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1

Antibody Profiling for Apoptosis Signaling

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Antibodies used for immunoblotting analyses in this study are listed below: rabbit anti-MCL-1 (1:500, ab32087), rabbit anti-BAX (1:1000, ab32503) were obtained from Abcam; mouse anti-BCL-2 (1:1000, #15071), rabbit anti-BIM (1:1000, #2933), rabbit anti-BCL-XL (1:1000, #2762), rabbit anti-BAK (1:1000, #12105), rabbit anti-AKT (1:1000, #4691), rabbit anti-p-AKT (1:1000, #4060), rabbit anti-mTOR (1:1000, #2983), rabbit anti-p-mTOR (1:1000, #5536), rabbit anti-p-4EBP1 (1:1000, #2855), rabbit anti-4EBP1 (1:1500, #9644), rabbit anti-FOXO3a (1:1000, #12829), rabbit anti-p-FOXO3a (1:1000, #9466) rabbit anti-cleaved PARP (1:1000, #5625) and rabbit anti-cleaved Caspase-3 (1:1000, #9664) were purchased from Cell Signaling Technology; mouse anti-β-actin (1:1000, sc-47778), mouse anti-GAPDH (1:1000, sc-32233) and rabbit anti-PUMA (1:1000, sc-28226) were from Santa Cruz Biotechnology; rabbit anti-p-4EBP1 (1:500, NB100-81769, used in Fig. 1b) and mouse anti-4EBP1 (1:1000, NBP1-47366, used in Fig. 1b) were obtained from Novus Biologicals. The compounds of BH3 mimetics (ABT263 and ABT199) and mTOR inhibitors (BEZ235, AZD8055, and Temsirolimus) were from AbMole Bioscience.
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2

Western Blot Analysis of Apoptosis Markers

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T cells with a >95% purity were purified using an EasySep mouse T cell enrichment kit (StemCell Technologies). T cell lysates were prepared in sample buffer (50 mM Tris-Cl [pH 6.8], 50mM 2-ME, 2% SDS, 0.2% bromophenol blue, and 10% glycerol). Antibodies used for Western blots were rabbit anti-LC3 (polyclonoal P014, MBL International), hamster anti-Bcl-2 (polyclonal, BD pharmingen), rabbit anti-Bcl-xL (polyclonal), rabbit anti-Mcl-1 (polyclonal, Rockland Immunochemicals), rabbit anti-Bim (polyclonal, Cell Signaling), rabbit anti-Bax (polyclonal, Cell Signaling), rabbit anti-Bak (polyclonal, Cell Signaling), rabbit anti-Bid (polyclonal, Abcam), rabbit anti-PARP-1 (polyclonal, Cell Signaling), rabbit anti-COX IV (polyclonal, Cell Signaling), mouse anti-cytochrome c (7H8.2C12, BioLegend), mouse anti-α-Tubulin (B-5-1-2, Sigma) and goat anti-β-Actin (polyclonal, Santa Cruz Biotechnology). For HRP-labeled western blot, the secondary antibodies were anti-rabbit IgG-HRP, anti-mouse IgG-HRP, anti-hamster IgG-HRP and anti-goat IgG-HRP (Jackson Immunoresearch). The development of the western blot was achieved with SuperSignal West Pico Chemiluminescent substrate (Thermo Scientific). For fluorescent western blot, the secondary antibodies were anti-rabbit IgG-Alexa Fluor 680, anti-mouse IgG-Alexa Fluor 680, and anti-goat IgG-Alexa Fluor 790 (Molecular Probes, Invitrogen).
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3

