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    JCRB Cell Bank kp2 cell line
    MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, <t>KLM1</t> (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.
    Kp2 Cell Line, supplied by JCRB Cell Bank, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/kp2+cell+line/kp2+cell+line/pmc11609825-125-28-35
    Average 90 stars, based on 1 article reviews
    kp2 cell line - by Bioz Stars, 2026-10
    90/100 stars

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    1) Product Images from "MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer"

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer

    Journal: Cancer Discovery

    doi: 10.1158/2159-8290.CD-23-1529

    MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, KLM1 (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.
    Figure Legend Snippet: MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, KLM1 (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.

    Techniques Used: Expressing, Quantitative Proteomics, Knock-Out, Infection, Staining, Flow Cytometry, Reporter Assay, Gene Knockout, ChIP-sequencing

    Related Articles

    Expressing:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Quantitative Proteomics:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Knock-Out:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Infection:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Staining:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Flow Cytometry:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Reporter Assay:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    Gene Knockout:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).

    ChIP-sequencing:

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
    Article Snippet: The KP2, 326 T3M-4, SUIT-2 and KLM-1 cell lines were purchased from the “Japanese Collection of Research 327 Bioresources Cell Bank” (JCRB).



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    MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, <t>KLM1</t> (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.
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    MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, <t>KLM1</t> (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.
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    KEY RESOURCES TABLE

    Journal: Developmental cell

    Article Title: Twist1 Activation in Muscle Progenitor Cells Causes Muscle Loss Akin to Cancer Cachexia

    doi: 10.1016/j.devcel.2018.05.026

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: REAGENTS or RESOURCES SOURCE IDENTIFIER Antibodies Atrogin1/Fbx32 Abcam ab168372 BrdU Cell Signaling 52925 Cleaved caspase 3 Cell Signaling 9661 Cytokeratin 19 Abcam ab52625 Dystrophin Abcam ab15277 elF3-f Abcam ab64177 MHC Abcam ab71808 Myostatin Abcam ab71808 Myostatin R&D Systems AF788 MuRF1 Cell Signaling 4305 Myc tag Cell Signaling 22765 Smad4 Santa Cruz sc-7966 Smad2 Cell Signaling 5339 pSmad2 Cell Signaling 3108 Twist1 Santa Cruz sc-81417 Pax7 Abcam Ab92317 Chemicals, Peptides, and Recombinant Proteins Activin A R&D Systems 338-AC-050 bFGF Sigma-Aldrich F3685 Collagenase D Sigma-Aldrich 11088858001 Collagenase type 1 Sigma-Aldrich SCR103 Dispase II Sigma-Aldrich 4942078001 D-luciferin Perkin Elmer 122799 JQ1 Sigma-Aldrich SML-1524 Myostatin R&D Systems 788-GB-010 puromycin Sigma-Aldrich P9620 Tamoxifen Sigma-Aldrich T5648 Critical Commercial Assays Activin A ELISA kit R&D Systems DAC00B SURVEYOR Mutation Detection Kit Integrated DNA Technologies 706025 Recombinant DNA Adenovirus-CMV.Cre (Ad.Cre) Baylor College Ad5-CMV-Cre Atrogin1-Luc This study N/A Mstn-Luc This study N/A MuRF1-Luc This study N/A pBABE-puro-mTwist1 Addgene 1783 pGIPZ-sh.Activin Dharmacon EG16323 pGIPZ-sh.control Dharmacon RHS4346 LentiCISPRv2 Addgene 52961 pSpCas9(BB)-2A-Puro (PX459) Addgene 62988 Experimental Models: Cell Lines B16 ATCC CRL-6322 Suit2 ATCC CRL-1687 MiaPaca2 ATCC CRL-1420 CT-26 ATCC CRL-2638 KP2 This study N/A KP1 This study N/A LLC ATCC CRL-1642 Experimental Models: Organisms/Strains CAG-Cre ERT2 Jackson Lab. 004682 CAG-Loxp-CAT-Loxp-Twist1 Jackson Lab. 018543 CAG-Loxp-Stop-Loxp-Luciferase NCI 01XAC Loxp-Stop-Loxp-Kras G12D NCI 01XJ6 NOD/SCID Jackson Lab. 001303 p16Ink4A-Luciferase Dr. Sharpless Burd et al., 2013 Pax7.Cre Jackson Lab. 010530 Pax7.Cre ERT2 Jackson Lab. 012476 Pdx1.Cre NCI 01XL5 Prrx1.Cre Jackson Lab. 005584 MCK.Cre Jackson Lab. 006475 Trp53.Loxp/Loxp Jackson Lab. 008462 Twist1.Loxp/Loxp Dr. Xu Baylor College of Medicine Open in a separate window KEY RESOURCES TABLE

    Techniques: Recombinant, Enzyme-linked Immunosorbent Assay, Mutagenesis

    MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, KLM1 (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.

    Journal: Cancer Discovery

    Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer

    doi: 10.1158/2159-8290.CD-23-1529

    Figure Lengend Snippet: MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, KLM1 (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.

    Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.

    Techniques: Expressing, Quantitative Proteomics, Knock-Out, Infection, Staining, Flow Cytometry, Reporter Assay, Gene Knockout, ChIP-sequencing