Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| TSG101 (mouse IgG1) | BD Transduction Laboratories™ | 612697 |
| TUJ1 (Mouse IgG2a, κ) | Biolegend | MMS-435P |
| LC3 (Rabbit IgG) | MBL | PM036 |
| P62 (Mouse IgG1, κ) | BD Transduction | 610832 |
| OPTN (Rabbit IgG) | Proteintech | 10837-1-AP |
| Phospho-TDP43(Ser409/410) (Rabbit IgG) | Proteintech | 22309-1-AP |
| PIP5K3 (Rabbit IgG) | Proteintech | 13361-1-AP |
| TFEB (Rabbit IgG) | Bethyl Laboratories® | A303-673A |
| Phospho-TFEB (Ser142) (Rabbit IgG) | Sigma-Aldrich | ABE1971-I-25UL |
| Huntingtin (Rabbit IgG) | Abcam | ab109115 |
| alpha Synuclein (Rabbit IgG) | Invitrogen | PA5-85791 |
| Fibrillarin (Rabbit IgG) | Abcam | ab166630 |
| HSP90 (Rabbit IgG) | Proteintech | 13171-1-AP |
| GR repeat (Rabbit IgG) | Proteintech | 23978-1-AP |
| PR repeat (Rabbit IgG) | Proteintech | 23979-1-AP |
| GA repeat (Rabbit IgG) | Proteintech | 24492-1-AP |
| TDP43 (Rabbit IgG) | ProteinTech | 10782-2-AP |
| Poly-GA (Mouse IgG) | Milipore | MABN889 |
| LysoSensor™ Green DND-189 | Invitrogen | L7535 |
| LysoTracker™ Deep Red | Invitrogen | L12492 |
| LC3B (Rabbit IgG) | Abcam | ab192890 |
| LAMP1 (Mouse IgG) | Abcam | ab25630 |
| CD63 (mouse IgG1, κ) | BD Transduction Laboratories™ | 556019 |
| RAB7 (Rabbit IgG) | Abcam | ab137029 |
| Phospho-TDP43(Ser409/410) (Rabbit IgG) | Cosmo Bio | CAC-TIP-PTD-P07 |
| Alexa Fluor® 647 Anti-LC3B antibody | Abcam | ab225383 |
| FUS (Goat IgG) | Bethyl Laboratories® | A303-839A |
| IBA1 (Goat IgG) | Abcam | ab5076 |
| MAP2 (Chicken IgY) | Abcam | ab5392 |
| TUJ1/Tubb3 (Mouse IgG) | Neuromics | CH23005 |
| NeuN (Mouse IgG) | Millipore | MAB377 |
| ChAT (Goat polyclonal) | Millipore Sigma | AB144P |
| Phospho TDP43(Ser403/404) (Mouse IgG2a) | ProteinTech | 66079-1-Ig |
| LAMP1 (Rabbit IgG) | Abcam | ab24170 |
| RAB7 (Mouse IgG1 κ) | Santa Cruz | sc-376362 |
| LC3B (Mouse IgG2a) | GeneTex | GT3612 |
| GFP (Chicken IgY) | Aves Lab | GFP-1010 |
| GFAP (Rabbit IgG) | Abcam | ab7260 |
| Iba1 (Rabbit IgG) | GeneTex | GT101495 |
| DAPI | Thermo Fisher | 62248 |
| NeuroTrace™ 500/525 Green Fluorescent Nissl Stain | Thermo Fisher | N21480 |
| Goat anti-Chicken IgY (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 405 | Thermo Fisher | A48260 |
| Donkey anti-Rabbit, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 488 | Invitrogen | A-21206 |
| Donkey anti-Mouse,IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 555 | Invitrogen | A31570 |
| Donkey anti-Mouse, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 488 | Invitrogen | A21202 |
| Donkey anti-Mouse, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 647 | Invitrogen | A32787 |
