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5 protocols using ab203832

1

Native PAGE Analysis of Mitochondrial Complexes

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As previously described (Riessland et al., 2019 ), for the assessment of mitochondrial complexes, cell lysates were prepared using the NativePAGE Sample Prep Kit (Life Technologies) and solubilized with 1% digitonin. A BCA assay (Thermo Scientific) was used to determine the protein concentrations as described above. Equal amounts of protein were then loaded onto a NativePAGE Novex 4-16% Bis-Tris Protein Gel (Life Technologies). A wet blotting method was used to transfer the proteins onto a PVDF membrane (Life Technologies, 0.45 μm), the membrane was then incubated with 8% acetic acid for 15min and washed with methanol and water before being blocked with 5% BSA in 20 mM Tris, 150 mM NaCl, and 0.1% (w/v) Tween 20, pH 7.5, for 2 hours. The membrane was subsequently immunoblotted with the respective primary antibody at 4 °C overnight. The primary antibodies used were NDUFA9 (a CI Subunit) (1/2500 by vol; ab14713: Abcam), UQCRC2 (a CIII Subunit) (1/2500 by vol; ab203832: Abcam), or MT-CO2 (a CIV Subunit) (1/2500 by vol; ab110258: Abcam). Primary antibodies were detected using either HRP-linked donkey anti–rabbit IgG (GE Healthcare, #NA934V; 1:10,000) or HRP-linked sheep anti–mouse IgG (GE Healthcare, #NA931V, 1:10,000) together with Western Lightning Plus-ECL (Perkin Elmer, #NEL105001EA).
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2

Mitochondrial Complex Assessment by Western Blot

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As previously described (Riessland et al., 2019 (link)), for the assessment of mitochondrial complexes, cell lysates were prepared using the NativePAGE Sample Prep Kit (Life Technologies) and solubilized with 1% digitonin. A BCA assay (Thermo Scientific) was used to determine the protein concentrations as described above. Equal amounts of protein were then loaded onto a NativePAGE Novex 4%–16% Bis‐Tris Protein Gel (Life Technologies). A wet blotting method was used to transfer the proteins onto a PVDF membrane (Life Technologies, 0.45 μm), the membrane was then incubated with 8% acetic acid for 15 min and washed with methanol and water before being blocked with 5% BSA in 20 mM Tris, 150 mM NaCl, and 0.1% (w/v) Tween 20, pH 7.5, for 2 h. The membrane was subsequently immunoblotted with the respective primary antibody at 4°C overnight. The primary antibodies used were NDUFA9 (a CI Subunit) (1/2500 by vol; ab14713: Abcam), UQCRC2 (a CIII Subunit) (1/2500 by vol; ab203832: Abcam), or MT‐CO2 (a CIV Subunit) (1/2500 by vol; ab110258: Abcam). Primary antibodies were detected using either HRP‐linked donkey anti–rabbit IgG (GE Healthcare, #NA934V; 1:10,000) or HRP‐linked sheep anti–mouse IgG (GE Healthcare, #NA931V, 1:10,000) together with Western Lightning Plus‐ECL (Perkin Elmer, #NEL105001EA).
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3

Mitochondrial Protein Expression Profiling

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Patient cell culture (FB862) and control cell culture (FB826), were grown to 90–95% confluence, and cells were harvested by trypsinization. Cell-free extract was made by using RIPA buffer and protease inhibitor cocktail (Sigma, Santa Fe, NM). Protein estimation of cell-free extract was done using DC Protein Assay kit (Bio-Rad Laboratories, Hercules, CA). Total of 10–40 μg of protein was loaded on the gel for Western blotting. Membranes were probed with antibodies to ETFDH (SC515202, Santa Cruz Biotechnologies Inc., Dallas, TX); VLCAD (SC271225); core protein 2 of Complex III (ab203832, Abcam, Cambridge, UK); TFPα and TFPβ (custom-made, Cocalico Biologicals Inc., Reamstown, PA); and GAPDH (ab8245). Protein levels were quantified by densitometric analysis of scanned blots with GAPDH as a control using NIH ImageJ software.
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4

Blue Native PAGE Analysis of Mitochondrial Proteins

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Blue Native gel electrophoresis (PAGE) was performed by isolating mitochondrial proteins from mutant and control cybrid cell lines as described elsewhere [21 (link)]. Samples containing 30 μg of proteins were separated on 3~12% Native PAGE gel. The primary antibodies applied for this experiment were NDUFA9 (Abcam, ab128744), SDHA (Abcam, ab14715), UQCRC2 (Abcam, ab203832), COX5A (Abcam, ab110262), and ATP5C (Abcam, ab119686). As a secondary detection antibody, an ECL system was used for band detection, after which densitometric calculations were performed as shown in Western blotting.
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5

Quantifying HIF1α, IL-8, and AMPK Signaling

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Total RNA from cells and tissues was extracted with TRIzol (10296010, Thermo Fisher Scientific), and reverse transcription was performed with a reverse transcription kit (R323-01, Vazyme). qPCR was performed with SYBR (TSE202, Vazyme) in an Applied Biosystems QuantStudio 5 Real-Time PCR system. Finally, the relative expression was calculated using GAPDH as a standard. The primers for qPCR are listed in Supplemental Table 1. Western blot analysis was conducted as reported previously. Briefly, cells and tissue samples were lysed in cell lysis buffer and tissue protein extraction reagent (78510, Thermo Fisher Scientific), respectively. A total of 40 μg protein was processed for subsequent analysis. Antibodies against HIF1α (36169T, Cell Signaling Technology), IL-8 (ab106350, Abcam), p-AMPK (2535T, Cell Signaling Technology), AMPK (ab32047, Abcam), FOXO3A (ab53287, Abcam), UQCRC2 (ab203832, Abcam), and tubulin (AF0001, Beyotime) were used.
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