| Antibodies |
| Total OXPHOS antibody cocktail |
Abcam |
ab110413 |
| Mouse monoclonal anti-C9orf72 |
Bio-Rad |
VMA00065 |
| Rabbit polyclonal anti-C9orf72 |
Proteintech Group |
22637-1-AP |
| Mouse monoclonal anti-TIMMDC1 |
Santa Cruz |
sc-514927 |
| Rabbit polyclonal anti-TIMMDC1 |
Sigma Aldrich |
HPA053214 |
| Rabbit monoclonal anti-NDUFB9 |
Abcam |
ab200198 |
| Rabbit monoclonal anti-NDUFB11 |
Abcam |
Ab183716 |
| Mouse monoclonal anti-UQCRC1 |
Abcam |
ab110252 |
| Mouse monoclonal anti-MTCO1 |
Abcam |
ab14705 |
| Mouse monoclonal anti-NDUFA8 |
Santa Cruz |
sc-398097 |
| Mouse monoclonal anti-AIFM1 |
Santa Cruz |
sc-13116 |
| Mouse monoclonal anti-CHCHD4 |
Santa Cruz |
sc-365137 |
| Rabbit polyclonal anti-AFG3L2 |
Abcam |
ab154990 |
| Mouse monoclonal anti-PHB1 |
Santa Cruz |
sc-377037 |
| Mouse monoclonal anti-PHB2 |
Santa Cruz |
sc-133094 |
| Rabbit monoclonal anti-PHB2 |
Cell Signaling |
14085 |
| Rabbit polyclonal anti-TOM70 |
Sigma Aldrich |
HPA014589 |
| Mouse monoclonal anti-TIM44 |
Santa Cruz |
sc-390755 |
| Rabbit polyclonal anti-SOD1 |
Enzo Life Sciences |
ADI-SOD-100 |
| Rabbit polyclonal anti-YME1L |
Proteintech Group |
11510-1-AP |
| Rabbit polyclonal anti-TIM23 |
Proteintech Group |
11123-1-AP |
| Mouse monoclonal anti-TIM23 |
Santa Cruz |
sc-514463 |
| Rabbit monoclonal anti-TOM20 |
Cell Signaling |
42406 |
| Rabbit monoclonal anti-GAPDH |
Cell Signaling |
2118 |
| Mouse monoclonal anti-His tag |
Santa Cruz |
sc-8036 |
| Mouse monoclonal anti-Flag tag |
Sigma Aldrich |
F1804 |
| Mouse monoclonal anti-GST tag |
Santa Cruz |
sc-138 |
| Mouse monoclonal anti-β-actin |
Santa Cruz |
sc-47778 |
| Rabbit monoclonal anti-β-tubulin |
Cell Signaling |
2128 |
| Bacterial and Viral Strains |
| Stbl3 competent E. coli |
Thermo Fisher Scientific |
C737303 |
| BL21(DE3) competent E. coli |
Agilent |
200131 |
| Biological Samples |
| Human spinal cord tissue |
See Table S6
|
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| Rock inhibitor Y27632 |
Stemgent |
04-0012 |
| N2 supplement |
Thermo Fisher Scientific |
17502048 |
| B27 supplement |
Thermo Fisher Scientific |
17504044 |
| Neurobasal medium |
Thermo Fisher Scientific |
21103049 |
| Glucose-free neurobasal medium |
Thermo Fisher Scientific |
A2477501 |
| Fetal bovine serum |
Thermo Fisher Scientific |
10438026 |
| Dialyzed fetal bovine serum |
Thermo Fisher Scientific |
26400044 |
| CHIR99021 |
Stemgent |
04-0004 |
| SB431542 |
Stemgent |
04-0010 |
| DMH-1 |
Tocris |
4126 |
| Retinoic acid |
Sigma Aldrich |
R2625 |
| Purmorphamine |
Stemgent |
04-0009 |
| Dispase |
Stemcell |
07923 |
| Compound E |
Sigma Aldrich |
530509 |
| Galactose |
Sigma Aldrich |
G5388 |
| Ascorbic acid |
Sigma Aldrich |
A4544 |
| Calcein AM |
Thermo Fisher Scientific |
C3099 |
| Image-iT TMRM |
Thermo Fisher Scientific |
I34361 |
| CCCP |
Sigma Aldrich |
C2759 |
|
13C6,15N4 L-Arginine |
Cambridge Isotope Laboratories |
CNLM-539-H |
|
13C6,15N2 L-Lysine |
Cambridge Isotope Laboratories |
CNLM-291-H |
| Tandem mass tag (TMT) reagents |
Thermo Fisher Scientific |
90061 |
| Digitonin |
Sigma Aldrich |
D141 |
| cOmplete protease inhibitor cocktail |
Roche |
11873580001 |
| Protein A/G beads |
Thermo Fisher Scientific |
88803 |
| IgG elution buffer |
Thermo Fisher Scientific |
21028 |
| TRIzol reagent |
Thermo Fisher Scientific |
15596026 |
| EasyTag L-[35S]-Methionine |
PerkinElmer |
NEG709A500UC |
| AMS |
Thermo Fisher Scientific |
A485 |
| Cycloheximide |
Sigma Aldrich |
C1988 |
| Recombinant human C9orf72 protein |
