Ribosome subunit attrition and activation of the p53–MDM4 axis dominate the response of MLL-rearranged cancer cells to WDR5 WIN site inhibition
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, United States
- Department of Biostatistics, Vanderbilt University Medical Center, United States
- Center for Quantitative Sciences, Vanderbilt University Medical Center, United States
- Mass Spectrometry Research Center, Vanderbilt University School of Medicine, United States
- Department of Biochemistry, Vanderbilt University School of Medicine, United States
- Department of Medicine, Vanderbilt University Medical Center, United States
- Department of Pharmacology, Vanderbilt University School of Medicine, United States
- Department of Chemistry, Vanderbilt University, United States
Figures
Figure 1 with 2 supplements
Impact of WIN site inhibitors (WINi) on the transcriptome of MLLr cancer cells.
(A) Chemical structures of C6 and C16. (B) Crystal structures of C6 or C16 bound to the WIN site of WDR5 with electrostatic surfaces mapped (PDB IDs: 6E23 [Aho et al., 2019a]; 6UCS [Tian et al., 2020…
-
Figure 1—source data 1
Output of RNA-seq analysis of MV4;11 cells treated with C6/C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig1-data1-v1.xlsx
-
Figure 1—source data 2
GSEA Hallmark and over-representation analysis (ORA) Hallmark enrichment analysis of differentially expressed genes in RNA-seq.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig1-data2-v1.xlsx
Figure 1—figure supplement 1
Transcript changes elicited by WIN site inhibitors (WINi) in MLLr cancer cells.
(A) Crystal structures of C6 or C16 bound to the WIN Site of WDR5 with electrostatic surfaces mapped (PDB IDs: 6E23 [Aho et al., 2019a]; 6UCS [Tian et al., 2020]). (B) Viabilities of MV4;11 cells …
Figure 1—figure supplement 2
Impact of WIN site inhibitors (WINi) on RPL22L1 and p53 target gene expression.
(A) Venn diagram, showing the overlap of consensus p53 target genes (Fischer, 2017) with genes significantly induced by C6 or C16 in MV4;11 cells. (B) Graph showing the changes in expression of the …
Figure 2 with 3 supplements
Impact of WIN site inhibitors (WINi) on the translatome of MLLr cancer cells.
(A) Volcano plots depicting alterations in translation efficiency (TE) induced by 48 hr treatment of MV4;11 cells with either 2 µM C6 (left) or 100 nM C16 (right) compared to DMSO (n = 2; red …
-
Figure 2—source data 1
Output of Ribo-seq analysis of MV4;11 cells treated with C6/C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig2-data1-v1.xlsx
-
Figure 2—source data 2
Hallmark, Reactome, and KEGG enrichment analysis of differentially translated genes in Ribo-seq.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig2-data2-v1.xlsx
-
Figure 2—source data 3
Enrichment analysis of differentially translated genes, broken down by mRNA level change direction.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig2-data3-v1.xlsx
Figure 2—figure supplement 1
WIN site inhibitors (WINi) suppress bulk protein synthesis.
(A) Representative histograms from protein synthesis assays in MV4;11 cells treated 24, 48, or 96 hr with either 0.1% DMSO (blue), 2 µM C6 (red), or 100 nM C16 (orange). Cells were pulsed with O-prop…
Figure 2—figure supplement 2
WIN site inhibitors (WINi) suppress translation.
(A) Distribution of ribosome-protected fragment (RPF) lengths in each Ribo-seq sample/replicate. The length distribution of RPFs in mammalian Ribo-seq experiments typically peaks at 30–31 …
Figure 2—figure supplement 3
WIN site inhibitors (WINi) impair translation of mitochondrial ribosomal proteins.
(A) Top: transcript level changes in mitochondrial ribosomal protein genes elicited by C6 or C16, as indicated. Bottom: translational efficiency (TE) changes in mitochondrial ribosomal protein genes …
Figure 3 with 4 supplements
Impact of WIN site inhibitors (WINi) on the ribosome inventory of MLLr cancer cells.
(A) Lysates from MV4;11 cells treated 24 or 72 hr with either 0.1% DMSO or 250 nM C16 were subjected to liquid chromatography coupled with tandem mass spectrometry and analyzed by label-free …
-
Figure 3—source data 1
Output of label-free quantitative mass spectrometry (LFQMS) analysis of MV4;11 cells treated with C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig3-data1-v1.xlsx
-
Figure 3—source data 2
Enrichment analysis of proteins altered in abundance by 24 or 72 hr of C16 treatment.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig3-data2-v1.xlsx
Figure 3—figure supplement 1
Distribution of peptide/protein intensities in label-free quantitative mass spectrometry (LFQMS) analysis.
