Reagents and resources

All the reagents including qPCR primers, antibodies, and software used are listed in Supplementary Table1

Human embryonic stem cell (H7-hESCs; WiCell, Madison, WI, https://www.wicell.org) reporter line with CRISPR-engineered multicistronic BRN3B-P2A-tdTomato-P2A-Thy1.2 construct into the endogenous RGC specific BRN3B locus was used for isogenic control20. CRISPR mutated H7-hESC reporter with OPTNE50K-homozygous mutation (H7-E50K) was done as explained previously25. Patient-derived induced pluripotent stem cells (iPSCs) with E50K mutation24 (iPSC-E50K), E50K mutation corrected to WT by CRISPR in the patient-derived iPSC (iPSC-E50Kcorr)25 with BRN3B::tdTomato reporter were obtained from the Jason Meyer lab. All the above cell lines were grown in mTeSR1 media (mT) at 37C in 5% CO2 incubator on matrigel (MG) coated plates. These cells were maintained by clump passaging using Gentle Cell Dissociation Reagent (GD) after 7080% confluency. Media was aspirated and GD was added to cells followed by incubation at 37C in 5% CO2 incubator for 5min. Next, mT was used to break up the colonies into small clumps by repeated pipetting and then seeded onto new MG plates.

For differentiation, stem cells were dissociated to single cells using accutase for 10min and then quenched with twice the volume of mT with 5M blebbistatin (blebb). The cells were centrifuged at 150xg for 6minutes and resuspended in mT with 5M blebb, then 100,000 cells were seeded per well of a 24-well MG coated plate. The next day, media was replaced with mT without blebb. After 24h, media was replaced with differentiation media (iNS) and further small molecule-based differentiation was carried out with iNS media as elucidated previously23. Differentiation of hRGCswas monitored by tdTomato expression and cells were purified during days 4555 using THY1.2 microbeads and magnetic activated cell sorting system (MACS, Miltenyi Biotec) as explained before20,23. Next, hRGCs were resuspended in iNS media, counted using a hemocytometer and seeded on MG-coated plates, coverslips, or MatTek dishes for experiments.

Purified hRGCs were seeded at 30,000 cells per well of a 96-well MG-coated plate and maintained for 3 days. For measuring mitochondrial mass, hRGCs were labeled with mitochondria-specific MTDR dye. To measure mitochondrial degradation, hRGCs were labeled with 10nM MTDR dye for 1h, washed, and then treated with 10M CCCP for a time course. To measure mitochondrial biogenesis, hRGCs were labeled with MTDR first, treated with 10M CCCP or equal amount of DMSO for 3h, then washed and incubated with fresh media with MTDR for the time course. After treatments, hRGCs were dissociated to single-cell suspension using accutase and analyzed using Attune NxT flow cytometer (Thermo Fisher).

Purified hRGCs were seeded at 500,000 cells per well of 24-well MG-coated plates and maintained for 3 days. Cells were then treated with indicated molecules and time points. DMSO was used as the control as the small molecules were dissolved in DMSO. The cells were lysed and collected in 100l of M-PER extraction buffer with 5mM EDTA and protease inhibitors. Protein quantification was done using a BSA standard following the DC Protein Assay Kit II (Bio-Rad) and measured on microplate reader. Loading samples were prepared with heat denaturation at 95C for 5minutes with laemmli sample buffer (1X). 1020g protein per sample were run on Bio-Rad Mini-PROTEAN TGX precast gels, in running buffer (Tris-Glycine-SDS buffer; Bio-Rad) at 100V until the dye front reached to the bottom. The transfer sandwich was made using PVDF membrane (activated in methanol) in Tris-Glycine transfer buffer (Bio-Rad) with 20% methanol and transferred for 2h at 30V, 4C. For the visualization of proteins, the membranes were blocked in 5% skim milk in TBST (TBS buffer with 20% Tween20) for 2h at room temperature and incubated overnight at 4C in 1:1000 dilution of primary antibodies for PGC1 (Abcam), Phospho-PGC1Ser571 (R&D Systems), PGC1 (Abcam), AMPK (Cell Signaling Technologies, CST), Phospho-AMPKThr172 (CST), LC3B (Sigma), GAPDH (CST), or ACTIN (CST). Membranes were then washed three times for 5minutes each in TBST, followed by 2h of incubation in 5% milk in TBST containing anti-rabbit HRP linked secondary antibody (CST) at 1:10,000 dilution. The membranes were again washed three times with TBST and then placed in Clarity Max Western ECL (Bio-Rad) substrate for 5min. The membranes were imaged in a Bio-Rad ChemiDoc Gel Imager, and the raw integrated density for each band was measured and normalized with respect to the corresponding GAPDH or actin loading control using Image J. Treatment conditions were further normalized to the corresponding DMSO control for each experiment. Complete blots of the representative western blot images, with protein molecular weight marker (Thermo Scientific), are provided in Supplementary Fig.6. Protein bands corresponding to the appropriate size were quantified following product datasheets and published literature.

