IPSC-MNs at differentiation D35 were harvested in cold Hypotonic buffer (20 mM HEPES pH 7.4, 10 mM KCl, 2 mM MgCl2, 1 mM EDTA, 1mM EGTA, 1 mM DTT and protease inhibitor cocktail (Roche)) and lysed by passing through G25 needles 25 times and then spun down at 700 x g for 10min at 4℃. The Supernatant was loaded onto pre-made 30% Percoll solution and re-centrifuged at 33,000 RPM using Beckman rotor SWI55 for 50min at 4℃. 300 ul aliquots were taken from top to bottom as fractions and all the collected samples were boiled with SDS-PAGE sample buffer and analyzed by western blot.

Consistent with PIKFYVE being the relevant target in the iMN survival assay, Apilimod increased C9ORF72 patient, but not control, iMN survival in either neurotrophic withdrawal conditions (Fig. 6d) or excess glutamate (n=4 patients, Supplementary Fig. 15f (n=3 controls, Supplementary Fig. 15g). Automated neuron tracking software independently verified Apilimod efficacy on C9ORF72 patient iMNs (Supplementary Fig. 15h). As further confirmation that PIKFYVE was the active target, ASO-mediated suppression of PIKFYVE also rescued C9ORF72 patient iMN survival (Fig. 6d and Supplementary Fig. 15i). In addition, we synthesized a structural analog of Apilimod with a reduced ability to inhibit PIKFYVE kinase activity in a biochemical assay using purified PIKFYVE protein (Fig. 6b and Supplementary Fig. 15j, 16). The reduced activity analog was significantly less effective at rescuing C9ORF72 patient iMN survival (Fig. 6e). Thus, small molecule inhibition of PIKFYVE can rescue patient motor neuron survival.
We wondered if reduced C9ORF72 activity renders motor neurons vulnerable to other insults that might be exacerbated by impaired endosomal-lysosomal system function, such as DPR toxicity. Without excess glutamate treatment, C9ORF72+/−, C9ORF72−/−, and C9ORF72 patient iMN survival was similar to control iMNs (Fig. 5a-d and Supplementary Fig. 14a, b). Exogenous expression of PR50 or GR50 DPRs using cassettes that do not contain the GGGGCC repeat expansion induced control iMN degeneration (Fig. 5a, b). Interestingly, C9ORF72+/−, C9ORF72−/−, and C9ORF72 patient iMNs (n=2 patients) degenerated significantly faster than controls in response to PR50 or GR50 expression (Fig. 5a-d and Supplementary Fig. 14a, b).
For experiments other than the comparison of Apilimod and the reduced-activity analog, Apilimod was purchased from Axon Medchem (cat. no. 1369). For the reduced-activity analog assays, Apilimod and the reduced activity analog were synthesized at Icagen, Inc. according to the schemes shown in Supplementary Fig. 16. PIKFYVE kinase inhibition was measured using the ADP-Glo kinase assay from SignalChem according to the manufacturer’s instructions, using purified PIKFYVE kinase (SignalChem cat. no. P17–11BG-05).
Hb9::RFP+ C9ORF72 ALS/FTD iMNs were generated in 96-well plates. On Day 15 post transduction, neurotrophic factors and RepSox were withdrawn and the small molecule library was added (EMD Millipore kinase collection and Stemselect library, 3.3 µM final concentration) and added fresh every other day until the screen was terminated on Day 25 post-transduction. Identification of neuroprotective compounds was identified using SVcell 3.0 (DRVision Technologies) and further verification by manual iMN tracking.
Biotinylation of plasma membrane localized glutamate receptors was performed using the Piece™ Cell Surface Protein Isolation Kit (Thermo Fisher Scientific) following the manufacturer’s instructions. Briefly, Dox-NIL iMNs were incubated with 0.25mg/ml Sulfo-NHS-SS-Biotin in cold room for 1~2 hrs with end-to-end shaking. After quenching, cells were harvested by scraping and lysed with lysis buffer from the Piece™ Cell Surface Protein Isolation Kit or the M-PER™ mammilian protein extraction buffer (Thermo Fisher Scientific). Cell lysate was incubated with High Capacity NeutrAvidin™ agorase beads (Thermo Fisher Scientific), and the bound protein was eluted in 2X SDS-PAGE sample buffer supplemented with 50mM DTT for 1 hr at room temperature with end-to-end rotation, and further analyzed by western blot.

We anticipate three key implications of our findings: 1) ALS/FTD caused by the C9ORF72 repeat expansion requires both gain- and loss-of-function mechanisms, 2) increasing C9ORF72 activity in motor neurons should mitigate disease and provides a new therapeutic target, and 3) PIKFYVE inhibition and other approaches that modulate vesicle trafficking may ameliorate C9ORF72 disease processes in both neurons and myeloid cells. The fact that mutations in FIG4 cause ALS, epilepsy, and Charcot-Marie-Tooth 55 illustrates the broad implications of impaired vesicle trafficking within the CNS. The identification of targets that effectively modulate vesicle trafficking in neurons, glia, and myeloid cells could hold tremendous therapeutic value for C9ORF72 ALS/FTD and other CNS disorders.