(A) Peptide intensities of all proteins detected in each mass spectrometry run before (left) and after normalization (right). (B) Magnitudes of significant protein level alterations within each …
Figure 3—figure supplement 2
Enrichment analysis of proteins with altered expression in response to C16 treatment.
(A) Graphs showing enrichment of proteins in GO BP (top) and Hallmark.MSigDB (bottom) pathways that are induced by C16 treatment at 24 (blue) or 72 (green) hr. The x-axis displays -Log10 (FDR); the …
Figure 3—figure supplement 3
WIN site inhibitors suppress rRNA levels.
(A) In-gel fluorescence assay detecting metabolically labeled rRNA (top) isolated from MV4;11 cells treated 24, 48, or 96 hr with either DMSO (0.1%), C6 (2 µM), or C16 (100 nM), and pulsed with …
-
Figure 3—figure supplement 3—source data 1
Raw unprocessed gel images corresponding to Figure 3—figure supplement 3A.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig3-figsupp3-data1-v1.pdf
Figure 3—figure supplement 4
C16 induces redistribution of nucleophosmin from the nucleolus to the nucleoplasm.
(A) Representative immunofluorescent images of MV4;11 cells treated with vehicle (DMSO control), C16 (100 nM), or ActD (5 nM) for the times indicated and stained for nucleophosmin (NPM1, green), …
Figure 4 with 1 supplement
A two-tier loss-of-function screen for modulators of the response to WIN site inhibitors (WINi).
(A) Two-tier screen design. In the first tier, Cas9-expressing MV4;11 cells were transduced with a genome-wide sgRNA library and treated with 2 µM C6 until a resistant cell population emerged. sgRNA …
-
Figure 4—source data 1
Output of the tier 1 screen.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig4-data1-v1.xlsx
-
Figure 4—source data 2
Output of the tier 2 screen.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig4-data2-v1.xlsx
Figure 4—figure supplement 1
Genome-wide CRISPR screen identifies genes that influence response to C6/C16.
(A) Tier 1 screen: daily cell counts of MV4;11 Cas9 and MV4;11 Cas9+GeCKOv2 (Library) populations treated with either DMSO or 2 µM C6. The two replicates of this screen are shown separately. (B) …
Figure 5 with 3 supplements
Identification of agents that synergize with WIN site inhibitors (WINi) in MLLr cells.
(A) Peak synergy (>0) and antagonism (<0) zero interaction potency (ZIP) delta (δ) scores from synergy assays in which MV4;11 cells were treated for 3 d with 49 unique dose combinations of C16 and …
-
Figure 5—source data 1
Peak synergy and antagonism scores for MV4:11 and MOLM13 cells treated with C16 in combination with 11 agents.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig5-data1-v1.xlsx
-
Figure 5—source data 2
Output of RNA-seq analysis of MV4;11 cells treated with C16, mivebresib, or both.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig5-data2-v1.xlsx
-
Figure 5—source data 3
Enrichment analysis of differentially expressed genes in RNA-seq of MV4;11 cells treated with C16, mivebresib, or both.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig5-data3-v1.xlsx
Figure 5—figure supplement 1
C16 is synergistic with multiple agents in MV4;11 cells.
(A) Heatmaps of MV4;11 cell growth inhibition at each dose of C16 and the indicated five compounds. (B) Heatmaps of δ scores from MV4;11 cells at each dose combination of C16 and the indicated agents.
Figure 5—figure supplement 2
C16 is synergistic with multiple agents in MOLM13 cells.
(A) Heatmaps of MOLM13 cell growth inhibition at each dose of C16 and the indicated five compounds. (B) Heatmaps of δ scores from MOLM13 cells at each dose combination of C16 and the indicated agents.
Figure 5—figure supplement 3
Impact of C16 and mivebresib on RPG and p53 target gene expression.
(A) Transcript level changes in WDR5-bound (left) and non-bound (right) RPGs elicited by C16 (top), mivebresib (Mivb; middle), or the combination (bottom). (B) Heatmap, showing significant changes …
Figure 6 with 3 supplements
WIN site inhibitors (WINi) inactivate MDM4 in an RPL22-dependent manner.
