3 (L2/3) of the motor cortex were obtained using high resolution confocal microscopy (Leica TCS SP8; 3144 × 3144 resolution, 150 nm optical z-step, 2 µm total thickness). Each field was subdivided in 10 μm x 10 μm regions of interest covering the area of the neuropil avoiding cell bodies and blood vessels. Images were cropped and segmented using automated local thresholding Fiji (Fiji, RRID:SCR_002285) algorithms. Segmentation parameters were exclusive for each channel but the same for all sections. To avoid false positive signal, objects that were not present in at least two consecutive sections were removed. Quantification of adjacent pre and post synaptic objects (object centers within 1 μm distance) in the tissue volume was obtained using an in-house MATLAB algorithm. Values were averaged for each animal and presented as synapses/mm3.
Array tomography
Images were obtained using a Zeiss AxioImager Z2 epifluorescent microscope with a CoolSnap digital camera and AxioImager software with array tomography macros (Carl Zeiss, Ltd, Cambridge UK). A tile scan of the ribbon is initially taken in low magnification followed by the generation of a position list that outlines the area of the ribbon. Serial high-resolution images are then taken with a 63 × 1.4 NA Plan Apochromat objective and aligned using MultiStackReg 1.4 Fiji plugin (Fiji, RRID:SCR_002285) [25]. Two to five image stacks were captured per tissue block per case. Synaptic quantification was performed as described above.
Mouse tissue
All sections were imaged using a Leica TCS SP8 confocal microscope. For cell density quantification 3–9 fields (150 μm x150μm each) were obtained from each section depending on the lesion size. Total number of cells was quantified in the lesion and perilesion area and represented as cells/mm2. Perilesion area was defined as the area spanning 150 μm from the lesion border. 3–5 sections were analyzed per animal and the numbers were averaged for each animal. For signal area quantification, the same size and number of areas were thresholded and automatically quantified using in-house Fiji macros (Fiji, RRID:SCR_002285).
Synaptic density quantification was done similarly to human tissue. 3 stacks (184.58 μm × 184.58 μm each) from L2/3 of the motor cortex were obtained using high resolution confocal microscopy (3144 × 3144 resolution, 150 nm optical z-step, 2 µm total thickness). 3–5 sections were analyzed per animal. Quantification of adjacent pre and post synaptic objects (object centers within 0.5 μm distance) in the tissue volume was obtained using an in-house MATLAB algorithm. Values were averaged for each animal and presented as synapses/mm3.
Images were randomised using the File randomizer Fiji (Fiji, RRID:SCR_002285) macro prior to analysis.
Illustrations created with BioRender.com.
In vitro slice electrophysiology
Slices containing LPC lesion and PBS control neurons were prepared from mice which had been implanted with cryogels overlaying the motor cortex (M1), as previously described [5, 6]. Briefly, mice were sedated with isofluorane, decapitated and their brains rapidly removed and placed in ice-cold sucrose-modified artificial cerebrospinal fluid (sucrose-ACSF; in mM: 87 NaCl, 2.5 KCl, 25 NaHCO3, 1.25 NaH2PO4, 25 glucose, 75 sucrose, 7 MgCl2, 0.5 CaCl2); saturated with carbogen (95% O2/5% CO2). 300 μm coronal brain slices were then sliced on a vibratome (VT1200S, Leica, Germany) covering the region that was overlain by the cryogel, as assessed by eye during dissections, then transferred to submerged holding chambers filled with sucrose-ACSF at 35 °C for 30 min, then room temperature until needed.
Whole-cell patch-clamp recordings were performed to record miniature EPSCs and IPSCs. Slices were transferred to a submerged recording chamber which was perfused with ACSF (in mM: 125 NaCl, 2.5 KCl, 25 NaHCO3, 1.25 NaH2PO4, 25 glucose, 1 MgCl2, 2 CaCl2, containing 500 nM tetrodotoxin,TTX) and bubbled with carbogen, at a rate of 4–6 mL.min−1, recordings were maintained at 30 ± 1 °C with an inline Peltier heating device (Scientifica, Brighton, UK). Slices were first visualised under low-power magnification (4 × Objective 0.2 NA, Neoplan, Olympus, Japan) with infrared differential-inference contrast microscopy using a digital camera (SciCamPro, Scientifica, UK) mounted on an upright microscope (SliceScope, Scientifica, UK) to the dorsal pole of the slice. Neurons were identified for recording with a high-power 40 × water-immersion objective lens (1.0 N.A., Olympus, Japan) and chosen based on having an ovoid soma located in the upper region of L2, with an apical dendrite oriented towards the pial surface. Recording pipettes were pulled from borosilicate glass capillaries (1.7 mm outer/1 mm inner diameter, Harvard Apparatus, UK) on a horizontal electrode puller (P-97, Sutter Instruments, CA, USA) and filled with a Cs-gluconate based intracellular solution (in mM 140 Cs-gluconate, 3 CsCl, 0.2 EGTA, 10 HEPES, 2 Na2ATP, 2 MgATP, 0.3 Na2GTP, 10 Na2Phosphocreatine, 2.7 Biocytin, 5 QX-314.Cl, pH = 7.4, 290–310 mOsm), which gave 3–5 MΩ resistance electrodes and a measured Cl− reversal of − 74 mV under these recording conditions. Liquid junction potential was not corrected. Cells were rejected from further recording, if they required more than 200pA current injection to maintain a -70 mV holding potential, series resistance > 30 MΩ, or series resistance changed by more than 20%. All recording was performed with a Multiclamp 700B amplifier (Molecular Devices, CA, USA) and filtered online at 2 kHz with the amplifiers 4-pole Bessel Filter and digitised at 20 kHz (Digidata1550B, Molecular Devices, CA, USA).)
All in the presence of 500 mM TTX, mEPSCs were recorded from -70 mV voltage clamp. 5 min of continuous recording were performed with series resistance measured before and after this period. Following mEPSC recordings, the membrane potential was switched to between 0 and 5 mV – depending on measured mEPSC reversal—and 5 min of mIPSCs recorded. Following recording, the series resistance was measured again to confirm recording stability. Out-side out patches were then performed on recorded neurons, to seal the included biocytin within cells. A further 2–3 cells were recorded from each slice and then slices fixed in 4% PFA in 0.1 M PB overnight, then transferred to PBS until processed for histology.
mPSCs were detected offline using a template fitting approach, whereby exemplary mini-PSCs were fit with a triexponential curve [10], with thresholds of 4–7 imposed for detection. Following signal extraction, individual traces were excluded for analysis if they failed to exceed the threshold of 3*SD of the baseline noise. EPSCs were detected as inward currents and ISPCs as outward currents. Traces were collected in pCLAMP 9 (Molecular Devices, CA, USA) and stored on a desktop computer. All analysis of electrophysiological data was performed offline using the Stimfit electrophysiological package [21]. All data collection and analysis were performed blind to treatment group.