Cell culture
The iPSC lines from CMT2A patients and healthy subjects were already available in our laboratory[33] and were maintained in culture on Matrigel-coated dishes with Essential 8 medium (Thermo Fisher Scientific). Lentiviral transductions, selection and expansion of stable iPSC lines were performed in mTeSR1 (Stem Cell Technologies). HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 supplemented with 15% fetal bovine serum, 1% penicillin/streptomycin (Pen-Strep), and 1% amphotericin B (all from Thermo Fisher Scientific). All cell cultures were maintained at 37°C in 5% CO2. All cell lines were tested for mycoplasma contamination once a month.
Plasmids
For transient knockdown, pSUPuro-MFN2-shRNAtg1 and pSUPuro-MFN2-shRNAtg2 were cloned by inserting double-stranded oligos into pSUPERpuro between the BglII and HindIII sites as described previously [35, 36]. The shRNAs expressed from pSUPuro-MFN2-shRNAtg1 and pSUPuro-MFN2-shRNAtg2 target nucleotides 1564-1582 (5’-CCTCAAGGTTTATAAGAAT-3’) and 2381-2399 (5-GCAAAGCTGCTCAGGAATA-3’) of MFN2 mRNA (numbering according to NM_014874.4). pSUPuro-scrambled (5’-ATTCTCCGAACGTGTCACG-3) is described elsewhere[37]. C-terminally Myc-DDK-tagged MFN2 was from Origene (pCMV6-MFN2-Myc-DDK; #RC202218; Myc-tag: EQKLISEEDL ~1202 Daltons; FLAG-tag: DYKDDDDK ~1012 Da).
To render the MFN2 cDNA RNAi-resistant, silent mutations were introduced into the shRNA target sites in the MFN2 cDNA using the Quikchange Lightning Multi-Site Kit (Agilent) and primers QC-MFN-t1 (5’-gacttccacccttctccagtagtgctgaaagtctacaaaaacgagctgcaccgccacatagagga-3’) and QC-MFN-t2 (5’- cttgactcacttcagagcaaagctaaactcctgagaaacaaagccggttggttggacagtga-3’) according to the manufacturer’s protocol to generate pCMV6-MFN2Rtg1-Myk-DDK and pCMV6-MFN2Rtg2-Myk-DDK, respectively.
For stable knockdown, the shRNAtg2 sequence was inserted into pEco-Lenti-H1-shRNA-Blasticidin (Gentarget). To increase the expression of blasticidin resistance in iPSCs, the RSV promoter between the MluI and KpnI sites of pEco-Lenti-H1-MFN2-shRNAtg2-shRNA-Blasticidin was replaced by a gene-synthesized fragment (GeneArt Gene Synthesis) containing a CMV promoter with a chimeric intron to generate pEco-Lenti-H1-MFN2-shRNAtg2-CMV-BSD.
To generate the lentiviral MFN2 cDNA expression construct (pLVX-EF1a-MFN2Rtg2-Myk-DDK-IRES-Puro), MFN2 cDNA was excised from pCMV6-MFN2Rtg2-Myk-DDK using EcoRI and PmeI (New England Biolabs) and cloned into the EcoRI-BamHI (Blunt) sites of PLVX-EF1a-IRES-Puro (Clontech). All constructs were verified by Sanger sequencing.