(A) Differential alternative splicing events affected by C6/C16 treatment of MV4;11 cells were quantified by rMATS. The types of alternative splicing events are cartooned at left, and the number of …
-
Figure 6—source data 1
Raw unprocessed gel images corresponding to Figure 6—figure supplement 1A.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data1-v1.pdf
-
Figure 6—source data 2
Output of rMATS analysis of MV4;11 cells treated with C6/C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data2-v1.xlsx
-
Figure 6—source data 3
Raw unprocessed gel images corresponding to Figure 6—figure supplement 1F.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data3-v1.pdf
-
Figure 6—source data 4
Raw unprocessed gel images corresponding to Figure 6—figure supplement 2A.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data4-v1.pdf
-
Figure 6—source data 5
Raw unprocessed gel images corresponding to Figure 6D.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data5-v1.pdf
-
Figure 6—source data 6
Output of RNA-seq analysis of NT and RPL22KO MV4;11 cells treated with C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data6-v1.xlsx
-
Figure 6—source data 7
GSEA Hallmark and GOBP enrichment analysis of differentially expressed genes in RNA-seq of NT and RPL22KO MV4;11 cells treated with C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data7-v1.xlsx
-
Figure 6—source data 8
Output of rMATS analysis of NT and RPL22KO MV4;11 cells treated with C16.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data8-v1.xlsx
-
Figure 6—source data 9
Raw unprocessed gel images corresponding to Figure 6G.
- https://cdn.elifesciences.org/articles/90683/elife-90683-fig6-data9-v1.pdf
Figure 6—figure supplement 1
WIN site inhibitors (WINi) alter the abundance of alternatively spliced mRNA isoforms.
(A) Western blots comparing the effects of 72 hr DMSO (DM) or C16 treatment of MV4;11 (top) or MOLM13 (bottom) cells on levels of p53 and GAPDH (loading control). Representative images from three …
Figure 6—figure supplement 2
Impact of RPL22 loss on the response of MLLr cells to WIN site inhibitors (WINi).
(A) Western blot analysis of RPL22 expression in MV4;11, MOLM13, and K562 cells electroporated with Cas9 and either scrambled non-targeting (NT) control or RPL22-targeting sgRNAs. GAPDH and …
Figure 6—figure supplement 3
Impact of RPL22 loss on the abundance of alternatively-spliced mRNA isoforms in MV4;11 cells.
(A) Differential alternative splicing events affected by C16 treatment of control (NT) or RPL22 knockout (KO) MV4;11 cells were quantified by rMATS. The types of alternative splicing events are …
Tables
Appendix 1—key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Homo sapiens) | RPL22 | NA | ENSEMBL:ENSG00000116251 | |
| Gene (H. sapiens) | RPL22L1 | NA | ENSEMBL:ENSG00000163584 | |
| Gene (H. sapiens) | MDM4 | NA | ENSEMBL:ENSG00000198625 | |
| Strain, strain background (Escherichia coli) | Endura ElectroCompetent Cells | Lucigen | Cat# 60242-2 | |
| Cell line (H. sapiens) | ‘MV4;11’ | ATCC | Cat# CRL-9591; RRID:CVCL_0064 | |
| Cell line (H. sapiens) | ‘MV4;11 NT’ | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | ‘MV4;11 RPL22 KO’ | This study | NA | See ’Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | ‘MV4;11 Cas9’ | This study | NA | See ‘Generation of Cas9-expressing MV4;11 cells’ |
| Cell line (H. sapiens) | MOLM13 | DMSZ | Cat# ACC554; RRID:CVCL_2119 | |