| Donkey Anti-Chicken IgY (IgG) (H+L) Alexa Fluor® 647 | Jackson ImmunoResearch | 703-605-155 |
| Goat anti-Chicken IgY (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488 | Invitrogen | A32931TR |
| Donkey anti-Goat, IgG (H+L) Highly Cross-Adsorbed , Alexa Fluor 555 | Invitrogen | A32816 |
| IRDye® 680RD Donkey anti-Rabbit IgG Secondary Antibody | LI-COR Biosciences | 926-68073 |
| IRDye® 800CW Donkey anti-Mouse IgG Secondary Antibody | LI-COR Biosciences | 926-32212 |
| CFSE dye | Thermo | C34554 |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM | Gibco | 11995-065 |
| Opti-MEM | Gibco | 31985-070 |
| FBS | GenClone | 25-514 |
| Trypsin | GenClone | 25-510 |
| Polybrene (Hexadimethrine bromide) | Sigma | H9268-5G |
| DMEM/F12 | Corning | 10-090-CV |
| Laminin | Invitrogen | 23017015 |
| Glutamax | Gibco | 35050-061 |
| N2 | Gibco | 17502048 |
| B27 | Gibco | 17504044 |
| Human FGF-beta | Peprotech | 100-18B |
| Repsox | Selleckchem | S7223 |
| human CNTF | R&D | 257-NT |
| human BDNF | R&D | 248BDB |
| human GDNF | R&D | 212-GD |
| Matrigel | Corning | 354277 |
| mTeSR | StemCell | 85851 |
| Accutase | Innovative Cell Technologies | AT4104 |
| Y-27632 2HCl | selleckchem | S1049 |
| Lenti-X concentrator | TaKaRa | 631232 |
| Polybrene (Hexadimethrine bromide) | Sigma | H9268-5G |
| Neurobasal-A | Life Technologies | 10888-022 |
| Apilimod | achemblock | O33822 |
| GW 4869 (hydrochloride hydrate) | Cayman Chemicals | 13127 |
| SB431542 | Cayman Chemical | 13031 |
| CHIR99021 | Cayman Chemical | 13122 |
| Retinoic Acid | Millipore Sigma | R2625 |
| DMH1 | selleckchem | S7146 |
| Purmorphamine | Cayman Chemical | 10009634 |
| Donor Equine Serum | HyClone | 16777-030 |
| BMP4 | Invitrogen | PHC9534 |
| VEGF | Invitrogen | PHC9394 |
| SCF | Miltenyi | 130-096-692 |
| X-VIVO15 | SLS (Lonza) | LZBE02-060F |
| M-CSF | Invitrogen | PHC9501 |
| IL-3 | Invitrogen | PHC0033 |
| 2-mercaptoethanol | Gibco | 21985023 |
| IL-34 | Biolegend | 577906 |
| Bafilomycin A1 | Cayman | 11038 |
| HEPES Stock Solution (1 M) | Cayman | 600212 |
| Citrate Buffer pH 6.0 | Electron Microscopy Sciences (EMS) | 64142-07 |
| Normal Donkey Serum | VWR | 102644-006 |
| cOmplete™, EDTA-free Protease Inhibitor Cocktail | Roche | 4693132001 |
| PhosSTOP™ | Roche | 4906845001 |
| Chameleon® Duo Pre-stained Protein Ladder | Licor | 928-60000 |
| Odyssey® One-Color Protein Molecular Weight Marker | Licor | 928-40000 |
| MEM media | Life Technologies | 10370088 |
| Urea | Sigma | U5378-100G |
| Thiourea | Sigma | T8656-50G |
| CHAPS | Sigma | 10810118001 |
| Tris-HCl 1.5M, pH=8.8 | Teknova | T1588 |
| Penicillin-streptomycin 50X | Corning | 30-001-CI |
| Compound E | Cayman Chemicals | 15579 |
| PEG 6000 | Sigma-Aldrich | 81253 |
