Dataset Information

KM-12 Whole Cell Lysate Proteomics

ABSTRACT: The KM-12 cell line, representative of colorectal cancer indications, was used to explore the effect that multiple compounds would have in the profile of transcription factor occupancy. Cells were dosed with 3 concentrations of each of the 5 compounds provided for 3 different timepoints. Both a chromatin fraction (ChESS) and a whole cell lysate preparation were performed. Resulting proteins were digested via SP3 digestion and resulting peptides were analyzed by data independent acquisition liquid chromatography mass spectrometry. (DIA-LCMS) in order to determine the effects of each of the provided compounds in both chromatin and whole cell lysate matrices on a variety of transcription factor proteins. The following dataset includes data corresponding to peptides resulting from nuclear isolation after a 6 hour treatment with 100 nanomolar concentration CG-428 (positive control, published TRK PROTAC), JWJ-378 (novel PROTAC developed by Nabet lab), and DMSO (negative control).

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Sebastian Paez

LAB HEAD: Alexander Federation

PROVIDER: PXD065035 | Pride | 2026-04-06

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	241220_CG428_0-1uM_2hr_Lysate_REP1.d.tar	Other
	241220_CG428_0-1uM_2hr_Lysate_REP2.d.tar	Other
	241220_CG428_0-1uM_2hr_Lysate_REP3.d.tar	Other
	241220_CG428_0-1uM_6hr_Lysate_REP1.d.tar	Other
	241220_CG428_0-1uM_6hr_Lysate_REP2.d.tar	Other

Items per page:

1 - 5 of 23

Publications

Development of PROTACs for targeted degradation of oncogenic TRK fusions.

Kumar Saurav S Jiang Jiewei J Donald-Paladino Mia S MS Chen Joy J Gutierrez Andrea A Federation Alexander J AJ Szulzewsky Frank F Holland Eric C EC Ferguson Fleur M FM Nabet Behnam B

RSC chemical biology 20260318 4

Chromosomal translocations leading to the fusion of tropomyosin receptor kinases (TRKs) with diverse partner proteins have been identified as oncogenic drivers in many adult and pediatric cancers. While first-generation TRK kinase inhibitors, such as entrectinib and larotrectinib, have shown positive responses in TRK fusion-positive cancers, resistance mutations against these inhibitors in the kinase domain limit their efficacy. Second-generation inhibitors are in clinical evaluation, highlighti ...[more]

PMID: 41908584

Similar Datasets

Project description:Although drug induced steatosis represents a mild type of hepatotoxicity, it can progress into more severe non-alcoholic steatohepatitis. Current models used for safety assessment in drug development and chemical risk assessment do not accurately predict steatosis in humans. Therefore, new models need to be developed to screen compounds for steatogenic properties. We have studied the usefulness of mouse precision-cut liver slices (PCLS) as an alternative to animal testing to gain more insight into the mechanisms involved in the steatogenesis. To this end, PCLS were incubated 24h with the model steatogenic compounds, amiodarone (AMI), valproic acid (VA), and tetracycline (TET). Transcriptome analysis using DNA microarrays was used to identify genes and processes affected by these compounds. AMI and VA upregulated lipid metabolism, whereas processes associated with extracellular matrix remodelling and inflammation were downregulated. TET downregulated mitochondrial functions, lipid metabolism, and fibrosis. From the transcriptomics data it was hypothesized that all 3 compounds affect peroxisome proliferator activated-receptor (PPAR) signalling. Application of PPAR reporter assays classified AMI and VA as PPARγ and triple PPARα/ (β/δ)/γ agonist, respectively, whereas TET had no effect on any of the PPARs. Some of the differentially expressed genes were considered as potential candidate biomarkers to identify PPAR agonists (i.e. AMI and VA) or compounds impairing mitochondrial functions (i.e. TET). Finally, comparison of our findings with publicly available transcriptomics data showed that a number of processes altered in the mouse PCLS was also affected in mouse livers and human primary hepatocytes exposed to known PPAR agonists. Thus mouse PCLS are a valuable model to identify mechanisms of action of compounds altering lipid metabolism. Two sets of candidate biomarkers could be used to screen compounds interfering with lipid metabolism by different mechanisms. Steatogenic compounds exposures Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic, cholestatic, and necrotic compounds selected based on published reports. As steatogenic model compounds amiodarone (AMI), valproic acid (VA), and tetracycline (TET) were selected. As model cholestatic compounds cyclosporin A (CsA), chlorpromazine (CPZ), and ethinyl estradiol (EE) were applied. As necrotic compounds acetaminophen (APAP), isoniazid (ISND), and paraquat (PQ) were applied. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: AMI 0-100 μM, VA 0-500 μM, TET 0-100 μM , CsA 0-100 μM, CPZ 0-80 μM, EE 0-100 μM, PQ 0-10 μM, APAP 0-3000 μM and ISND 0-1000 μM. CsA, CPZ, AMI, PQ, EE were dissolved in DMSO, VA and TET were dissolved in ethanol (EtOH), and ISND was dissolved in PBS. The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in an appropriate solvent (DMSO, EtOH, or PBS). Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein. Dose selection for the three steatogenic, cholestatic, and necrotic exposures were performed in 5 independent experiments with slices obtained from 5 mice. Concentrations that did not cause a decrease of the ATP level normalized on protein, compared to controls, were selected. For transcriptome analysis, PCLS were cultured at the same conditions as described above. The selected concentrations for steatogenic, cholestatic, and necrotic drugs were tested again in liver slices obtained from 5 different mice to re-confirm that the selected concentrations for the exposure experiments were not toxic. The concentrations used in the exposure experiments were for the steatogenic compounds: 50 μM for AMI, 200 μM for VA, and 40 μM for TET. For the cholestatic exposures 40 μM CsA, 20 μM CPZ, and 10 μM EE. For the necrotic compounds: 1000 μM APAP, 1000 μM ISND, and 5 μM PQ. Thereafter, RNA was extracted from three slices per each condition and after processing, the samples were hybridized on the HT Mouse Genome 430 PM array plate(s) using the Affymetrix GeneTitan system (CA, USA).