| Cell line (H. sapiens) | MOLM13 NT | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | MOLM13 RPL22 KO | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | K562 | ATCC | Cat# CCL-243; RRID:CVCL_0004 | |
| Cell line (H. sapiens) | K562 NT | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | K562 RPL22 KO | This study | NA | See ‘Generation of RPL22-null cell lines’ |
| Cell line (H. sapiens) | HEK293T | ATCC | Cat# CRL-11268; RRID:CVCL_1926 | |
| Antibody | Anti-p53 (DO-1) (mouse monoclonal) | Santa Cruz Biotechnology | Cat# sc-126; RRID:AB_628082 | (1:2000) |
| Antibody | Anti-RPL22 (52) (mouse monoclonal) | Santa Cruz Biotechnology | Cat# sc-136413; RRID:AB_10658965 | (1:1000) |
| Antibody | Anti-RPL22L1 (rabbit polyclonal) | Thermo Fisher Scientific | Cat# PA5-63266; RRID:AB_2646731 | (1:1000) |
| Antibody | Anti-MDMX (mouse monoclonal) | Sigma-Aldrich | Cat# M0445; RRID:AB_532256 | (1:1000) |
| Antibody | Anti-p21 Waf1/Cip1 (12D1) (rabbit monoclonal) | Cell Signaling Technology | Cat# 2947; RRID:AB_823586 | (1:1000) |
| Antibody | Anti-⍺-actinin (HRP) (rabbit monoclonal) | Cell Signaling Technology | Cat# 12413; RRID:AB_2797903 | (1:1000) |
| Antibody | Anti-GAPDH (HRP) (rabbit monoclonal) | Cell Signaling Technology | Cat# 8884; RRID:AB_11129865 | (1:2000) |
| Antibody | Anti-nucleophosmin (mouse monoclonal) | Abcam | Cat# ab10530; RRID:AB_297271 | (1:500) |
| Antibody | Anti-Phospho-Histone H2A.X (Ser139) (20E3) (rabbit monoclonal) | Cell Signaling Technology | Cat# 9718; RRID:AB_2118009 | (1:250) |
| Antibody | Goat anti-mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A-11001; RRID:AB_2534069 | (1:500) |
| Antibody | Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | Cat# A-11037; RRID:AB_2534095 | (1:500) |
| Antibody | Anti-GAPDH (HRP) (rabbit monoclonal) | Cell Signaling Technology | Cat# 8884; RRID:AB_11129865 | (1:2000) |
| Antibody | Goat anti-mouse IgG, Light chain specific (HRP) | Jackson ImmunoResearch Laboratories, Inc | Cat# 115-035-174; RRID:AB_2338512 | (1:5000) |
| Antibody | Goat anti-rabbit IgG, HRP-linked antibody | Cell Signaling Technology | Cat# 7074; RRID:AB_2099233 | (1:5000) |
| Recombinant DNA reagent | lentiCas9-Blast | PMID:25075903 | Addgene plasmid# 52962; RRID:Addgene_52962 | |
| Recombinant DNA reagent | psPAX2 | Addgene | Addgene plasmid# 12260; RRID:Addgene_12260 | |
| Recombinant DNA reagent | pMD2.G | Addgene | Addgene plasmid# 12259; RRID:Addgene_12259 | |
| Recombinant DNA reagent | Human GeCKOv2 CRISPR Knockout Pooled Library (A+B) in lentiGuide-PURO | PMID:25075903 | Addgene plasmid# 1000000048 | |
| Recombinant DNA reagent | lentiGuide-PURO | PMID:25075903 | Addgene plasmid# 52963; RRID:Addgene_52963 | |
| Commercial assay or kit | cOmplete, EDTA-free, Protease Inhibitor Cocktail | Roche | Cat# 11873580001 | |
| Commercial assay or kit | PhosSTOP | Roche | Cat# 4906837001 | |
| Commercial assay or kit | Pefabloc SC | Roche | Cat# 11429868001 | |
| Commercial assay or kit | TURBO DNase (2 U/µL) | Invitrogen | Cat# AM2238 | |
| Commercial assay or kit | RNase I, E. coli | Lucigen | Cat# N6901K | |
| Commercial assay or kit | SUPERaseIn RNase Inhibitor | Invitrogen | Cat# AM2694 | |
| Commercial assay or kit | TRIzol Reagent | Invitrogen | Cat# 15596018 | |
| Commercial assay or kit | SYBR Gold Nucleic Acid Gel Stain | Invitrogen | Cat# S11494 | |
| Commercial assay or kit | T4 Polynucleotide Kinase | New England BioLabs | Cat# M0201S | |
| Commercial assay or kit | T4 RNA Ligase 2, truncated K227Q | New England BioLabs | Cat# M0351S | |
| Commercial assay or kit | SuperScript III Reverse Transcriptase | Invitrogen | Cat# 18080085 | |