Transient transfection, lentiviral vector production, and transduction
HeLa cells were transfected with 7.5 µg shRNAtg1 or shRNAtg2 using Lipofectamine LTX reagent (ThermoFisher Scientific) or Dreamfect (OZ Biosciences). Twenty-four hours after transfection, cells were selected in DMEM/F12 medium supplemented with 1.5 µg/mL puromycin (Sigma Aldrich). Co-transfection experiments with 7.5 µg shRNAtg1/MFN2Rtg1 or shRNAtg2/MFN2Rtg2 were performed in parallel in a 1:1 (3.75 µg shRNA to 3.75 µg pCMV6) ratio. After 24 hours, cells were cultured in the presence of 500 µg/mL G418 (Sigma Aldrich). Cells were transfected with pSUPuro-SCR under the same conditions as controls. Virus production for protein expression was essentially performed as follows. HEK 293T cells were transfected with pEco-Lenti-H1-shRNAt2-CMV-BSD supplemented with Lentiviral Packaging plasmid (Gentarget; #HT-Pack) or pLVX-EF1a-MFN2Rtg2-MycDDK-IRES-Puro supplemented with Lenti-X HTX packaging mix (Clontech: #631248) according to the manufacturer’s protocol and established methods [38]. Lentiviral supernatants were collected 48 and 72 h post-transfection, filtered through a 0.45-μM polyethersulfone sterile filter (Millipore), followed by concentration using Lenti-X-Concentrator (Clontech: #631232). CMT2A iPSCs were transduced three times with pEco-Lenti-H1-shRNAt2-CMV-BSD supernatant. Eight hours after the final transduction, cells were expanded under blasticidin selection at a final concentration of 2.5-5 μg/mL, followed by a final 5-day selection with 40 µg/mL blasticidin. To rescue MFN2 expression, pLVX-EF1a-MFN2Rtg2-MycDDK-IRES-Puro viral supernatant was added twice to pEco-Lenti-H1-shRNAt2-CMV-BSD transduced cells. Forty-eight hours after the final transduction, cells were expanded with puromycin to a final concentration of 0.5 μg/mL.
Differentiation of iPSCs into MNs
iPSCs were differentiated into MNs using a multistep protocol modified from Maury et al[39].To induce embryoid body formation from iPSCs, on day 0, iPSCs were dissociated with accutase and resuspended in differentiation N2B27 medium (1:1 DMEM/F12-Neurobasal media, supplemented with N2, B27, 2 mM L-glutamine, 1% Pen-Strep, 0.1 mM β-ME; all from ThermoFisher Scientific), with 10 μM Y-27632 (Cell Signaling Technology), 0.1 μM LDN 193189 (MiltenyiBiotec), 20 μM SB431542, and 3 μM CHIR-99021 (both from Sigma Aldrich). The media was replaced every 2 days, adding small molecules as follows: on day 2, 1 μM LDN 193189 (MiltenyiBiotec), 20 μM SB431542, 3 μM CHIR-99021, and 100 nM retinoic acid (RA, all three from Sigma Aldrich); on day 4: 0.1 μM LDN 193189, 20 μM SB431542, 3 μM CHIR-99021, 100 nM RA, and 500 nM Smoothened Agonist (SAG, Sigma Aldrich); on day 7: 100 nM RA and 500 nM SAG; finally, on day 9: 100 nM RA, 500 nM SAG, and 10 μM DAPT (Stem Cell Technologies). BDNF (20 ng/mL) and GDNF (10 ng/mL; both from Peprotech) were added to the differentiation medium on day 10. On day 11 or 14, EBs were dissociated and the cells seeded on poly-L-ornithine (20 µg/mL) and laminin (20 µg/mL; both from Sigma Aldrich) coated plates. Three or four days after seeding, cells were stained for live imaging analyses, and 5-8 days after seeding, they were fixed for immunocytochemistry and harvested for mtDNA and Western blot analysis.
Immunocytochemistry of iPSCs and MNs
Cells were fixed in 4% paraformaldehyde for 20 min at 37°C, permeabilized with 0.25% Triton X-100, and then blocked with 10% bovine serum albumin in phosphate-buffered saline (PBS) containing 0.25% Triton X-100 (all from Sigma Aldrich) for 1 h at room temperature. We incubated the cells with primary antibodies (Table S1) overnight at 4°C, and then with secondary antibodies (Table S2) for 1 h at room temperature. The nuclei were stained with 0.5 µg/mL DAPI (Sigma Aldrich). Images were acquired using a laser-scanning Leica TCS SP5 confocal microscope (Leica Microsystems, Wetzlar, Germany) or a LED-based Nikon ECLIPSE Ti/CREST microscope (Nikon).
Mitochondrial area analysis
Accurate analysis of the area occupied by mitochondrial structures requires sharp, high contrast images with minimal background noise. Single maximum intensity projection images of TOM20 immunolabeled MNs obtained by laser-scanning confocal microscopy (Leica TCS SP5, Leica Microsystems) were pre-processed in Fiji software using an unsharp mask filter and then binarized by thresholding (Otsu threshold 20560-65535). To perform single cell analysis of the mitochondrial area, each cell was subdivided into seven adjacent regions of interest (ROIs), the first spanning from the center of the cells to the axon hillock (7x10 µm) and the other six covering the axon (3x10 µm), for a total length of 70 µm. The mean fluorescence intensity (Iaverage) was measured.