Purified hRGCs were seeded on MG-coated coverslips (1.5 thickness) at a density of 30,00040,000 cells per coverslip and grown for 3 days. Next, hRGCs were treated with indicated molecules and time points. After treatment the media was aspirated, the cells were washed with 1 PBS, and then fixed with 4% Paraformaldehyde for 15min at 37C. Fixed cells were permeabilized with 0.5% Triton-X100 in PBS for 5min and then washed with washing buffer (1% donkey serum, 0.05% Triton-X100 in PBS) three times for 5min each. Cells were blocked with blocking buffer (5% donkey serum, 0.2% Triton-X100 in PBS) for 1h. After blocking, antibodies against TOM20 (Mouse, Santa Cruz), Tubulin 3 (mouse, Biolegend), RBPMS (rabbit, GeneTex) and Optineurin (Rabbit, Cayman Chemicals) were added (1:200 in blocking buffer) and the coverslips were incubated overnight at 4C. Next, coverslips were washed with washing buffer three times for 5min each and incubated for 2h at room temperature in the dark with fluorophore conjugated anti mouse or rabbit secondary antibodies (1:500). The coverslips were washed with washing buffer three times for 5min each, with 1.43M DAPI added to the second wash. The coverslips were then mounted onto slides with DAKO mounting medium. Visualization of above proteins and nucleus was done by confocal immunofluorescence microscopy using Zeiss LSM700 with 63x/1.4 oil objective. Analysis was carried out using ImageJ with maximum projections of DAPI channel (number of nuclei) and sum projections of TOM20 and OPTN channels for the corresponding confocal z-stacks. For OPTN aggregate size, we analyzed particles from 0.02 a.u. to infinity to account for the small and big aggregates.

Purified hRGCs were seeded at 300,000 cells per well of 24-well MG-coated plates and maintained for 3 days. Cells were then treated with indicated molecules and durations. Media was aspirated and cells were incubated in 200l accutase for 10min and then quenched with 400l iNS media. Cells were centrifuged at 150xg for 6min, media aspirated, and the cell pellets were stored at 20C. RNA was extracted from cell pellets following the kit protocol (Qiagen 74104). The RNA concentration was measured using Nanodrop 2000c (Thermo) and 6l of RNA was used to prepare cDNA following the kit protocol (Abm #G492). Primers were designed as detailed in TableS1 and qPCR were performed using BlasTaq qPCR MasterMix with 100ng total cDNA in a 20l reaction mixture using QuantStudio6 Flex RT PCR system (Applied Biosystems). GAPDH or actin was used as a housekeeping gene in every plate to calculate the Ct values. The Ct was calculated with respect to (w.r.t) the average Ct of the control sample. All conditions were measured by averaging three technical repeats for each biological repeat with total three biological replicates.

Purified hRGCs were seeded at 50,00075,000 cells per well of 96-well MG-coated plates and maintained for 3 days. Cells were then treated with indicated molecules for the designated durations. Media was aspirated and cells were incubated in 30l accutase for 10min and then quenched with 100l iNS media. Cells were centrifuged at 150xg for 6min, media aspirated, and the cell pellets were stored at 20C. DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen) and eluted with 30l elution buffer. DNA concentration was measured using Nanodrop 2000c (Thermo). 10ng of DNA was used to measure both mitochondrial ND1 gene and internal control, human nuclear RNase P gene copy numbers, as done previously23.

hRGCs were seeded on MG-coated glass bottom (1.5 thickness)MatTek dishes at 40,000 cells per dish and maintained for 3 days. For the experiments in Fig.2ac, cells were incubated with 250l of JC1 media (1:100 in iNS) for 30min in the incubator, then an additional 1.75ml of dilute JC1 (1:1000 in iNS) was added to the dish. The dish was then transferred to the live cell chamber (5% CO2, 37C, Tokai Hit) and confocal z-stacks were acquired prior to (before) and 10minutes after CCCP (10M) treatment using Zeiss LSM700 with 63x/1.4 oil objective. For experiments in Fig.2df, cells were treated with 10M CCCP or equivalent DMSO for 30min. Next, cells were washed with iNS media, and then incubated with 250l of JC1 media (1:100 in iNS) for 30min in the incubator. The JC1 media was then removed, cells were washed again, and 2ml of new iNS was added to the dish. The dish was then transferred to the live cell chamber and imaged. Analysis was carried out using ImageJ with sum projections of red and green channels. The red fluorescence from the tdTomato expressed by the hRGCs was much less intense than the JC1 red staining of mitochondria, thus the red fluorescence measured from the cytoplasm was considered background and subtracted out of the measurements. For the green fluorescence, background was measured from outside the cell. Red-to-Green ratios were calculated by dividing the red intensity by green intensity. These values were then normalized to the control condition, hRGCWT-before (Fig.2c) or average DMSO ratio for each cell line (Fig.2f).