| Experimental models: Cell lines | ||
| ND03231 (CTRL1) | NINDS Biorepository | 3231 |
| ND05280 (CTRL2) | NINDS Biorepository | 5280 |
| ND03719 (CTRL3) | NINDS Biorepository | 3719 |
| ND00184 (CTRL4) | NINDS Biorepository | 00184 |
| ND41865 (CTRL5) | NINDS Biorepository | 41865 |
| ND06769 (C9-ALS 1) | NINDS Biorepository | 6769 |
| ND10689 (C9-ALS 2) | NINDS Biorepository | 10689 |
| ND12099 (C9-ALS 3) | NINDS Biorepository | 12099 |
| ND50000 (C9-ALS 4) | NINDS Biorepository | 50000 |
| ND10739 (sALS1) | NINDS Biorepository | 10739 |
| ND13454 (sALS2) | NINDS Biorepository | 13454 |
| ND11813 (sALS3) | NINDS Biorepository | 11813 |
| ND09711 (sALS4) | NINDS Biorepository | 9711 |
| ND14185 (sALS5) | NINDS Biorepository | 14185 |
| ND08705 (sALS6) | NINDS Biorepository | 8705 |
| ND09292 (sALS7) | NINDS Biorepository | 9292 |
| ND09329 (sALS8) | NINDS Biorepository | 9329 |
| ALS93E (sALS9) | This Manuscript | N/A |
| ND35663 (FUS H517Q) | NINDS Biorepository | 35663 |
| ND39034 (FUS R522R) | NINDS Biorepository | 39034 |
| ND50007 (TDP-43 G298S) | NINDS Biorepository | 50007 |
| Experimental models: Animal Models | ||
| C. elegans: TDP-43A315T | Parker lab | N/A |
| Drosophila: Wild type (w1118) | Zarnsecu and Dickman labs | N/A |
| Drosophila: GR.100 larvae (w;OK6-Gal4/UAS-100xGR) | Dickman lab | N/A |
| Drosophila: w1118 ; UAS-TDP-43G298S- YFP | Zarnescu lab | N/A |
| Drosophila: y[1]v[1]; P{Y[+(7.7) = GSYP}attP2 | Bloomington Drosophila Stock Center | BDSC # 8622 |
| Drosophila: y[1] sc[*] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.GL00246}attP2 | Bloomington Drosophila Stock Center | BDSC # 35793 |
| Drosophila: P{UAS-poly-GR.PO-100}attP40 | Bloomington Drosophila Stock Center | BDSC#58696 |
| Mice: TDP-43 transgenic mice | Jackson Laboratory | 012836 |
| Mice: B6.Cg-PIKFYVE<tm1.1Ashi>/J | Jackson Laboratory | 029331 |
| Mice: B6.C-Tg(CMV-Cre)1Cgn/J | Jackson Laboratory | 006054 |
| Mice: C57BL/6J mice | Jackson Laboratory | 000664 |
| Oligonucleotides | ||
| sgRNA-1 targeting upstream of repeat expansion | This Manuscript | GUAACCUACGGUGUCCCGCU |
| sgRNA-2b targeting downstream of repeat expansion | This Manuscript | ACCCCAAACAGCCACCCGCC |
| Primer 1 for repeat primed PCR | This Manuscript | FAM-tgtaaaacgacggccagtCAAGGAGGGAAACAACCGCAGCC |
| Primer 2 for repeat primed PCR | This Manuscript | caggaaacagctatgaccGGGCCCGCCCCGACCACGCCCCGGCCCCGGCCCCGG |
| Primer 3 for repeat primed PCR | This Manuscript | caggaaacagctatgacc |
| Forward primer for Southern Probe | This Manuscript | AGAACAGGACAAGTTGCC |
| Reverse primer for Southern Probe | This Manuscript | AACACACACCTCCTAAACC |
| qPCR primer for RAB27A, Forward | This Manuscript | AGAGGCCAGAGAATCCACCT |