Quantification of the mitochondrial area was performed according to the specifications of Valente et al [40]. The mitochondrial area represents the total area in the image covered by signal after being separated from the background and consists of the number of pixels in the binary image containing the signal multiplied by the area of a pixel. I represents the pixel intensity in the binarized image, x represents the width of the image in pixels, y represents the height of the image in pixels, and s represents the calibrated length of one pixel:
Data were graphed and two groups of data compared by multiple Student’s unpaired t-tests using GraphPad Prism 8 (GraphPad Software, San Diego, California, USA). Data were considered to be significantly different if p<0.05.
Live cell imaging of lysosomes and mitochondria
For mitochondrial and lysosome live cell analysis, MNs plated in optical 4- or 8-well µ-Slides (Ibidi GmbH) pre-coated with poli-L-ornithine and laminin (both from Sigma Aldrich) were transduced with CellLight™ Mitochondria-RFP BacMam 2.0 and/or CellLight™ lysosome-GFP BacMam 2.0 reagents (both from ThermoFisher Scientific) (30 particles per cell) and incubated for approximately 48 hours at 37°C. Imaging was performed with a Crest Optics Spinning Disk module (Crest-Crisel Instruments) mounted on a fully automated inverted Nikon ECLIPSE Ti microscope (Nikon) and acquisitions achieved with an Andor DU-888 EM-CCD camera (Andor) for fast recordings and NIS-Elements v.5 software (Nikon). Time-lapse parameters were determined based on the speed of transport of the mitochondria and lysosomes in MNs [41] and set at 5 s intervals, for a total of 2-3 min. A time series of 6-µm z-sections (0.3 µm z-steps) was acquired at 60x magnification (using 60x oil, NA 1.40 objective, Nikon) and matched pinhole (70 μm) with spinning disk and processed by equalization over time (with NIS-Elements v.5 software, Nikon) with background subtraction using Fiji software. Data were exported as a sequential time-lapse in AVI format (speedback: 5 frames per second).
mtDNA analysis
Total DNA was extracted from MNs using a standard protocol (Flexigene, Qiagen). The mtDNA was quantified by quantitative real-time PCR using the ΔΔCt method on a 7500 Real Time PCR system (Software 2.01, Applied Biosystems, ThermoFisher Scientific) and the Taqman assay with probes for human mitochondrial genes CYTB (VIC- CAC CAG ACG CCT CAA CCG CCT T - TAMRA) and ND4 (FAM- CCG ACA TCA TTA CCG GGT TTT CCT CTT G - MGB), normalizing for nuclear APP (FAM- CCC TGA ACT GCA GAT CAC CAA TGT GGT AC - TAMRA) and RNAseP (TaqMan™ Copy Number Reference Assay, human, RNase P; 4403326) genes, respectively. All quantifications were carried out in triplicate using 25 ng of total DNA as the template. The mtDNA levels were normalized to nuclear DNA and expressed as relative values using the amount of mtDNA in the cells of healthy controls as a reference (relative quantification = 1).
AAV vectors
AAV9 vectors were produced by Virovek Laboratories (Hayward, CA). The shRNAtg2 vector was used to generate self-complementary (sc)AAV9-KD (AAV9-KD) containing shRNAtg2 to silence MFN2. AAV9-KD incorporated a GFP tag. shRNAtg2 sequence and MFN2 cDNA mutated to be resistant to the shRNA incorporating a DDK tag were used to produce single-stranded (ss)AAV9-KD-rMFN2 (AAV9-KD-rMFN2). As a control, a third vector was generated with a non-coding sequence under the CMV promoter to generate the AAV9-null vector.