(Liu et al., 2018) |
N/A |
| Recombinant human PHB1 protein |
Abnova |
H00005245-P01 |
| Recombinant human PHB2 protein |
Abnova |
H00011331-P02 |
| Recombinant SUMO protein |
MyBioSource |
MBS2553243 |
| Critical Commercial Assays |
| Seahorse XF cell mito stress test kit |
Agilent |
103708-100 |
| NativePAGE Novex Bis-Tris gel system |
Thermo Fisher Scientific |
BN2001; BN2002; BN1002BOX; BN2008; LC0725 |
| Gibson assembly cloning kit |
New England Biolabs |
E5510S |
| Cell counting kit-8 (CCK-8) |
Abcam |
Ab228554 |
| TNT coupled reticulocyte lysate systems |
Promega |
L4611 |
| Complex I enzyme activity microplate assay kit |
Abcam |
ab109721 |
| Mitochondrial Complex I activity colorimetric assay kit |
Biovision |
K968 |
| QuantiTect reverse transcription kit |
Qiagen |
205313 |
| iQ SYBR green PCR mix |
Bio-Rad |
1708880 |
| ATP determination kit |
Thermo Fisher Scientific |
A22066 |
| Extracellular oxygen consumption assay |
Abcam |
ab197243 |
| Experimental Models: Cell Lines |
| Human HEK293 |
ATCC |
CRL-1573 |
| Mouse embryonic fibroblasts control |
(Ugolino et al., 2016) |
N/A |
| Mouse embryonic fibroblasts C9orf72 KO |
(Ugolino et al., 2016) |
N/A |
| Human HAP1 control |
Horizon Discovery |
C631 |
| Human HAP1 C9orf72 KO |
Horizon Discovery |
HZGHC003729c002 |
| Human B lymphocytes |
See Table S6
|
N/A |
| Human iPSCs |
See Table S6
|
N/A |
| Experimental Models: Organisms/Strains |
| B6.Tg(Sox2-cre)1Amc/J mice |
The Jackson Laboratory |
008454 |
| C57BL/6J mice |
(Ugolino et al., 2016) |
N/A |
| C57BL/6J C9orf72 KO mice |
(Ugolino et al., 2016) |
N/A |
| Oligonucleotides |
| Human AIFM1 siRNA GGGCAAAAUCGAUAAUUCU |
(Hangen et al., 2015) |
N/A |
| Human CHCHD4 siRNA GCAUGGAUUGAUACUGCCATT |
(Hangen et al., 2015) |
N/A |
| Mouse TIMMDC1 qPCR FWD AGTACTCCGGTGAGACGGTT |
This study |
N/A |
| Mouse TIMMDC1 qPCR REV TGCAGACTGCTTCTCCACTC |
This study |
N/A |
| Mouse Actin qPCR FWD GGCTGTATTCCCCTCCATCG |
This study |
N/A |
| Mouse Actin qPCR REV CCAGTTGGTAACAATGCCATGT |
This study |
N/A |
| Recombinant DNA |
| Plasmid: mouse TIMMDC1 shRNA |
Sigma Aldrich |
TRCN0000202057 |
| Plasmid: human NDUFS5 shRNA 1# |
Sigma Aldrich |
TRCN0000036639 |
| Plasmid: human NDUFS5 shRNA 2# |
Sigma Aldrich |
TRCN0000036643 |
| Plasmid: mouse PHB1 shRNA 1# |
Sigma Aldrich |
TRCN0000088457 |
| Plasmid: mouse PHB1 shRNA 2# |
Sigma Aldrich |
TRCN0000088455 |
| Plasmid: mouse PHB2 shRNA 1# |
Sigma Aldrich |
TRCN0000054428 |
| Plasmid: mouse PHB2 shRNA 2# |
Sigma Aldrich |
TRCN0000054429 |
| Plasmid: human AFG3L2 shRNA |
Sigma Aldrich |
TRCN0000051489 |
| Plasmid: mouse AFG3L2 shRNA |
Sigma Aldrich |
TRCN0000241172 |
| Plasmid: mouse YME1L shRNA |
Sigma Aldrich |
TRCN0000031200 |
| Plasmid: human C9orf72 shRNA |
(Ugolino et al., 2016) |
N/A |
| Plasmid: pLenti-CMV-Puro-DEST |
(Campeau et al., 2009) |
Addgene # 17452 |
| Plasmid: pLenti-CMV-Puro-C9orf72 |
This Study |
N/A |
| Plasmid: GW1-PercevalHR |
(Tantama et al., 2013) |
Addgene #49082 |
| Plasmid: pGEM-7Zf(+)-C9orf72 |
This Study |
N/A |
| Plasmid: pGEM-7Zf(+)-NDUFS8 |
This Study |
N/A |
| Plasmid: pGEM-7Zf(+)-NDUFA8 |
This Study |
N/A |
| Plasmid: pSATL-C9orf72-His-SUMO |
(Liu et al., 2018) |
N/A |
| Software and Algorithms |
| Quantity One |
Bio-Rad |
https://www.bio-rad.com/en-us/product/quantity-one-1-d-analysis-software
|
| GraphPad Prism |
GraphPad |
https://www.graphpad.com/
|
| Fiji |
N/A |
https://fiji.sc/
|
| Image-Pro Plus |
Media Cybernetics |
https://www.mediacy.com/imageproplus
|
