1. Cancer Biology

Experiments from unfinished Registered Reports in the Reproducibility Project: Cancer Biology

  1. Timothy M Errington  Is a corresponding author
  2. Alexandria Denis
  3. Anne B Allison
  4. Renee Araiza
  5. Pedro Aza-Blanc
  6. Lynette R Bower
  7. Jessica Campos
  8. Heidi Chu
  9. Sarah Denson
  10. Cristine Donham
  11. Kaitlyn Harr
  12. Babette Haven
  13. Elizabeth Iorns
  14. Jennie Kwok
  15. Elysia McDonald
  16. Steven Pelech
  17. Nicole Perfito
  18. Amanda Pike
  19. Darryl Sampey
  20. Michael Settles
  21. David A Scott
  22. Vidhu Sharma
  23. Todd Tolentino
  24. Angela Trinh
  25. Rachel Tsui
  26. Brandon Willis
  27. Joshua Wood
  28. Lisa Young
  1. Center for Open Science, United States
  2. Piedmont Virginia Community College, United States
  3. University of California, Davis, United States
  4. Independent consultant, United States
  5. Applied Biological Materials, Canada
  6. University of Georgia, United States
  7. University of Virginia, United States
  8. Absorption Systems, United States
  9. Science Exchange, United States
  10. Drexel University College of Medicine, United States
  11. Kinexus Bioinformatics, Canada
  12. University of British Columbia, United States
  13. BioFactura, United States
  14. Sanford Burnham Prebys Medical Discovery Institute, United States
https://doi.org/10.7554/eLife.73430
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Cite this article
  1. Timothy M Errington
  2. Alexandria Denis
  3. Anne B Allison
  4. Renee Araiza
  5. Pedro Aza-Blanc
  6. Lynette R Bower
  7. Jessica Campos
  8. Heidi Chu
  9. Sarah Denson
  10. Cristine Donham
  11. Kaitlyn Harr
  12. Babette Haven
  13. Elizabeth Iorns
  14. Jennie Kwok
  15. Elysia McDonald
  16. Steven Pelech
  17. Nicole Perfito
  18. Amanda Pike
  19. Darryl Sampey
  20. Michael Settles
  21. David A Scott
  22. Vidhu Sharma
  23. Todd Tolentino
  24. Angela Trinh
  25. Rachel Tsui
  26. Brandon Willis
  27. Joshua Wood
  28. Lisa Young
(2021)
Experiments from unfinished Registered Reports in the Reproducibility Project: Cancer Biology
eLife 10:e73430.
https://doi.org/10.7554/eLife.73430
  2. Download BibTeX
  3. Download .RIS
7 figures, 1 table and 1 additional file

Figures

Figure 1 with 1 supplement
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Replication attempt of Sharma et al., 2010.

Growth characteristics of PC9 cells treated with various doses of erlotinib. (A) PC9 cells were plated at equal density and treated with dimethyl sulfoxide(DMSO) or the indicated dose of erlotinib …

Figure 1—figure supplement 1
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Growth characteristics of PC9 cells treated with erlotinib hydrochloride (HCl).

(A) PC9 cells were plated at equal density and treated with DMSO or the indicated dose of erlotinib HCl (2 or 20 µM) for 9 days (fresh erlotinib was added every 3 days). Representative microscopic …

Figure 2
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Replication attempt of Ricci-Vitiani et al., 2010.

(A) Tie2 expression in patient-derived glioblastoma neurospheres (GSC83), a glioblastoma cell line (U87MG), and an endothelial cell line (human dermal microvascular endothelial cells, HMVEC). …

Figure 3
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Replication of Kan et al., 2010.

(A) Anchorage-independent growth of human mammary epithelial cells (HMECs). HMECs were left uninfected or stably expressing empty vector (EV), wild-type (WT) GNAO1, or GNAO1-R243H. Number of …

Figure 4
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Replication attempt of Heidorn et al., 2010.

ERK activation following treatment with BRAF inhibitors in A375 cells (mutant BRAF; wild-type NRAS) and D04 cells (wild-type BRAF; mutant NRAS). (A) A375 cells were treated with DMSO, sorafenib (10 …

Figure 5 with 1 supplement
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Replication attempt of Johannessen et al., 2010.

(A) Cellular dose–response curves for RAF inhibitor (PLX4720) in BRAF(V600E) cell lines, A375, HT29, and RPMI-7951. Absolute half-maximum growth inhibition (GI50) values (µM) were determined for …

Figure 5—figure supplement 1
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Cellular dose–response curves for each biological repeat and representative Western blot image of ERK and MEK phosphorylation.

(A) This is the same experiment as in Figure 5A. The dose–response curve of each biological repeat [n = 3] for A375, HT29, and RPMI-7951 cells treated with PLX4720 for this replication attempt are …

Figure 6
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Replication attempt of Kang et al., 2011.