| Commercial assay or kit | Random Hexamers | Invitrogen | Cat# N8080127 | |
| Commercial assay or kit | CircLigase II ssDNA Ligase | Lucigen | Cat# CL9021K | |
| Commercial assay or kit | LD-Dithiothreitol | MilliporeSigma | Cat# D9779 | |
| Commercial assay or kit | Iodoacetamide | MilliporeSigma | Cat# I1149 | |
| Commercial assay or kit | o-Phosphoric acid, 85% | Fisher Scientific | Cat# A260-500 | |
| Commercial assay or kit | Water, Optima LC/MS Grade | Fisher Scientific | Cat# W6-4 | |
| Commercial assay or kit | Methanol, Optima LC/MS Grade | Fisher Scientific | Cat# A456 | |
| Commercial assay or kit | Triethylammonium bicarbonate buffer | MilliporeSigma | Cat# T7408 | |
| Commercial assay or kit | Trypsin Gold, Mass Spectrometry Grade | Promega | Cat# V5280 | |
| Commercial assay or kit | Formic Acid, LC/MS Grade | Thermo Scientific Pierce | Cat# 28905 | |
| Commercial assay or kit | Acetonitrile, Optima LC/MS Grade | Fisher Scientific | Cat# A955-1 | |
| Commercial assay or kit | Phusion High Fidelity DNA polymerase | New England BioLabs | Cat# M0530S | |
| Commercial assay or kit | BsmBIv2 | New England BioLabs | Cat# R0739S | |
| Commercial assay or kit | DNase I (RNase-free) | New England BioLabs | Cat# M0303S | |
| Commercial assay or kit | RNA Clean and Concentrator-25 | Zymo Research | Cat# R1017 | |
| Commercial assay or kit | RNasin Ribonuclease Inhibitor | Promega | Cat# N2515 | |
| Commercial assay or kit | SYBR Safe DNA Gel Stain | Invitrogen | Cat# S33102 | |
| Commercial assay or kit | Click-iT Cell Reaction Buffer Kit | Invitrogen | Cat# C10269 | |
| Commercial assay or kit | Neon Transfection System 10 µL Kit | Thermo Scientific | Cat# MPK1096 | |
| Commercial assay or kit | Gene Knockout Kit v2 – human – RPL22 | Synthego | NA | |
| Commercial assay or kit | Negative Control, Scrambled sgRNA#1, mod-sgRNA | Synthego | NA | |
| Commercial assay or kit | ProLong Gold Antifade Mountant | Thermo Fisher Scientific | Cat# P36934 | |
| Commercial assay or kit | Lipofectamine 3000 Transfection Reagent | Invitrogen | Cat# L3000075 | |
| Commercial assay or kit | QuantiGene Plex panel | Thermo Fisher Scientific | NA | |
| Commercial assay or kit | QuantiGene Sample Processing Kit for cultured cells | Thermo Fisher Scientific | Cat# QS0100 | |
| Commercial assay or kit | QuantiGene Plex Assay kits | Thermo Fisher Scientific | Cat# QP1013 | |
| Commercial assay or kit | Pierce BCA Protein Assay Kit | Thermo Scientific | Cat# PI23225 | |
| Commercial assay or kit | Clarity Western ECL Substrate | Bio-Rad | Cat# 1705061 | |
| Commercial assay or kit | Qubit RNA High Sensitivity Assay Kit | Invitrogen | Cat# Q32852 | |
| Commercial assay or kit | Direct-zol RNA Miniprep | Zymo Research | Cat# R2050 | |
| Commercial assay or kit | RiboCop rRNA Depletion Kit V1.2 | Lexogen | Cat# 037.24 | |
| Commercial assay or kit | Quick-DNA MidiPrep Plus Kit | Zymo Research | Cat# D4075 | |
| Commercial assay or kit | NEBNext High Fidelity 2X PCR Master Mix | New England BioLabs | Cat# M0541L | |
| Commercial assay or kit | Zymo-Spin V Columns with Reservoir | Zymo Research | Cat# C1016-25 | |
| Commercial assay or kit | NucleoSpin Gel and PCR Clean-up | Macherey-Nagel | Cat# 740609.250 | |
| Commercial assay or kit | Gibson Assembly Master Mix | New England BioLabs | Cat# E2611S | |
| Commercial assay or kit | NucleoBond Xtra Maxi EF | Macherey-Nagel | Cat# 740424.10 | |
| Commercial assay or kit | Q5 DNA Polymerase | New England BioLabs | Cat# M0491S | |
