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7 protocols using pf 670462

1

Circadian Rhythm Monitoring in Zebrafish

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Progeny of a homozygous Tg(per3:luc)g1, Tg(elavl3:EGFP)knu3 incross (Kaneko and Cahill, 2005 (link)) were injected at the single-cell stage with RNPs targeting csnk1db. At 4 dpf, using a P1000 pipet set at 150 μL with a tip whose end was cut-off, individual larvae were transferred to a white 96-round well plate (Greiner Bio-One). No animals were added in the last two columns of wells to serve as blanks. 50 mM (100×) Beetle luciferin (Promega) in water was mixed with 0.1% DMSO in water or 0.1 mM PF-670462 (Sigma-Aldrich) in DMSO to obtain a 4× luciferin/4 μM PF-670462 or 4× luciferin/0.004% DMSO solution. 50 μL of this solution was added on top of each well. Blank wells were topped with the luciferin/DMSO solution. Final concentrations in the wells were: luciferin 0.5 mM; DMSO 0.001%; PF-670462 1 µM. The plate was sealed and transferred to a Packard NXT Topcount plate reader (Perkin Elmer). Recording was performed in constant dark during 123 hr, starting around 12 noon the first day, or CT3, i.e. 3 hr after the last Zeitgeber. Temperature in the room was 25–28°C.
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2

Screening Drug Concentrations for Cell Viability

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For each drug, cell viability and morphology were initially screened over a period of 2 to 4 days using a range of concentrations. Concentrations of the drug that did not result in hemolysis or altered viability or morphology under our experimental conditions (following Henslee et al., 2017 (link)) were chosen for subsequent time-course experiments. The drugs used in this study—staurosporine, PF-670462, D4476 (all Sigma-Aldrich), and TTP22 (Tocris Biosciences; Bristol, UK)—were prepared in DMSO according to the manufacturer’s instructions. Drugs were diluted in KHB and delivered as a 10X concentration bolus to RBC suspensions to achieve the final concentration. In each case, an equivalent % of DMSO was used as a vehicle control. Drugs were added to RBC suspensions at ZT0 on day 1 (staurosporine) or circadian time (CT)-0 on day 3 (PF-670462, D4476, TTP22), as indicated in the figure legend. For human U2OS cells, PF-670462 was diluted from a 10 mM DMSO stock directly into recording medium, and was delivered to cells through a media change at the beginning of the recording. This was compared with vehicle control (between 0.03% to 0.1% DMSO).
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3

Pharmacological Compound Preparation Protocol

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SP600125 (Sigma-Aldrich), KL001 (Tocris), PF-670462 (Sigma-Aldrich), Chir99021
(Tocris), and etoposide (Santa Cruz Biotech), were prepared in 100% dimethyl
sulfoxide (DMSO; Sigma-Aldrich) at a concentration of 50 mM and stored at −20 °C
in single-use aliquots. When dosing cells, each was diluted in culture media (or
recording media for bioluminescence recording) to a final DMSO concentration of
0.2%. The solution was mixed well and added to the seeded cells.
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4

Antibody Procurement and Reagent Sources

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The antibodies used in this study are listed in Appendix Table S2. PF‐670462 was purchased from Sigma‐Aldrich. All other chemicals were purchased from Nacalai Tesque.
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5

Synthesis and Cellular Evaluation of Novel Compounds

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Compounds 14 and NECA were designed and synthesized at the School of Pharmacy of Camerino University (Italy) and dissolved as reported before [28 (link)]. Briefly, the 10 mM stock solutions were prepared in dimethylsulfoxide (DMSO) and then diluted with water to reach the desired concentration. In any case, the DMSO concentration in each well was equal to or lower than 0.5% and did not affect cell viability. PF 670462 and TC199 medium (with Hank’s salts and L-glutamine, without NaHCO3) were purchased from Sigma-Aldrich (Milan, Italy). All material used for cell maintenance was bought from EuroClone S.p.A. (Milan, Italy), and CellTiter 96® Aqueous One Solution Cell Proliferation and CellTiter-Glo® Luminescent Cell Viability Assays were obtained from Promega (Milan, Italy).
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6

TDP-43 Stress Granule Formation Assay

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All chemicals were purchased from Fisher Scientific (Loughborough, Leicestershire, UK) unless otherwise stated. Pharmacological inhibitors were sourced as indicated: tunicamycin (Cat T7765), PF670462 (Cat SML0795) (Sigma-Aldrich, Gillingham, Dorset, UK), sodium arsenite (Cat #12897692), sorbitol (Cat #10396733) (Fisher Scientific), and D 4476 (Cat CAY13305) (Cambridge Bioscience, Cambridge, UK). Dimethyl sulphoxide was used as a vehicle in cell culture treatments.
Primary antibodies used were for the TDP-43 N-terminus (Proteintech Group, Manchester, UK; RRID:AB_615042, 1:500 (ICC) or 1:1000 (IB)), Phospho(409/410)-TDP-43 (Proteintech Group; RRID:AB_66318, 1:500), BiP/Grp78, (Proteintech; RRID: AB_2119855, 1:500), TIAR (BD Biosciences; RRID:AB_397742, 1:500), G3BP1 (Proteintech Group; RRID: AB_2232034, 1:500) and β-actin (Sigma-Aldrich; RRID:AB_476692, 1:1000).
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7

Small Molecule Treatments in DMSO

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Small molecules were dissolved in DMSO and treatments were carried out using the indicated concentrations with vehicle controls. The following substances were used: Pyrvinium pamoate (Sigma, Taufkirchen, Germany), IC261 (Sigma), D4476 (Sigma), PF670462 (Sigma). Doxycycline hyclate (Applichem, Darmstadt, Germany) was dissolved in ddH2O and used at the indicated concentrations.
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