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Trans isrib

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Trans-ISRIB is a small molecule compound that functions as a selective and reversible inhibitor of the integrated stress response (ISR) pathway. It acts by binding to and modulating the activity of the eIF2B complex, a key regulator of protein synthesis initiation.

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Lab products found in correlation

Rnaimax, by Thermo Fisher Scientific (2 mentions) Lipofectamine 3000, by Thermo Fisher Scientific (2 mentions) Revertaid first strand cdna synthesis kit, by Thermo Fisher Scientific (2 mentions) Phenformin, by Merck Group (1 mentions) Aminooxyacetic acid, by Merck Group (1 mentions) Oligomycin, by Merck Group (1 mentions) Gcn2ib, by MedChemExpress (1 mentions) Iacs 10759, by Selleck Chemicals (1 mentions) Mycoalert plus, by Lonza (1 mentions) High glucose dmem, by Thermo Fisher Scientific (1 mentions) Dimethyl sulfoxide (dmso), by Merck Group (1 mentions) Fetal bovine serum (fbs), by Corning (1 mentions) Toyocamycin, by Cayman Chemical (1 mentions) Mss205172, by Thermo Fisher Scientific (1 mentions) Mss205173, by Thermo Fisher Scientific (1 mentions) Stealth rnai, by Thermo Fisher Scientific (1 mentions) 1 glutamine, by Merck Group (1 mentions) Penicillin, by Corning (1 mentions) Streptomycin, by Corning (1 mentions) Sodium pyruvate, by Corning (1 mentions)

7 protocols using trans isrib

1

Characterization of Murine Pancreatic Tumor Clones

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The clonal cell lines described (E, H, V, K, M, N and T) were isolated from pancreatic tumors from KPC mice and have been previously described30 . Clonal lines 6419c5, 6694c2, 2838c3 and 6499c4 were derived from KPC mice and have also been previously described24 (link). KPC7940B cells were a gift from G. Beatty (University of Pennsylvania). KPC-MT3 cells were a gift from D. Tuveson (Cold Spring Harbor Laboratory). PATC53 cells were obtained from ATCC. Cells were maintained in high-glucose DMEM (Gibco) supplemented with 10% fetal bovine serum (Corning) and routinely tested for mycoplasma contamination using MycoAlert Plus (Lonza). DMSO, oligomycin, phenformin and aminooxyacetic acid were obtained from Sigma, trans-ISRIB was obtained from Cayman Chemical and GCN2iB was obtained from MedChemExpress. IACS-10759 was obtained from Selleck Chem. KPC clonal lines were genotyped for KrasG12D recombination using primer sets from Jackson Laboratories.
Halbrook C.J., Thurston G., Boyer S., Anaraki C., Jiménez J.A., McCarthy A., Steele N.G., Kerk S.A., Hong H.S., Lin L., Law F.V., Felton C., Scipioni L., Sajjakulnukit P., Andren A., Beutel A.K., Singh R., Nelson B.S., Van Den Bergh F., Krall A.S., Mullen P.J., Zhang L., Batra S., Morton J.P., Stanger B.Z., Christofk H.R., Digman M.A., Beard D.A., Viale A., Zhang J., Crawford H.C., Pasca di Magliano M., Jorgensen C, & Lyssiotis C.A. (2022). Differential integrated stress response and asparagine production drive symbiosis and therapy resistance of pancreatic adenocarcinoma cells. Nature Cancer, 3(11), 1386-1403.
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2