(A–F) Quantification of Nras-, p21-, and p16-positive cells on liver sections from C.B-17 or C.B-17 SCID/beige mice six or 30 days after intrahepatic delivery of NrasG12V or NrasG12V/D38A. Percent …

Figure 7 with 2 supplements
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Replication attempt of Lu et al., 2012.

(A) HEK293T cells transfected with wild-type (WT) or the indicated mutant of IDH1 or IDH2, or empty vector, were analyzed for intracellular metabolites 72 hr after transfection by gas …

Figure 7—figure supplement 1
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Replication attempt of Lu et al., 2012.

(A) This is the same experiment as in Figure 7B. Representative Western blots (experiment performed independently six times) of histone extractions from HEK293T cells transfected with the indicated …

Figure 7—figure supplement 2
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Meta-analyses of effects from replication attempt of Lu et al., 2012.

Meta-analysis of each effect reported in Figure 7. Effect size and 95 % confidence intervals are presented for Lu et al., 2012, this replication study (Reproducibility Project: Cancer Biology, …

Tables

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Cell line (Homo sapiens, male)PC9Sigma-Aldrichcat# 90071810;RRID:CVCL_B260lot# 14A030
Chemical compound, drugerlotinibCayman Chemicalcat# 10,483lot# 0459700-31
Chemical compound, drugerlotinib-HClLC Laboratoriescat# E-4007lot# BBE-108
Software, algorithmCellometer Auto T4 SoftwareNexcelom BioscienceRRID:SCR_021656Version 3.1.1
Software, algorithmImage Studio SoftwareLI-COR BiosciencesRRID:SCR_015795
Antibodyrabbit-anti-phospho-EGFR (Y1068)Cell Signaling Technologycat# 3777; clone D7A5;RRID:AB_20962701:1000 dilution
Antibodymouse anti-GAPDHThermo Fisher Scientificcat# MA5-15738; clone GA1R; RRID:AB_109773871:2000 dilution
AntibodyIRDye 680RD-conjugated donkey anti-mouseLI-COR Biosciencescat# 926-68072;RRID:AB_109536281:15,000 dilution
AntibodyIRDye 800CW-conjugated donkey anti-rabbitLI-COR Biosciencescat# 926-32213;RRID:AB_6218481:15,000 dilution
Software, algorithm2,100 Bioanalyzer SoftwareAgilent TechnologiesRRID:SCR_019389Version 1.03
Cell line (Homo sapiens, male)U87MGATCCcat#HTB-14; RRID:CVCL_0022
Cell line (Homo sapiens, male)HMVECLonzaCC-2516
Cell line (Homo sapiens, male)GSC83doi:10.1038/nature09557RRID:CVCL_A9TLShared by Ricci-Vitiani lab, Istituto Superiore di Sanità
Cell line (Homo sapiens, female)HMECApplied Biological Materialscat# T0454; RRID:CVCL_B0CIlot# RZ824921; infected with SV40 large T and small T antigen
Recombinant DNA reagentpRetroX-IRES-ZsGreen1-empty vectorClontechcat# 632,520
Recombinant DNA reagentpRetroX-FLAG-GNAO1WT-IRES-ZsGreen1This paper
Recombinant DNA reagentpRetroX-FLAG-GNAO1R243H-IRES-ZsGreen1This paper
Cell line (Homo sapiens, female)PhoenixATCCcat# CRL-3213; RRID:CVCL_H716
Antibodymouse anti-FLAGSigma-Aldrichcat# F1804; clone M2; RRID:AB_2620441:500 dilution
Antibodymouse anti-β-ACTINSigma-Aldrichcat# A5441; clone AC-15; RRID:AB_4767441:1000 dilution
AntibodyHRP-conjugated rabbit anti-mouseAbcamcat# ab6728; RRID:AB_9554401:10,000 dilution
Software, algorithmFACSDivaBD BiosciencesRRID:SCR_016722Version 6.1.2
Software, algorithmImageJdoi:10.1038/nmeth.2089RRID:SCR_003070Version 1.51p
Cell line (Homo sapiens, female)D04ABN Cell Line Bank, QIMR
Berghofer Medical
Research Institute		RRID:CVCL_H604
Cell line (Homo sapiens, female)A375ATCCcat# CRL-1619; RRID:CVCL_0132
Chemical compound, drugsorafenibSelleckchemcat# S7397
Chemical compound, drugSB590885Selleckchemcat# S2220
Chemical compound, drugPD184352Selleckchemcat# S1020
Antibodymouse anti-phospho-ERK1/2 (T202/Y204)Cell Signaling
Technology		cat# 9106; clone E10; RRID:AB_3317681:1000 dilution
AntibodyRabbit anti-ERK1/2Cell Signaling