| Commercial assay or kit | Taq DNA Polymerase with Standard Taq Buffer | New England BioLabs | Cat# M0273S | |
| Commercial assay or kit | SYBR Safe DNA Gel Stain | Invitrogen | Cat# S33102 | |
| Commercial assay or kit | KAPA SYBR Fast qPCR Master Mix (2×) | Roche | Cat# 07959397001 | |
| Commercial assay or kit | CellTiter-Glo Luminescent Cell Viability Assay | Promega | Cat# G7572 | |
| Chemical compound, drug | Blasticidin S Hydrochloride Powder | Research Products International | Cat# B12200-0.05 | |
| Chemical compound, drug | DMSO | Sigma | Cat# D2650 | |
| Chemical compound, drug | C6 | PMID:30865883 | N/A | |
| Chemical compound, drug | C16 | PMID:31858797 | N/A | |
| Chemical compound, drug | 2’-Azido-2’-deoxycytidine | Biosynth | Cat# NA05412 | |
| Chemical compound, drug | Actinomycin D | Cayman Chemical Company | Cat# 11421-10mg | |
| Chemical compound, drug | MB 680R DBCO | Vector Laboratories | Cat# CCT-1462 | |
| Chemical compound, drug | Cycloheximide | Research Products International | Cat# C81040-1.0 | |
| Chemical compound, drug | OPP (O-propargyl-puromycin) | Invitrogen | Cat# C10459 | |
| Chemical compound, drug | Hoechst 33342 | Thermo Fisher Scientific | Cat# H3570 | |
| Chemical compound, drug | Alexa Fluor 647 Azide, Triethylammonium Salt | Invitrogen | Cat# A10277 | |
| Chemical compound, drug | Cycloheximide | Sigma | Cat# C4859-1ML | |
| Chemical compound, drug | Nutlin-3a | Cayman Chemical Company | Cat# 18585 | |
| Chemical compound, drug | Rapamycin | MedChem Express | Cat# HY-10219 | |
| Chemical compound, drug | Pinometostat | Cayman Chemical Company | Cat# 16175 | |
| Chemical compound, drug | Harmine | Sigma-Aldrich | Cat# 286044 | |
| Chemical compound, drug | Mivebresib | Cayman Chemical Company | Cat# 21033 | |
| Chemical compound, drug | Venetoclax | Cayman Chemical Company | Cat# 16233 | |
| Chemical compound, drug | Etoposide | Cayman Chemical Company | Cat# 12092 | |
| Chemical compound, drug | Olaparib | Cayman Chemical Company | Cat# 10621 | |
| Chemical compound, drug | VE-821 | Cayman Chemical Company | Cat# 17587 | |
| Chemical compound, drug | Pemrametostat | Selleck Chemicals | Cat# S8664 | |
| Chemical compound, drug | Alvespimycin | Cayman Chemical Company | Cat# 11036 | |
| Software, algorithm | R | The R Foundation | RRID:SCR_001905 | https://www.r-project.org |
| Software, algorithm | drc | Ritz et al., 2015; Ritz and Streibig, 2021 | NA | https://github.com/DoseResponse/drc |
| Software, algorithm | CHOPCHOP | Labun et al., 2019 | RRID:SCR_015723 | https://chopchop.cbu.uib.no |
| Software, algorithm | count_spacers.py | Joung et al., 2017; Joung, 2017 | NA | https://github.com/fengzhanglab/Screening_Protocols_manuscript/blob/master/design_targeted_library.py |
| Software, algorithm | SynergyFinder Plus | Zheng et al., 2022 | RRID:SCR_019318 | https://synergyfinder.org/ |
| Software, algorithm | PASWR | Ugarte et al., 2015; Arnholt, 2022 | NA | https://github.com/cran/PASWR |
| Software, algorithm | cutadapt | Martin, 2011 | RRID:SCR_011841 | https://github.com/marcelm/cutadapt/ |
| Software, algorithm | sabre | NA | RRID:SCR_011843 | https://github.com/najoshi/sabre |
| Software, algorithm | bowtie2 | Langmead and Salzberg, 2012 | RRID:SCR_016368 | https://github.com/BenLangmead/bowtie2 |
| Software, algorithm | STAR | Dobin et al., 2013 | RRID:SCR_004463 | https://github.com/alexdobin/STAR |
| Software, algorithm | UMI-tools | Smith et al., 2017 | RRID:SCR_017048 | https://github.com/CGATOxford/UMI-tools |