| qPCR primer for RAB27A, Reverse | This Manuscript | CACACCGTTCCATTCGCTTC |
| qPCR primer for HPRT, Forward | This Manuscript | GACTTTGCTTTCCTTGGTCAG |
| qPCR primer for HPRT, Reverse | This Manuscript | GGCTTATATCCAACACTTCGTGGG |
| qPCR primer for VAMP7, Forward | This Manuscript | CGGTTCAAGAGCACAGACAGCA |
| qPCR primer for VAMP7, Reverse | This Manuscript | ATCCACTTGGGCTTGAGTCTCC |
| qPCR primer for RAB8A, Forward | This Manuscript | TCAGGAACGGTTTCGGACGATC |
| qPCR primer for RAB8A, Reverse | This Manuscript | GCTCCTCAATGTTGCGAATCCAG |
| qPCR primer for HSP8A, Forward | This Manuscript | TCCTACCAAGCAGACACAGACC |
| qPCR primer for HSP8A, Reverse | This Manuscript | CAGGAGGTATGCCTGTGAGTTC |
| qPCR primer for NSMAF, Forward | This Manuscript | GTCTGAACACCTTCACGAGTGG |
| qPCR primer for NSMAF, Reverse | This Manuscript | CTGTTCAAGTCTACACCTCCTTC |
| qPCR primer for ATG7, Forward | This Manuscript | CGTTGCCCACAGCATCATCTTC |
| qPCR primer for ATG7, Reverse | This Manuscript | CACTGAGGTTCACCATCCTTGG |
| qPCR primer for MCOLN1, Forward | This Manuscript | CTGATGCTGCAAGTGGTCAAG |
| qPCR primer for MCOLN1, Reverse | This Manuscript | GGTGTTCTCTTCCCGGAATGTC |
| qPCR primer for GORASP1, Forward | This Manuscript | CACGGGGATGTGGAACCATC |
| qPCR primer for GORASP1, Reverse | This Manuscript | ATCAGCTTCAAGGGCTTCCC |
| qPCR primer for SMPD3, Forward | This Manuscript | GAAGCACACCTCAGGACCAAAG |
| qPCR primer for SMPD3, Reverse | This Manuscript | CAGCCAGTCCTGAAGCAGGTC |
| qPCR primer for PIKFYVE, Forward | This Manuscript | GGCTCACGCCTATAATCCTATC |
| qPCR primer for PIKFYVE, Reverse | This Manuscript | GCTGGAATGCAATGGTGTAATC |
| qPCR primer for GAPDH, Forward | This Manuscript | CGAGATCCCTCCAAAATCAA |
| qPCR primer for GAPDH, Reverse | This Manuscript | GTCTTCTGGGTGGCAGTGAT |
| qPCR primer for MAP2, Forward | This Manuscript | GGAACCAACTCTCTCTGGATTT |
| qPCR primer for MAP2, Reverse | This Manuscript | GCATTCTCTCTTCAGCCTTCT |
| qPCR primer for truncated STMN2, Forward | This Manuscript | GGACTCGGCAGAAGACCTTC |
| qPCR primer for truncated STMN2, Reverse | This Manuscript | GCAGGCTGTCTGTCTCTCTC |
| qPCR primer for Pikfyve, Forward (exon 6) | This Manuscript | GAAGCAATATTGGATGCCAGA |
| qPCR primer for Pikfyve, Reverse (exon 6) | This Manuscript | CCCATAAATTTTCCAGGGATT |
| qPCR primer for Pikfyve, Forward | This Manuscript | ACAGTGCTGAAGAAGGGCTC |
| qPCR primer for Pikfyve, Reverse | This Manuscript | ACAGATCAGGGCTCTTCCCT |
| qPCR primer for PPIA, Forward | This Manuscript | TCCTGGACCCAAAACGCTCC |
| qPCR primer for PPIA, Reverse | This Manuscript | CCATGGCAAATGCTGGACCA |
| DNA primer for S0 genotyping, Forward | This Manuscript | GTGACTAGTGAACCTAGCACATTG |
| DNA Common primer, TDP-43 genotyping | This Manuscript | TGAAATCCGGGTGGTATTGG |