Animal procedures
The MitoCharc1 transgenic mice (B6;D2-Tg(Eno2-MFN2*R94Q)L51Ugfm/J) harbor the neuron- specific rat Eno2 promoter, driving the expression of human R94Q (arginine to glutamine) MNF2 mainly in neurons, mimicking the most common mutation found in CMT2A patients[34]. Hemizygous mutant mice (MFN2) and WT littermates were used for the experiments and analyses. The genotypes of the mice were confirmed using a PCR-based assay as described previously [34]. All transgenic animals were purchased from the Jackson Laboratory, and they were maintained according to standard conditions, including ad libitum access to food and water and 12-hour dark/light cycle. All animal experiments were approved by the Italian Ministry of Health review boards in compliance with U.S. National Institutes of Health Guide for the Care and Use of Laboratory Animals. AAV9-KD or AAV9-KD-rMFN2 (1.8 × 1013 µg/kg) were injected into MitoCharc1 pups (P1, n=3) via intracerebroventricular injection[42]. AAV9::null was used as a control vector (n=3). To evaluate MFN2 expression, brains were collected after 2 weeks.
Mouse behavioral analysis
Survival and weight were monitored in MFN2 (n=26) versus WT mice (n=22) from 1 to 24 months. The animals were sacrificed at 24 months.
Rotarod test. Motor functions of MFN2 (n=9) and WT (n=10) mice were tested once a month by an accelerating test on a rotarod device (4 to 40 rpm, Rota-Rod 7650, UgoBasile Biological Instruments, Varese, Italy).
Hot plate test. MFN2 (n=9, P270) and WT mice (n=10, P270) were placed on a hot plate analgesimeter (UgoBasile Biological Instruments, Varese, Italy) with the surface temperature maintained at 50±0.2°C. The latency before the first licking or lifting of the posterior paw was recorded as the withdrawal latency time. Immediately after the initial reaction, the trial was halted and the mouse removed from the hotplate. To avoid any injury to the tissues, if the animal was not responsive, the test was stopped using a cut-off time of 45 s. Each animal was tested twice with a 30 min interval between the sessions. All tests were performed blinded to the mouse genotype.
Nerve conduction velocity
Tail motor and sensory conductions were studied in MFN2 mice (n=8, P270) versus WT mice (n=3, P270) as described by Leandri et al [43]. Briefly, the tail sensory nerve was stimulated by inserting the cathode 1 cm from the tail tip and anode 0.5 cm distally using a square-wave pulse of 0.1-ms duration at supramaximal intensity. Sensory nerve action potentials were recorded by inserting an active electrode 4 cm proximally from the cathode and the reference electrode 0.5 cm more proximally. The sensory nerve conduction velocity was calculated by measuring the latency to the peak of the initial negative deflection and the distance between stimulating and recording electrodes. Motor tail nerve conduction was measured using a bipolar recording configuration. An active electrode was placed 1 cm from the tail tip and reference electrode 0.5 cm distally. The motor tail nerve was stimulated first 2.5 cm proximally from the active recording electrode and then 5 cm proximally. Motor nerve conduction velocity was calculated by subtracting the distal from the proximal compound motor action potential’s first negative peak latency measured in milliseconds, and the difference was divided by the distance between the two stimulating electrodes in millimeters. All of the neurophysiological determinations were performed under standard conditions in a temperature-controlled room; animals were maintained under deep isoflurane anesthesia during the recordings.
DRG culture
Adult DRG neurons were rapidly dissected on ice-cold DMEM (ThermoFisher Scientific) and centrifuged for 3 min at 300 g. They were digested for 20 min in 2.5% collagenase in Ca2+- and Mg2+-free Hank’s Buffer Saline Solution (HBSS, GIBCO, ThermoFisher Scientific) at 37°C. Additional digestion was carried out for 20 min in 0.25% trypsin (ThermoFisher Scientific) and stopped by washing in DMEM (GIBCO, Life Technologies) containing 15% serum (GIBCO, ThermoFisher Scientific). DRG were dissociated with a pipette and centrifuged at 300 g before re-suspension in DMEM containing 15% FBS and counted. Cells were then plated on 12-mm-diameter glass coverslips in 24-well plates previously coated with Matrigel and left to adhere for 24 hours. The following day, the medium was replaced with neurobasal medium (GIBCO, ThermoFisher Scientific) supplemented with B27, 2 mM L-glutamine, and 1% Pen-Strep (all from ThermoFisher Scientific), and the cells were left to spread for 3-4 days before immunocytochemical analyses.