Atherosclerosis in Apoe and Parkin Mice

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C57BL/6.129P2-Apoetm1Unc/J mice (Apoe−/− mice; received from Jackson Laboratory, Bar Harbor, Maine, and created by Nabuyo Maeda, University of North Carolina), and C57BL/6.129S4-Prkntm1Shn/J (parkin−/− mice; received from Jackson Laboratory and created by Jie Shen, Harvard Medical School) and C57BL/6-eIF2αk3tm2201(G646N,M886A)Arte mice (PERK_ASKA [ATP-analog sensitive kinase allele] mice; received from J.R. Lipford at Amgen, Thousand Oaks, California, and created by Taconic Artemis, Cologne, Germany); G646N/M886A mutations were introduced by Cre-Lox system and bred with Apoe−/−. Apoe−/− mice were injected with GSK2606414 (30 mg/kg/day; Atomole Scientific, Wuhan, China) or trans-ISRIB (1 to 2 mg/kg/day; Cayman Chemical, Ann Arbor, Michigan). PERK_ASKA mice were injected with 4-amino-1-tert-butyl-3-(1-naphthyl)pyrazolo[3,4-d]pyrimidine (1-NAPP1) (60 mg/kg/day; Taconic Artemis). Weight and blood glucose were measured weekly 7 (link), 15 . The experimental animal ethical care committees at Bilkent University and Cedars Sinai Medical Center approved all animal experiment protocols.
Onat U.I., Yildirim A.D., Tufanli Ö., Çimen I., Kocatürk B., Veli Z., Hamid S.M., Shimada K., Chen S., Sin J., Shah P.K., Gottlieb R.A., Arditi M, & Erbay E. (2019). Intercepting the Lipid-Induced Integrated Stress Response Reduces Atherosclerosis. Journal of the American College of Cardiology, 73(10), 1149-1169.
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3

Combination Treatments for Cell Viability

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Cytarabine (AraC) (77 (link)), trans-ISRIB (4 (link), 63 (link)), FX-1 (49 (link)), and toyocamycin (64 (link), 65 (link)) were obtained from Cayman Chemicals. FXR1 OE and control cells were treated with 1 μM trans-ISRIB for 24 hours. For cell viability that was measured by trypan blue staining and cell counts (1 (link)), FXR1 OE and control cells were treated individually or with a combination of 5 μM AraC and 1 μM trans-ISRIB for 24 hours, 100 nM toyocamycin and 1 μM AraC, and 10 μM FX-1 and 5 μM AraC.
Datta C., Truesdell S.S., Wu K.Q., Bukhari S.I., Ngue H., Buchanan B., Le Tonqueze O., Lee S., Kollu S., Granovetter M.A., Boukhali M., Kreuzer J., Batool M.S., Balaj L., Haas W, & Vasudevan S. (2022). Ribosome changes reprogram translation for chemosurvival in G0 leukemic cells. Science Advances, 8(43), eabo1304.
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4

Myogenic Differentiation of C2C12 and Primary Myoblasts

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A mouse myoblast cell line, C2C12, was cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum at 37 °C under 5% CO2. Mouse primary myoblasts were isolated from lower extremity muscles of 8-week-old C57BL6J mice as described previously [48 (link)]. Myogenic differentiation of C2C12 cells and primary myoblasts were induced by replacing the medium with the differentiation medium, DMEM supplemented with 2% or 5% horse serum, respectively. Cells were transfected with 50 nM of Stealth RNAi (Thermo Fisher Scientific, Waltham, MA, USA) using Lipofectamine 3000 (Thermo Fisher Scientific, Waltham, MA, USA) or RNAiMax (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol. The following siRNAs were used: Stealth RNAi siRNA negative control (negative control, Med GC, Thermo Fisher Scientific, Waltham, MA, USA), Stealth RNAi for Myoparr, and Stealth RNAi siRNAs specific for hnRNPK (MSS205172 and MSS205173, Thermo Fisher Scientific, Waltham, MA, USA). The siRNA sequences are listed in Table S1. At 24 h after siRNA transfection, myogenic differentiation was induced. At 24 h or 72 h after differentiation induction, cells were collected for the analysis of RNAs and proteins. For ISRIB treatment, the differentiation medium was added either with or without 1 µM trans-ISRIB (No.16258, Cayman Chemical Company, Ann Arbor, MI, USA).
Hitachi K., Kiyofuji Y., Nakatani M, & Tsuchida K. (2021). Myoparr-Associated and -Independent Multiple Roles of Heterogeneous Nuclear Ribonucleoprotein K during Skeletal Muscle Cell Differentiation. International Journal of Molecular Sciences, 23(1), 108.
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5

