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10 protocols using micro bca protein assay kit

1

Assessing Lysosomal Glycosidase Inhibition

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The effect of 1 mM concentration
of 14, 15, and 33·HCl was
assayed toward six lysosomal glycosidases other than GCase, namely,
α-mannosidase, β-mannosidase, α-galactosidase, β-galactosidase,
α-fucosidase from leukocytes isolated from healthy donors (controls)
and α-glucosidase from lymphocytes isolated from healthy donors’
flesh blood (controls). Isolated leukocytes or lymphocytes were disrupted
by sonication, and a micro BCA protein assay kit (Sigma-Aldrich) was
used to determine the total protein amount for the enzymatic assay,
according to the manufacturer’s instructions (for more details,
see the Supporting Information section).
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2

HDAC Activity Measurement in Human Enterocytes

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To assess HDAC activity, human enterocytes were treated with 10 nmol/L TSA (Sigma‐Aldrich) and with butyrate (Sigma‐Aldrich) at different doses (0.1; 0.5; 0.75; 1; and 2 mM) for 48 hours. The cell nuclear extracts (3 × 107 cells/well in 10 mL of culture medium) were prepared by using the Nuclei EZ Prep Kit (Sigma‐Aldrich) and quantified by using the Micro BCA Protein Assay Kit. HDAC activity was measured with the EpiQuik HDAC Activity/ Inhibition Assay Kit (EpiGentek), according to the manufacturer's instructions.
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3

Screening Compounds for GCase Inhibition

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The compounds 14, 15, and 33·HCl were screened toward GCase in leukocytes isolated
from healthy donors (controls). Isolated leukocytes were disrupted
by sonication, and a micro BCA protein assay kit (Sigma-Aldrich) was
used to determine the total protein amount for the enzymatic assay,
according to the manufacturer instructions. Enzyme activity was measured
in a flat-bottomed 96-well plate. Compound solution (3 μL),
4.29 μg/μL leukocytes homogenate (7 μL), and substrate
4-methylumbelliferyl-β-d-glucoside (3.33 mM, 20 μL,
Sigma-Aldrich) in citrate/phosphate buffer (0.1:0.2, M/M, pH 5.8)
containing sodium taurocholate (0.3%) and Triton X-100 (0.15%) at
37 °C were incubated for 1 h. The reaction was stopped by addition
of sodium carbonate (200 μL; 0.5 M, pH 10.7) containing Triton
X-100 (0.0025%), and the fluorescence of 4-methylumbelliferone released
by β-glucosidase activity was measured in SpectraMax M2 microplate
reader (λex = 365 nm, λem = 435
nm; Molecular Devices). Percentage GCase inhibition is given with
respect to the control (without compound). Data are mean SD (n = 3).
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4

Screening for Enzymatic Activity in Leukocytes

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All experiments on biological materials were performed in accordance with the ethical standards of the institutional research committee and with the 1964 Helsinki Declaration and its later amendments. In keeping with ethical guidelines, all blood and cell samples were obtained for storage and analyzed only after written informed consent of the patients (and/or their family members) was obtained, using a form approved by the local Ethics Committee (Project ID code: 16774_bio, 5 May 2020, Comitato Etico Regionale per la Sperimentazione Clinica della Regione Toscana, Area Vasta Centro, Florence, Italy). Controls and patients’ samples were anonymized and used only for research purposes.
The new compounds were screened at 1 mM concentration towards β-galactosidase (β-Gal) and β-glucosidase (GCase) in leukocytes isolated from healthy donors (controls). Isolated leukocytes were disrupted by sonication, and a Micro BCA Protein Assay Kit (Sigma–Aldrich, St. Louis, MO, USA) was used to determine the total protein amount for the enzymatic assay, according to the manufacturer’s instructions.
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5

Lysosomal Disorder Diagnostic Procedure

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All experiments on biological materials were performed in accordance with the ethical standards of the institutional research committee and with the 1964 Helsinki Declaration and its later amendments. In keeping with ethical guidelines, all blood and cell samples were obtained for storage and analysed only after written informed consent of the patients (and/or their family members) was obtained, using a form approved by the local Ethics Committee (Codice Protocollo: Lysolate “Late onset Lysosomal Storage Disorders (LSDs) in the differential diagnosis of neurodegenerative diseases: development of new diagnostic procedures and focus on potential pharmacological chaperones (PCs). Project ID code: 16774_bio, 5 May 2020, Comitato Etico Regionale per la Sperimentazione Clinica della Regione Toscana, Area Vasta Centro, Florence, Italy).
Controls and patients’ samples were anonymized and used only for research purposes.
The new compounds were screened at 1 mM concentration towards β-Galactosidase (β-Gal) and β-Glucosidase (GCase) in leukocytes isolated from healthy donors (controls).
Isolated leukocytes were disrupted by sonication, and a Micro BCA Protein Assay Kit (Sigma–Aldrich, St. Louis, MO, USA) was used to determine the total protein amount for the enzymatic assay, according to the manufacturer’s instructions.
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6