The 96-well seahorse plate was coated with MG and hRGCs were seeded at 250,000 cells per well and maintained for 2 days. 24h before measurements, media was exchanged with 100l iNS with 1g/ml BX795 or equivalent vehicle control DMSO. A day prior to the assay, the sensor cartridge was fully submerged with 200l of sterile water to hydrate it overnight in a non-CO2, 37C incubator. The next day, sterile water was replaced with pre-warmed XF calibrant buffer(Agilent) and the sensors were again submerged and incubated in the non-CO2, 37C incubator for 4560min. Seahorse media was made by adding stock solutions to XF DMEM to have final concentrations of 21.25mM glucose, 0.36mM sodium pyruvate, and 1.25 mM L-glutamine (Agilent), with pH adjusted to 7.387.42. Depending upon the assay, 20M Oligomycin (Oligo), 20M FCCP, 2.5g/ml Rotenone plus 5M Antimycin A (Rot/AA), and/or 175mM 2-deoxy-d-glucose (2-DG) solutions were then prepared in Seahorse media. In the Seahorse plate with hRGCs, iNS media was carefully exchanged to Seahorse media by removing, 60l iNS from all wells and adding 140l of Seahorse media. Next, 140l of the mixed media was removed by pipette and then an additional 140l seahorse media was added to each well to have a final volume of 180l. 180l of Seahorse media was then added to any empty wells. The plate was placed in Incucyte S3 (Sartorius) and one image of each well was taken for cell area normalization using brightfield and red fluorescence (tdTomato) channels. The hRGC seahorse plate was then placed into a non-CO2, 37C incubator for at least 45min. The reagents were added into their respective ports in the cartridge with the final concentrations in the wells as follows. For ATP rate assay, 2.0M Oligo and 0.25g/ml Rotenone plus 0.5M Antimycin A; for the glycolytic rate assay, 0.25g/ml Rotenone plus 0.5M Antimycin A and 17.5mM 2-DG; and for the Mito stress test, 2.0M Oligo, 2.0M FCCP (optimal concentration from FCCP titration), and 0.25g/ml Rotenone plus 0.5M Antimycin A. After loading all ports, the cartridge was placed into a non-CO2, 37C incubator while the experiment was setup in WAVE software (Agilent). The cartridge was then placed into the XFe96 analyzer (Agilent) and run for calibration. After the machine calibrations were successful, the hRGC seahorse plate was placed into the machine and the assay was run (ATP rate assay, glycolytic rate assay, or Mito stress test). Cell area from Incucyte images were measured using Image J and extrapolated for the total cell area in each well for normalization. The assay results were then exported into the appropriate excel macro using Seahorse Wave Desktop software (Agilent) for analysis.

hRGCs were seeded at 25,000 cells per well of a 96-well clear bottom black-walled plate and maintained for 3 days. The cells were then treated with indicated molecules for the designated time points. The caspase activity was measured using the ApoTox-Glo Triplex assay kit (Promega). 100l of Caspase-Glo 3/7 reagent was added to all wells and incubated for 30minutes at room temperature before measuring luminescence (Caspase). Measurements were normalized to DMSO control.

hRGCs were seeded at 250,000 cells per well on MG-coated 6-well plates and maintained for 3 days. The cells were then treated with 1 g/ml BX795 or equivalent DMSO for 24h. Media was aspirated, 500 l of fixative solution (3% Glutaraldehyde, 0.1M Cacodylate) was added, and the cells were incubated for 15min. Next, hRGCs were scraped and pelleted by centrifugation at 10,000xg for 20minutes. The pellets were fixed overnight at 4C, then rinsed the next day in 0.1M cacodylate buffer, followed by post fixation with 1% osmium tetroxide, 0.1M cacodylate buffer for 1h. After rinsing again with 0.1M cacodylate buffer, the cell pellets were dehydrated through a series of graded ethyl alcohols from 70 to 100%, and 2 changes of 100% acetone. The cell pellets were then infiltrated with a 50:50 mixture of acetone and embedding resin (Embed 812, Electron Microscopy Sciences, Hatfield, PA) for 72h. Specimen vial lids were then removed, and acetone allowed to evaporate off for 3h. Then the pellets were embedded in a fresh change of 100% embedding resin. Following polymerization overnight at 60C the blocks were then ready for sectioning. All procedures were done in centrifuge tubes including the final embedding. Sections with cut at 85nm, placed on copper grids, stained with saturated uranyl acetate, viewed, and imaged on a Tecnai Spirit (ThermoFisher, Hillsboro, OR) equipped with an AMT CCD camera (Advanced Microscopy Techniques, Danvers, MA). 49000X images were analyzed using Image J to measure mitochondrial parameters as explained in Fig.5.

Samples were treated with CCCP or BX795 at different time points as independent biological samples. Statistical tests between two independent datasets were done by Students t-test, each data point within a dataset is from an independent culture wellor cell (Figs.1cf, h, 1m; j, l, 2c, f, 3ad, fi, 4bd, fi, 5b, 6b, e, hl, Supplementary Figs.3b, 4bc). We used t-test rather than ANOVA because we did not want to assume that each group has the same variance. For non-normal data distribution, we performed MannWhitney U test to compare between two independent data sets (Fig.5ce, Supplementary Fig.5b). Graphs were made using GraphPad Prism 9.0 softwareand figures were made using Adobe Illustrator.

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