Immunohistochemical analysis of murine tissues
MFN2 (n=6) and WT mice (n=6) were euthanized at P270. Excised tissues (quadriceps, tibial anterior, and DRG) were fixed in 4% paraformaldehyde for 24 h, soaked in 20% sucrose solution overnight, and then frozen in liquid nitrogen-cooled isopentane [44]. Frozen tissues were cryosectioned (20 µm) and mounted on gelatinized glass slides. Every tenth section was collected and analyzed. All sections were saturated with 10% bovine serum albumin and 0.3% Triton X-100 for 1 h at room temperature before incubation with primary antibodies overnight at 4°C (Table S1). The next day, slides were incubated with Alexa Fluor secondary antibodies ( Table S2). A Leica TCS SP5 confocal microscope (Leica Microsystems) or Nikon ECLIPSE Ti/CREST microscope (Nikon) was used to acquire images.
RNA isolation and quantitative RT-PCR
Total RNA was extracted from the lumbar spinal cords of MFN2 (n=8, P30) and WT mice (n=4, P30) using the RNeasy Mini Kit (Qiagen). Concentrations were measured on a Nanodrop spectrophotometer. Only samples with ratios between 1.8 and 2.0 were further analyzed. A reverse-transcribed 1 μg of total RNA for each sample using the Ready-To-Go kit (GE Healthcare).
RNA extraction and 3′-mRNA sequencing
Total RNA was extracted from the lumbar spinal cords of MFN2 (n=8, P30) and WT mice (n=4, P30) using the RNeasy Mini Kit (Qiagen). Concentrations were measured on a Nanodrop spectrophotometer. Only samples with ratios between 1.8 and 2.0 were further analyzed. We reverse-transcribed 1 μg of total RNA for each sample using the Ready-To-Go kit (GE Healthcare). Total RNA extracted from samples was subjected to poly(A) mRNA sequencing. Libraries were constructed using the SMARTer-Stranded Total RNA Kit (Clontech) according to the manufacturer’s instructions. Sequencing was performed on a NextSeq 500 (Illumina). All libraries were sequenced in paired-end mode (75-bp length).
mRNA sequencing analysis
Raw reads were preprocessed for adapter trimming. Quality was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the reference genome (EnsemblMus musculus release GRC38) using the STAR algorithm [45]. Differential expression analysis was performed using the Generalized Linear Model approach implemented in the R/Bioconductor edgeR (Robinson et al., 2010) package (R version 3.5; edgeR version 3.24.3) using an FDR ≤ 0.05. The fold change ranked gene list was subjected to GSEA Preranked [46], using the c2.all.v7.5.1 and c5.all.v7.5.1 gene sets with classical enrichment statistics and phenotype permutation.
Protein analysis
Western blotting was performed as described previously[33, 47]. Protein lysate was separated by 4-12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) in MES SDS Running Buffer 20x (B0002; life Technologies) for 30 min at 200 V. To separate endoMFN2 and exoMFN2, the gel ran in MOPs SDS Running Buffer 20x (B0001; Life Technologies) for 90 min at 130 V and then 30 min at 90 V. Proteins were transferred to a nitrocellulose membrane (GE Healthcare) and incubated with primary antibodies (Table S1) overnight at 4°C. The membranes were then incubated in secondary antibodies (Table S2) and the immune complexes revealed using the Odyssey® Fc Imaging System (LI-COR Biosciences). Anti-actin antibody was used as a loading control. Semi-quantitative analysis was performed using Image Studio™ Lite software (LI-COR Biosciences).
Statistical analysis
Statistical analysis was carried out utilizing StatsDirect for Windows (version 2.6.4) or GraphPad Prism 8 software. Multiple comparisons on a single data set were performed with one-way analysis of variance (ANOVA) and, when several variables were considered, two-way ANOVA was used, followed by appropriate post hoc analysis. Two-tailed, unpaired Student's t-test was employed to compare two groups. All experiments were carried out at least in triplicate. The experimental results are shown as mean + SEM or mean + SD as needed. The null hypothesis was rejected at the 0.05 level of significance.