Screening of Compound CV82 for β-Galactosidase Inhibition

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The compound CV82 was screened at a 1 mM concentration towards β-Galactosidase (β-Gal) in leukocytes isolated from healthy donors (controls). Isolated leukocytes were disrupted by sonication, and a Micro BCA Protein Assay Kit (Sigma-Aldrich, St. Louis, MO, USA) was used to determine the total protein amount for the enzymatic assay, according to the manufacturer’s instructions. β-Gal activity was measured in a flat-bottomed 96-well plate. Compound-CV82 solution (3 μL), 4.29 μg/μL of leukocyte homogenate 1:10 (7 μL), and substrate 4-methylumbelliferyl β-d-Galactopyranoside (1.47 mM, 20 μL, Sigma-Aldrich) in acetate buffer (0.1 M, pH 4.3) containing NaCl (0.1 M) and sodium azide (0.02%) were incubated at 37 °C for 1 h. The reaction was stopped by the addition of sodium carbonate (200 μL; 0.5M, pH 10.7) containing Triton X-100 (0.0025%), and the fluorescence of 4-methylumbelliferone released by β-Gal activity was measured in a SpectraMax M2 microplate reader (λex = 365 nm, λem = 435 nm; Molecular Devices, San Jose, CA, USA). The percentage of β-Gal inhibition is given with respect to the control (Ctrl, without compound). Data are mean ± S.D. (n = 3).
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7

Western Blot Protein Quantification

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Proteins obtained using lysis buffer (200 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5% NP-40, 10% glycerol, 1 mM sodium fluoride, 1 mM sodium orthovanadate; Protease Inhibitor Cocktail (Sigma-Aldrich)) were quantified with Micro BCA™ Protein Assay Kit following the manufacturer's instructions (Sigma-Aldrich). Equal protein amounts were separated with SDS-polyacrylamide gel and transferred to a PVDF membrane (Life Technologies). After blocking, the membranes were incubated overnight at 4 • C with primary antibodies and after washes, with secondary antibodies (1 h at RT). The signal was visualized using chemiluminescence PDS kit (GeneSpin, Milan, IT) and CL-XPosure Film (Thermo Scientific). The densitometry was performed using ImageJ software.
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8

Western Blot Analysis of Protein Expression

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Cell lysate was prepared in RIPA lysis buffer. The protein concentration was determined with Micro BCA™ protein assay kit (Millipore, MA, USA). 35 μg protein was loaded into acrylamide gels and then transferred onto polyvinylidene fluoride membranes (Amersham Biosciences, Piscataway, NJ) after electrophoresis. The membranes were incubated with horseradish peroxidase-conjugated secondary antibody and probed with ECL western blotting detection system (Millipore, MA, USA) and visualized with the BioSpectrum AC imaging system.
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9

Protein Expression Analysis by Western Blotting

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Antibodies against CD133 (Abcam, Cambridge, UK), CD44 (Abcam), EpCAM (Santa Cruz Biotechnology, Santa Cruz, CA, USA), mTOR (Epitomics, Burlingame, CA, USA), CD24 (Epitomics), CD13 (Epitomics), PARP (Cell Signaling Technology, Beverly, MA, USA), phosphor-AMPK (Cell Signaling Technology), AMPK (Cell Signaling Technology) and β-actin (Chemicon, Inc., Pittsburgh, PA, USA) were used in western blotting. Cell extracts were harvested in RIPA lysis buffer and the protein concentration was determined with Micro BCA™ protein assay kit (Millipore, Billerica, MA, USA). Protein extracts (35 μg) were fractionated by SDS-PAGE and transferred to polyvinylidene fluoride membranes (Amersham Biosciences, Piscataway, NJ, USA) using a transfer apparatus according to the manufacturer's instruction (Hoefer Pharmacia Biotech, San Francisco, CA, USA). After incubation with 5% non-fat milk, the membranes were incubated with specific primary antibody and horseradish peroxidase-conjugated secondary antibody. The membranes were then probed with ECL western blotting detection system (Millipore) and visualized with the BioSpectrum AC imaging system.
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10

Western Blot Analysis of ACSL1 Protein

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Cell lysate was harvested in RIPA lysis buffer and the amount of protein was determined with Micro BCA Protein Assay kit (Millipore, MA, USA). 30μg protein lysate was loaded into acrylamide gels and then transferred onto polyvinylidene fluoride membranes (Amersham Biosciences, Piscataway, NJ). The membrane was blocked with 5% nonfat dry milk and incubated with primary antibody for specific protein overnight. The membranes were incubated with horseradish peroxidase-conjugated secondary antibody and probed with ECL western blotting detection system (Millipore, MA, USA) and visualized with the BioSpectrum AC imaging system. The catalog number of antibody was as the following: the anti-ACSL1 antibody (#4047, Cell Signaling) and the anti-β-actin antibody (GTX109639, GeneTex).
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