To study the pathogenic mechanism of the C9ORF72 repeat expansion in human motor neurons, we used the forced expression of the transcription factors Ngn2, Isl1, Lhx3, NeuroD1, Brn2, Ascl1, and Myt1l, to convert control and C9ORF72 ALS/FTD patient induced pluripotent stem cells (iPSCs)(for iPSC characterization, see Supplementary Fig. 1 and Supplementary Tables 3, 4) into iMNs (Supplementary Fig. 2a, b) 10,24. Control and patient iMNs labeled with an Hb9::RFP+ lentiviral reporter construct (Supplementary Fig. 2b-d)25 co-expressed spinal motor neuron markers including TUJ1, HB9, and VACHT; were produced at similar rates amongst different iPSC lines; and possessed electrophysiological properties of motor neurons (Supplementary Fig. 2c-i). Depolarizing voltage steps induced currents characteristic of sodium and potassium channels and iMNs fired single or repetitive action potentials (patient - 90%, n=10; control – 100%, n=10)(Supplementary Fig. 2g-i). When co-cultured with primary chick muscle, channel rhodopsin-expressing control and patient iMNs repeatedly induced myotube contraction upon depolarization with green light, indicating they formed neuromuscular junctions and actuated muscle contraction (Supplementary Fig. 2j and Supplementary Videos 1, 2).
We anticipate three key implications of our findings: 1) ALS/FTD caused by the C9ORF72 repeat expansion requires both gain- and loss-of-function mechanisms, 2) increasing C9ORF72 activity in motor neurons should mitigate disease and provides a new therapeutic target, and 3) PIKFYVE inhibition and other approaches that modulate vesicle trafficking may ameliorate C9ORF72 disease processes in both neurons and myeloid cells. The fact that mutations in FIG4 cause ALS, epilepsy, and Charcot-Marie-Tooth 55 illustrates the broad implications of impaired vesicle trafficking within the CNS. The identification of targets that effectively modulate vesicle trafficking in neurons, glia, and myeloid cells could hold tremendous therapeutic value for C9ORF72 ALS/FTD and other CNS disorders.

(a) The levels of C9ORF72 variant 2 mRNA transcript (encoding isoform A). Values are mean ± s.e.m., two-tailed t-test with Welch’s correction. t-value: 5.347, degrees of freedom: 11.08. n= 9 biologically independent iMN conversions from 3 control lines and 12 biologically independent iMN conversions from 5 C9-ALS lines. (b–d) iMN survival in excess glutamate following introduction of C9ORF72 (C9 isoform A or B) into C9ORF72 patient iMNs (b), but not control (b, d) or SOD1-ALS iMNs (c). For (b), n=50 iMNs per line for 2 control and 3 C9-ALS lines, iMNs quantified from 3 biologically independent iMN conversions per line. For (c), n=50 iMNs per condition, iMNs scored from 3 biologically independent iMN conversions. For (d), n=50 iMNs per line per condition for 2 control lines, iMNs quantified from 3 biologically independent iMN conversions. Each trace includes iMNs from 2–3 donors with the specified genotype (except SOD1-ALS (c)); see full details in Methods. (e) Strategy for knocking out C9ORF72 from control iPSCs using CRISPR/Cas9. (f) Survival of control (CTRL2) iMNs, the isogenic heterozygous (C9+/−) and homozygous (C9−/−) iMNs and C9ORF72 patient (C9-ALS) iMNs in excess glutamate. n=50 biologically independent iMNs per line per condition for one control and two C9-ALS lines, iMNs quantified from 3 biologically independent iMN conversions. (g) Control iMN survival in excess glutamate with scrambled or C9ORF72 antisense oligonucleotides (ASO). Each trace includes control iMNs from 2 donors. n=50 biologically independent iMNs per line per condition for 2 control lines, iMNs quantified from 3 biologically independent iMN conversions. All iMN survival experiments were analyzed by two-sided log-rank test, and statistical significance was calculated using the entire survival time course. iMN survival experiments in (b, d, and g) were performed in a Nikon Biostation, and (e and f) were performed in a Molecular Devices ImageExpress.

Consistent with previous studies 3,4,6–8, patient iMNs (n=5 patients) had reduced C9ORF72 expression compared to controls (n=3; Fig. 2a and Supplementary Fig. 4a, 5b). While previous studies have linked low C9ORF72 levels to changes in vesicle trafficking or autophagy 18,20,30–33, it remains unknown if loss of C9ORF72 protein directly contributes to degeneration. Thus, we re-expressed C9ORF72 (isoform A or B) in iMNs using a retroviral cassette (Supplementary Fig. 4b) and found that both isoforms rescued C9ORF72 patient iMN survival in response to glutamate treatment (n=3 patients Fig. 2b and Supplementary Fig. 4c). This effect was specific for C9ORF72 iMNs, as forced expression of C9ORF72 did not rescue SOD1A4V iMN survival (Fig. 2c), nor did it improve the survival of control iMNs (n=2 controls Fig. 2d and Supplementary Fig. 4d).