Project description:Although drug induced steatosis represents a mild type of hepatotoxicity, it can progress into more severe non-alcoholic steatohepatitis. Current models used for safety assessment in drug development and chemical risk assessment do not accurately predict steatosis in humans. Therefore, new models need to be developed to screen compounds for steatogenic properties. We have studied the usefulness of mouse precision-cut liver slices (PCLS) as an alternative to animal testing to gain more insight into the mechanisms involved in the steatogenesis. To this end, PCLS were incubated 24h with the model steatogenic compounds, amiodarone (AMI), valproic acid (VA), and tetracycline (TET). Transcriptome analysis using DNA microarrays was used to identify genes and processes affected by these compounds. AMI and VA upregulated lipid metabolism, whereas processes associated with extracellular matrix remodelling and inflammation were downregulated. TET downregulated mitochondrial functions, lipid metabolism, and fibrosis. From the transcriptomics data it was hypothesized that all 3 compounds affect peroxisome proliferator activated-receptor (PPAR) signalling. Application of PPAR reporter assays classified AMI and VA as PPARγ and triple PPARα/ (β/δ)/γ agonist, respectively, whereas TET had no effect on any of the PPARs. Some of the differentially expressed genes were considered as potential candidate biomarkers to identify PPAR agonists (i.e. AMI and VA) or compounds impairing mitochondrial functions (i.e. TET). Finally, comparison of our findings with publicly available transcriptomics data showed that a number of processes altered in the mouse PCLS was also affected in mouse livers and human primary hepatocytes exposed to known PPAR agonists. Thus mouse PCLS are a valuable model to identify mechanisms of action of compounds altering lipid metabolism. Two sets of candidate biomarkers could be used to screen compounds interfering with lipid metabolism by different mechanisms. Cholestatic compounds exposures Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic, cholestatic, and necrotic compounds selected based on published reports. As steatogenic model compounds amiodarone (AMI), valproic acid (VA), and tetracycline (TET) were selected. As model cholestatic compounds cyclosporin A (CsA), chlorpromazine (CPZ), and ethinyl estradiol (EE) were applied. As necrotic compounds acetaminophen (APAP), isoniazid (ISND), and paraquat (PQ) were applied. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: AMI 0-100 μM, VA 0-500 μM, TET 0-100 μM , CsA 0-100 μM, CPZ 0-80 μM, EE 0-100 μM, PQ 0-10 μM, APAP 0-3000 μM and ISND 0-1000 μM. CsA, CPZ, AMI, PQ, EE were dissolved in DMSO, VA and TET were dissolved in ethanol (EtOH), and ISND was dissolved in PBS. The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in an appropriate solvent (DMSO, EtOH, or PBS). Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein. Dose selection for the three steatogenic, cholestatic, and necrotic exposures were performed in 5 independent experiments with slices obtained from 5 mice. Concentrations that did not cause a decrease of the ATP level normalized on protein, compared to controls, were selected. For transcriptome analysis, PCLS were cultured at the same conditions as described above. The selected concentrations for steatogenic, cholestatic, and necrotic drugs were tested again in liver slices obtained from 5 different mice to re-confirm that the selected concentrations for the exposure experiments were not toxic. The concentrations used in the exposure experiments were for the steatogenic compounds: 50 μM for AMI, 200 μM for VA, and 40 μM for TET. For the cholestatic exposures 40 μM CsA, 20 μM CPZ, and 10 μM EE. For the necrotic compounds: 1000 μM APAP, 1000 μM ISND, and 5 μM PQ. Thereafter, RNA was extracted from three slices per each condition and after processing, the samples were hybridized on the HT Mouse Genome 430 PM array plate(s) using the Affymetrix GeneTitan system (CA, USA).