| Software, algorithm | BEDTools | Quinlan and Hall, 2010 | RRID:SCR_006646 | https://github.com/arq5x/bedtools2 |
| Software, algorithm | Xtail | Xiao et al., 2016; xryanglab, 2016 | NA | https://github.com/xryanglab/xtail |
| Software, algorithm | riboWaltz | Lauria et al., 2018 | RRID:SCR_016948 | https://github.com/LabTranslationalArchitectomics/riboWaltz |
| Software, algorithm | featureCounts | Liao et al., 2014 | RRID:SCR_012919 | http://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| Software, algorithm | DESeq2 | Love et al., 2014 | RRID:SCR_015687 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Software, algorithm | MAGeCK | Li et al., 2014; Li and Song, 2022 | NA | https://sourceforge.net/p/mageck/wiki/Home/ |
| Software, algorithm | Maxquant | Cox and Mann, 2008 | RRID:SCR_014485 | https://cox-labs.github.io/coxdocs/maxquant_instructions.html |
| Software, algorithm | Andromeda | Cox et al., 2011 | NA | https://cox-labs.github.io/coxdocs/andromeda_instructions.html |
| Software, algorithm | Msstats | Choi et al., 2014 | RRID:SCR_014353 | https://msstats.org/ |
| Software, algorithm | fgsea | Korotkevich et al., 2021 | RRID:SCR_020938 | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| Software, algorithm | Biorender | NA | RRID:SCR_018361 | https://biorender.com |
| Software, algorithm | PyMOL | NA | RRID:SCR_000305 | https://pymol.org/2/ |
| Software, algorithm | rMATS | Shen et al., 2014 | RRID:SCR_013049 | https://rnaseq-mats.sourceforge.net |
| Software, algorithm | Molecular Signatures Database | Liberzon et al., 2011 | RRID:SCR_016863 | https://www.gsea-msigdb.org/gsea/msigdb/index.jsp |
| Software, algorithm | Universal Protein Resource | Bateman et al., 2021 | RRID:SCR_002380 | https://www.uniprot.org |
| Software, algorithm | FlowJo | NA | RRID:SRC_008520 | https://www.flowjo.com/solutions/flowjo |
| Software, algorithm | Empiria Studio | LI-COR | RRID:SCR_022512 | https://www.licor.com/bio/empiria-studio/ |
| Software, algorithm | NIS-Elements AR 5.42.03 64-bit | Nikon Instruments | RRID:SCR_014329 | https://www.nikoninstruments.com/Products/Software |
| Software, algorithm | Fiji | Fiji/ImageJ | RRID:SCR_002285 | http://fiji.sc |
| Other | S-Trap Micro Columns | ProtiFi | Cat# C02-micro-80 | |
| Other | Jupiter 3 um C18 300A, Bulk packaging | Phenomenex | Cat# 04A-4263 | |
| Other | Molex Polymicro Capillary 100 um × 363 um | Fisher Scientific | Cat# 50-110-8623 | |
| Other | Neon Transfection System | Thermo Fisher Scientific | Cat# MPK5000 | |
| Other | Luminex FLEXMAP 3D System | Invitrogen | Cat# APX1342 | |
| Other | 4–20% Mini-PROTEAN TGX Precast Gel | Bio-Rad | Cat# 4561096 | |
| Other | Amersham Protran Western Blotting Membranes, Nitrocellulose | Cytiva | Cat# GE10600001 | |
| Other | C1000 Touch Thermal Cycler Chassis | Bio-Rad | Cat# 1841100 | |
| Other | CFX96 Optical Reaction Module for Real-Time PCR System | Bio-Rad | Cat# 1845097 | |
| Other | ChemiDoc Imaging System | Bio-Rad | Cat# 17001401 | |
| Other | Thick-wall Polycarbonate Tubes, 13 × 51 mm | Beckman-Coulter | Cat# 349622 | |
| Other | Novex TBE-Urea Gels 15%, 12 well | Invitrogen | Cat# EC68852BOX | |
| Other | Costar Spin-X Centrifuge Tube Filters | Corning | Cat# CLS8162 | |
| Other | Novex TBE Gels, 8%, 15 well | Invitrogen | Cat# EC62155BOX | |
| Other | GloMax Explorer Multimode Microplate Reader | Promega | Cat# GM3500 | |
| Other | Orbitrap Exploris 480 Mass Spectrometer | Thermo Scientific | Cat# BRE725533 |