Technology		cat# 9102; RRID:AB_3307441:1000 dilution
Cell line (Homo sapiens, female)RPMI-7951ATCCcat# HTB-66; RRID:CVCL_1666
Cell line (Homo sapiens, male)OUMS-23JCRBcat# JCRB1022; RRID:CVCL_3088
Cell line (Homo sapiens, female)HT-29ATCCcat# HTB-38; RRID:CVCL_0320
Chemical compound, drugPLX4720Selleckchemcat# S1152
Chemical compound, drugMAP3K8 kinase inhibitorEMD Milliporecat# 616,373
Antibodyrabbit anti-phospho MEK1/2 (S217/221)Cell Signaling
Technology		cat# 9154; clone 41G9; RRID:AB_21380171:1000 dilution
Antibodymouse anti-ERK1/2Cell Signaling
Technology		cat# 4696; clone L34F12; RRID:AB_3907801:1000 dilution
Antibodyrabbit anti-MEK1/2Cell Signaling
Technology		cat# 8727; clone D1A5; RRID:AB_108294731:1000 dilution
Antibodyrabbit anti-VinculinSigma-Aldrichcat# V4139; RRID:AB_2620531:20,000 dilution
AntibodyHRP-conjugated goat anti-rabbitCell Signaling
Technology		cat# 7074; RRID:AB_20992331:1000 dilution
AntibodyHRP-conjugated horse anti-mouseCell Signaling
Technology		cat# 7076; RRID:AB_3309241:1000 dilution
Strain, strain background (M. musculus, C.BKa-lghb/lcrCrl, female)C.B-17 wild-typeCharles RiverRRID:IMSR_CRL:251
Strain, strain background (M. musculus, CB17.Cg-PrkdcscidLystbg/Crl, female)SCID/beigeCharles RiverRRID:IMSR_CRL:250
Strain, strain background (M. musculus, C57BL/6 J, female)BL/6 wild-typeThe Jackson
Laboratory		RRID:IMSR_JAX:000664
Strain, strain background (M. musculus, B6.129S2-Cd4tm1Mak/J, female)CD4−/−The Jackson
Laboratory		RRID:IMSR_JAX:002663
Recombinant DNA reagentpPGK-SB13doi:10.1038/nature10599Shared by Zender lab, University of Tuebingen
Recombinant DNA reagentpT/CaggsNrasG12Vdoi:10.1038/nature10599Shared by Zender lab, University of Tuebingen
Recombinant DNA reagentpT/CaggsNrasG12V/D38Adoi:10.1038/nature10599Shared by Zender lab, University of Tuebingen
Antibodymouse anti-p16Abcamcat# ab54210; clone 2D9A12; RRID:AB_8818191:50 dilution
Antibodymouse anti-p21BD Biosciencescat# 556431; clone SXM30; RRID:AB_3964151:50 dilution
Antibodymouse anti-NrasSanta Cruz
Biotechnology		cat# sc-31; clone F155; RRID:AB_6280411:100 dilution
Antibodymouse IgG1 isotype controlSigma-Aldrichcat# M5284; clone MOPC21; RRID:AB_11636851:50 dilution
Antibodybiotinylated goat anti-mouseThermo Fisher Scientificted goat anti-mouse (Thermo Fisher Scientific)
Software, algorithmCaseViewer3DHISTECHRRID:SCR_017654Version 2.2
Cell line (Homo sapiens, female)HEK293TATCCcat# CRL-3216; RRID:CVCL_0063
Cell line (M. musculus, male)3T3-L1ATCCcat# CL-173; RRID:CVCL_0123
Recombinant DNA reagentpLPC empty vectorThis paper
Recombinant DNA reagentpLPC-IDH1 wildtypeThis paper
Recombinant DNA reagentpLPC-IDH1R132HThis paper
Recombinant DNA reagentpLPC-IDH2 wildtypeThis paper
Recombinant DNA reagentpLPC-IDH2R172KThis paper
Antibodyrabbit anti-H3Cell Signaling
Technology,		cat# 4499; clone D1H2; RRID:AB_105445371:1000 dilution
Antibodyrabbit anti-H3K4me3Milliporecat# 17–614; RRID:AB_112127701:2000 dilution
Antibodyrabbit anti-H3K36me3Abcamcat# ab9050; RRID:AB_3069661 µg/ml dilution
Antibodyrabbit anti-H3K79me2Cell Signaling
Technology		cat# 9757; RRID:AB_21184481:1000 dilution
Antibodyrabbit anti-H3K9me2Cell Signaling
Technology		cat# 9753; RRID:AB_6598481:1000 dilution
Antibodyrabbit anti-H3K9me3Abcamcat# ab8898; RRID:AB_3068481 µg/ml dilution
Antibodyrabbit anti-IDH1Proteintechcat# 12332-1-AP; RRID:AB_21231591:1500 dilution
Antibodymouse anti-IDH2Abcamcat# ab55271; clone 5F11; RRID:AB_9437931 µg/ml dilution
Software, algorithmR project for statistical computinghttps://www.r-project.orgRRID:SCR_001905Version 4.1.0
Software, algorithmmetafordoi:10.18637/jss.v036.i03RRID:SCR_003450Version 3.0-2

Additional files

Transparent reporting form
https://cdn.elifesciences.org/articles/73430/elife-73430-transrepform1-v1.docx

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