Project description:Although drug induced steatosis represents a mild type of hepatotoxicity, it can progress into more severe non-alcoholic steatohepatitis. Current models used for safety assessment in drug development and chemical risk assessment do not accurately predict steatosis in humans. Therefore, new models need to be developed to screen compounds for steatogenic properties. We have studied the usefulness of mouse precision-cut liver slices (PCLS) as an alternative to animal testing to gain more insight into the mechanisms involved in the steatogenesis. To this end, PCLS were incubated 24h with the model steatogenic compounds, amiodarone (AMI), valproic acid (VA), and tetracycline (TET). Transcriptome analysis using DNA microarrays was used to identify genes and processes affected by these compounds. AMI and VA upregulated lipid metabolism, whereas processes associated with extracellular matrix remodelling and inflammation were downregulated. TET downregulated mitochondrial functions, lipid metabolism, and fibrosis. From the transcriptomics data it was hypothesized that all 3 compounds affect peroxisome proliferator activated-receptor (PPAR) signalling. Application of PPAR reporter assays classified AMI and VA as PPARγ and triple PPARα/ (β/δ)/γ agonist, respectively, whereas TET had no effect on any of the PPARs. Some of the differentially expressed genes were considered as potential candidate biomarkers to identify PPAR agonists (i.e. AMI and VA) or compounds impairing mitochondrial functions (i.e. TET). Finally, comparison of our findings with publicly available transcriptomics data showed that a number of processes altered in the mouse PCLS was also affected in mouse livers and human primary hepatocytes exposed to known PPAR agonists. Thus mouse PCLS are a valuable model to identify mechanisms of action of compounds altering lipid metabolism. Two sets of candidate biomarkers could be used to screen compounds interfering with lipid metabolism by different mechanisms. Necrotic compounds exposures Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic, cholestatic, and necrotic compounds selected based on published reports. As steatogenic model compounds amiodarone (AMI), valproic acid (VA), and tetracycline (TET) were selected. As model cholestatic compounds cyclosporin A (CsA), chlorpromazine (CPZ), and ethinyl estradiol (EE) were applied. As necrotic compounds acetaminophen (APAP), isoniazid (ISND), and paraquat (PQ) were applied. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: AMI 0-100 μM, VA 0-500 μM, TET 0-100 μM , CsA 0-100 μM, CPZ 0-80 μM, EE 0-100 μM, PQ 0-10 μM, APAP 0-3000 μM and ISND 0-1000 μM. CsA, CPZ, AMI, PQ, EE were dissolved in DMSO, VA and TET were dissolved in ethanol (EtOH), and ISND was dissolved in PBS. The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in an appropriate solvent (DMSO, EtOH, or PBS). Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein. Dose selection for the three steatogenic, cholestatic, and necrotic exposures were performed in 5 independent experiments with slices obtained from 5 mice. Concentrations that did not cause a decrease of the ATP level normalized on protein, compared to controls, were selected. For transcriptome analysis, PCLS were cultured at the same conditions as described above. The selected concentrations for steatogenic, cholestatic, and necrotic drugs were tested again in liver slices obtained from 5 different mice to re-confirm that the selected concentrations for the exposure experiments were not toxic. The concentrations used in the exposure experiments were for the steatogenic compounds: 50 μM for AMI, 200 μM for VA, and 40 μM for TET. For the cholestatic exposures 40 μM CsA, 20 μM CPZ, and 10 μM EE. For the necrotic compounds: 1000 μM APAP, 1000 μM ISND, and 5 μM PQ. Thereafter, RNA was extracted from three slices per each condition and after processing, the samples were hybridized on the HT Mouse Genome 430 PM array plate(s) using the Affymetrix GeneTitan system (CA, USA).