GCN2 KO T-cell Metabolism

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T-cells from WT and GCN2 KO mice were isolated as aforementioned and were treated in 5 different medias, complete RPMI [10% FBS (HyClone), 10 mM HEPES–sodium pyruvate (Sigma), 1 mM sodium pyruvate (Corning), 0.01% 2-ME, 2 mM 1-glutamine (Sigma), 100 U/ml penicillin, and 100 μg/ml streptomycin (Corning)], +TRP, −TRP, 200nM trans-ISRIB +TRP and 200 nM trans-ISRIB (Cayman Chemicals) −TRP, for 24, 48 and 72 hours. After each time point, cells were lifted and analyzed via flow cytometry.
Rashidi A., Miska J., Lee-Chang C., Kanojia D., Panek W.K., Lopez-Rosas A., Zhang P., Han Y., Xiao T., Pituch K.C., Kim J.W., Talebian M., Fares J, & Lesniak M.S. (2019). GCN2 is Essential for CD8+ T-cell Survival and Function in Murine Models of Malignant Glioma. Cancer immunology, immunotherapy : CII, 69(1), 81-94.
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6

Combination Chemotherapy and Translational Inhibitors

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Doxorubicin, Gemcitabine, Paclitaxel, Cytarabine (AraC) (Kojima et al., 2005 (link)), Trazodone, and Trans-ISRIB (Costa-Mattioli and Walter, 2020 ; Zyryanova et al., 2021 (link)), were obtained from Cayman Chemicals and used as described. Sal003 10uM was obtained from selleckchem. Cells were treated with 1 μM Trans-ISRIB or 5 μM Trazodone for 18–24 h. For cell viability that was measured by Trypan blue staining and cell counts (Lee et al., 2020 (link)), cells were treated individually or with a combination of chemotherapies and 1 μM Trans-ISRIB or trazodone for 18–24 h.
Bukhari S.I., Truesdell S.S., Datta C., Choudhury P., Wu K.Q., Shrestha J., Maharjan R., Plotsker E., Elased R., Laisa S., Bhambhani V., Lin Y., Kreuzer J., Morris R., Koh S.B., Ellisen L.W., Haas W., Ly A, & Vasudevan S. (2023). Regulation of RNA methylation by therapy treatment, promotes tumor survival. bioRxiv.
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7

Regulation of Inflammation by ORMDL Proteins

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The following reagents were used. Dulbecco's modified Eagle's medium (Gibco), RPMI (Gibco), GSK 2656157, PERK inhibitor (Cayman chemical), trans-ISRIB (Cayman chemical), Lipofectamine 3000 Transfection kit (Invitrogen), Percoll (Sigma-Aldrich), Clarity Western ECL substrate (Bio-rad), Protease Inhibitor Cocktail kit(MP Biomedicals), Pierce Protein A/G PLUS-Agarose (Thermo Fisher Scientific), XF Base Medium (Agilent Seahorse), Human IL-1β/IL-1F2 Duoset ELISA (R &D), Human IL-10 Duoset ELISA (R&D), Human TNF-alpha Duoset ELISA (R&D), Mouse IL-1β & TNF-alpha Duoset ELISA (R&D), RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher scientific), Maxima SYBR Green/ROX qPCR Master mix (Thermo Fisher scientific), lipopolysaccharide (LPS, Sigma-Aldrich), MSU (InvivoGen), nigericin (Cayman Chemical), ATP (Cayman Chemical), Lipofectamine RNAiMAX reagent (Invitrogen), M-CSF Human (GenScript Biotech,), siRNA negative control (Dharmacon and Santa Cruz Biotechnology); siRNA ORMDL1, ORMDL2, ORMDL3 (Dharmacon and Santa Cruz Biotechnology).
Sharma J., Khan S., Singh N.C., Sahu S., Raj D., Prakash S., Bandyopadhyay P., Sarkar K., Bhosale V., Chandra T., Kumaravelu J., Barthwal M.K., Gupta S.K., Srivastava M., Guha R., Ammanathan V., Ghoshal U.C., Mitra K, & Lahiri A. (2024). ORMDL3 regulates NLRP3 inflammasome activation by maintaining ER-mitochondria contacts in human macrophages and dictates ulcerative colitis patient outcome. The Journal of Biological Chemistry, 300(4), 107120.
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