| DNA WT primer, TDP-43 genotyping | This Manuscript | GGTGAGTTTAACCTTCAAGGGCT |
| DNA Transgene primer, TDP-43 genotyping | This Manuscript | AGCTTGCTAGCGGATCCAGAC |
| DNA primer for S1 genotyping, Forward | This Manuscript | GCCTGAGTTCTGAGAGTGAGTG |
| DNA primer for S2 genotyping, Forward | This Manuscript | CTGAAGCAATATTGGATGCCAGATAGC |
| DNA primer for S3 genotyping, Forward | This Manuscript | GTAAAGGTTGACTTGACTTACATGATAG |
| DNA primer for A1 genotyping, Reverse | This Manuscript | CTATGATGGGAAGAGTGGACAGTC |
| DNA primer for Cre Control, Forward | This Manuscript | CTAGGCCACAGAATTGAAAGATCT |
| DNA primer for Cre Control, Reverse | This Manuscript | GTAGGTGGAAATTCTAGCATCATCC |
| DNA primer for Cre Transgene, Forward | This Manuscript | GCGGTCTGGCAGTAAAAACTATC |
| DNA primer for Cre Transgene, Reverse | This Manuscript | GTGAAACAGCATTGCTGTCACTT |
| Negative control ASO | This Manuscript | mG*mC*mG*mA*mC*T*A*T*A*C*G*C*G*C*A*mA*mU*mA*mU*mG |
| PIKFYVE ASO1 | This Manuscript | mU*mG*mG*mC*mC*T*C*C*T*T*C*T*G*C*T*mC*mU*mC*mU*mC |
| PIKFYVE ASO2 | This Manuscript | mG*mC*mU*mG*mG*T*C*C*A*A*C*T*T*C*C*mA*mC*mU*mC*mA |
| RAB27A ASO | This Manuscript | mG*mA*mA*mA*mC*C*T*C*T*C*C*T*G*C*C*mC*mU*mG*mC*mU |
| VAMP7 ASO | This Manuscript | mC*mU*mA*mG*mG*C*T*A*A*A*C*A*G*G*T*mG*mG*mC*mU*mA |
| RAB8A ASO | This Manuscript | mU*mG*mG*mU*mU*G*A*C*C*T*G*G*T*C*C*mC*mA*mG*mU*mC |
| HSPA8 ASO | This Manuscript | mC*mA*mA*mG*mG*A*A*G*G*T*A*G*T*T*G*mC*mC*mA*mA*mC |
| NSMAF ASO | This Manuscript | mA*mU*mC*mU*mG*C*C*C*T*A*A*G*A*G*A*mA*mU*mA*mG*mC |
| ATG7 ASO | This Manuscript | mG*mU*mU*mG*mA*G*T*G*C*C*A*T*A*C*C*mA*mG*mU*mA*mG |
| MCOLN1 ASO | This Manuscript | mG*mG*mU*mU*mA*G*A*T*G*T*A*C*C*T*T*mC*mA*mC*mA*mU |
| GORASP1 ASO | This Manuscript | mG*mG*mA*mU*mA*G*A*C*C*T*A*G*T*C*A*mG*mG*mU*mA*mG |
| SMPD3 ASO | This Manuscript | mG*mG*mA*mU*mU*G*T*C*A*A*A*A*A*C*A*mG*mU*mC*mC*mC |
| Negative control ASO (in vivo) | This Manuscript | /52MOErC/*/i2MOErC//i2MOErT//i2MOErA//i2MOErT/A*G*G*A*C*T*A*T*C*C*/i2MOErA//i2MOErG//i2MOErG/*/i2MOErA/*/32MOErA/ |
| Pikfyve ASO (in vivo) | This Manuscript | /52MOErG/*/i2MOErC//i2MOErA//i2MOErT//i2MOErC/T*T*G*T*G*G*A*A*C*T*/i2MOErC//i2MOErT//i2MOErC/*/i2MOErC/*/32MOErC/ |
| Deposited data | ||
| Bulk RNA-seq data (DMSO or AP treatment) | This Manuscript | GEO: GSE221015 |
| Bulk RNA-seq data (Negative control or PIKFYVE ASO treatment) | This Manuscript | GEO: GSE221016, GSE221017 |
| Software and Algorithms | ||
| ImageJ | Schneider et al.68 | https://imagej.nih.gov/ij/index.html |
| Prism | Graphpad | https://www.graphpad.com/scientific-software/prism/ |
| Enrichr | Kuleshov et al.60 | https://maayanlab.cloud/Enrichr/ |