(a) Super-resolution microscopy images of immunofluorescence shows NR1+ puncta on neurites of iMNs overexpressing eGFP or C9ORF72 isoform B-eGFP. Scale bar: 5 µm. This experiment was repeated 3 times with similar results. (b-d) Number of NR1+ puncta per unit area in control (b-d), patient (b), C9ORF72+/− (c), and C9ORF72+/− (d) iMNs. Mean ± s.d. Each grey open circle represents the number of NR1+ puncta per area unit on a single neurite (one neurite quantified per iMN). For (b), n=75 (CTRL + GFP), 84 (C9-ALS + GFP), 95 (C9-ALS + isoA), and 111 (C9-ALS + isoB) iMNs quantified from two biologically independent iMN conversions of 3 CTRL or 4 C9-ALS lines. For (c), n=37 (CTRL + GFP), 37 (C9ORF72+/− + GFP), 25 (C9ORF72+/− + isoA), and 27 (C9ORF72+/− + isoB) iMNs quantified from two biologically independent iMN conversions per condition. For (d), n=37 (CTRL + GFP), 37 (C9ORF72−/− + GFP), 38 (C9ORF72−/− + isoA), and 23 (C9ORF72−/− + isoB) iMNs quantified from two biologically independent iMN conversions per condition. One-way ANOVA with Tukey correction for all comparisons. F-value (DFn, DFd): (3, 360) = 56.63 (b), (3, 122) = 13.42 (c), (3, 131) = 17.11 (d). (e-h) Immunoblotting analysis of surface NR1 after surface protein biotinylation in control (e-h), C9ORF72+/− (e-f), and C9-ALS patient (g-h) iMNs generated with 3 factors (NGN2, ISL1, and LHX3). In (f), n=4 biologically independent iMN conversions from CTRL2 and 2 biologically independent iMN conversions from the C9ORF72+/− line. Mean +/− s.d. In (h), two-tailed Mann-Whitney test. n=11 biologically independent motor neuron cultures from 11 independent control lines and 4 biologically independent motor neuron cultures from 4 independent C9-ALS patient lines. Experiments in (e-h) were repeated twice with similar results. Mean +/− s.e.m. (i-j) Immunoblotting analysis of surface Nr1 and Glur1 in post-synaptic densities (PSDs) from C9orf72 control and knockout mice, two-tailed t-test. t-value: 4.424 (Nr1), 4.632 (Glur1), degrees of freedom: 4 (Nr1), 4 (Glur1). n= 3 control PSD preparations isolated from 3 control mice and 3 C9orf72−/− PSD preparations isolated from 3 C9orf72−/− mice. This experiment was repeated twice with similar results. Mean +/− s.e.m. (k-l) Immunoblotting analysis of surface NR1 and GLUR1 in post-synaptic densities (PSDs) from post mortem control and C9-ALS patient motor cortices, n=3 control and 2 C9-ALS patient PSD preparations isolated from 3 control and 2 C9-ALS patients. This experiment was repeated twice with similar results. Mean +/− s.d. (m) Average Ca2+ flux in the presence of glutamate per minute. n=28 (CTRL1), 15 (CTRL2), 15 (CTRL3), 26 C9-ALS1), 20 (C9-ALS2), 24 (C9-ALS3), and 15 (C9ORF72+/−) iMNs analyzed from two biologically independent iMN conversions for each line. Mean ± s.e.m. One-way ANOVA with Tukey correction between all controls and all patients and C9ORF72+/−. F-value (DFn, DFd): (6, 136) = 11.21.
Removal of TTX and TEA during glutamate receptor agonist treatment revealed additional increases in Gcamp6 activation in C9ORF72+/− iMNs compared to controls, suggesting that C9ORF72+/− iMNs also fire action potentials more frequently than controls (Supplementary Fig. 13a), although we did not detect large changes in sodium or potassium current amplitudes in C9ORF72+/− iMNs (Supplementary Fig. 13b, c). To determine if increased neuronal activity due in part to elevated glutamate receptor levels contributes to neurodegeneration in C9ORF72 patient and C9ORF72+/− iMNs, we measured iMN survival in the presence or absence of retigabine. Retigabine is approved by the U.S. Food and Drug Administration for the treatment of epilepsy and reduces neuronal excitability by activating Kv7 potassium channels 48. In the glutamate treatment assay, retigabine increased the survival of C9ORF72 patient (n=2 patients) and C9ORF72-deficient iMNs, but not controls (n=2 controls)(Supplementary Fig. 13d-g).
In advanced traditional Chinese kung fu (martial arts), Neijing (Traditional Chinese: 內勁; pinyin: nèijìng) refers to the conscious control of the practitioner's qi, or "life energy", to gain advantages in combat.[1] Nèijìng is developed by using "Neigong" (Traditional Chinese: 內功; pinyin: nèigōng) (內功), or "internal exercises," as opposed to "wàigōng" (外功), "external exercises."
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