Mitochondrial Dysfunction and Apoptosis in Retina

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The retinas were collected at 1, 3, 5, and 7 days after the intravitreal injection of mtDNA or control solution. The retinas processed with the Mitochondria Isolation Kit for Tissue as previously described [4 (link)] and the proteins collected from the supernatant and sediment were used for the detection of cytochrome c. Western blotting was performed according to methods described in previous study [4 (link)]. The following primary antibodies were used: rabbit anti-BAX (#2772, Cell Signaling Technology), rabbit anti-BAK (#12105, Cell Signaling Technology), rabbit anti-caspase 9 (AF6348, Affinity Biosciences Ltd), rabbit anti-cleaved caspase 9 (AF5240, affbiotech), rabbit anti-caspase 3 (ab44976, Abcam), rabbit anti-cleaved caspase 3 (ab49822, Abcam), anti-β-actin (ab8227, Abcam), anti-cGAS (ab179785, Abcam), rabbit anti-STING (D1V5L) (#50,494, Cell Signaling Technology), rabbit anti-TBK1/NAK (D1B4) (#3504, Cell Signaling Technology), rabbit anti-phospho-TBK1/NAK (Ser172) (D52C2) XP® (#5483, Cell Signaling Technology), rabbit anti-IRF3 (D83B9) (#4302, Cell Signaling Technology), rabbit anti-phospho-IRF3 (Ser396) (D6O1M) (#29047, Cell Signaling Technology), anti-interferon β (ab140211, Abcam), rabbit anti-cytochrome c (10993-1-AP, Proteintech), and rabbit anti-VDAC1 (ab154856; Abcam). Three eyes from each group were tested.
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4

Evaluating Apoptosis Markers in Leukemic Cells

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HL60 and HL-60R cells were seeded at a density of 1.5 × 105 cells/well in six-well plates for 36 h. Next, the cells were treated with or without 10 μM MK-4, MKH-DMG, or MKH-SUC for 24, 48, or 72 h. The cells were washed with PBS after removing the drug-containing medium and lysed with RIPA buffer (0.5% NP-40, 0.25% sodium deoxycholate, 0.05% SDS, 150 mM NaCl, and 50 mM HEPES, pH 7.4) containing a protease inhibitor cocktail (Nacalai Tesque, Kyoto, Japan). Each cell lysate was combined with sample loading buffer (Nacalai Tesque), separated on 15% SDS-PAGE gels (SuperSep Ace, FUJIFILM Wako), and transferred onto PVDF membranes (BIO-RAD, Hercules, CA, USA). After blocking, the membranes were incubated with the following primary antibodies: anti-pro/p17-caspase-3, anti-cleaved PARP1 (1:2000) (ab136812; Abcam, Cambridge, UK), rabbit anti-Bak (1:2000) (#12105; Cell Signaling Technology, Danvers, MA, USA), and mouse anti-GAPDH antibody (1:2000) (G8795; Sigma-Aldrich, St. Louis, MO, USA). After washing, the membranes were treated with appropriate secondary antibodies and visualized using Immunostar LD or Immunostar Zeta (FUJIFILM Wako).
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5

Mitochondrial Dysfunction in Retinal Injury

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The retinas were collected at 1, 3, 5, and 7 days after the intravitreal injection of mtDNA or control solution. The retinas processed with the Mitochondria Isolation Kit for Tissue (C3606, Beyotime, Shanghai, China), as previously described [14] and the proteins collected from the supernatant and sediment were used for the detection of cytochrome c. Western blotting was performed according to methods described in previous study [14] . The following primary antibodies were used: rabbit anti-BAX (#2772, Cell Signaling Technology), rabbit anti-BAK (#12105, Cell Signaling Technology), rabbit anticaspase 9 (AF6348, A nity Biosciences Ltd), rabbit anti-cleaved caspase 9 (AF5240, affbiotech), rabbit anti-caspase 3 (ab44976, Abcam), rabbit anti-cleaved caspase 3 (ab49822, Abcam), anti-β-actin (ab8227, Abcam), anti-cGAS (ab179785, Abcam), rabbit anti-STING (D1V5L) (#50494, Cell Signaling Technology), rabbit anti-TBK1/NAK (D1B4) (#3504, Cell Signaling Technology), rabbit anti-phospho-TBK1/NAK (Ser172) (D52C2) XP® (#5483, Cell Signaling Technology), rabbit anti-IRF3 (D83B9) (#4302, Cell Signaling Technology), rabbit anti-phospho-IRF3 (Ser396) (D6O1M) (#29047, Cell Signaling Technology), anti-interferon β (ab140211, Abcam), rabbit anti-cytochrome c (10993-1-AP, Proteintech), rabbit anti-VDAC1 (ab154856; Abcam). Three eyes from each group were tested.
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