National Cancer Institute - US
https://discover.nci.nih.gov/
RRID: RRID:SCR_025664
1.) Arakawa Y, Elloumi F, Varma S, Khandagale P, Jo U, Kumar S, Roper N, Reinhold WC, Robey RW, Takebe N, Gottesman MM, Thomas CJ, Boeva V, Berruti A, Abate A, Tamburello M, Sigala S, Hantel C, Weigand I, Wierman ME, Kiseljak-Vassiliades K, Del Rivero J, Pommier Y (2024 Sep 1). A Database Tool Integrating Genomic and Pharmacologic Data from Adrenocortical Carcinoma Cell Lines, PDX, and Patient Samples. Cancer research communications, 4(9), 2384-2398. . PMID: 39162009.
2.) Mizunuma M, Redon CE, Saha LK, Tran AD, Dhall A, Sebastian R, Taniyama D, Kruhlak MJ, Reinhold WC, Takebe N, Pommier Y (2024 Aug 1). Acetalax (Oxyphenisatin Acetate, NSC 59687) and Bisacodyl Cause Oncosis in Triple-Negative Breast Cancer Cell Lines by Poisoning the Ion Exchange Membrane Protein TRPM4. Cancer research communications, 4(8), 2101-2111. . PMID: 39041239.
3.) Tlemsani C, Heske CM, Elloumi F, Pongor L, Khandagale P, Varma S, Luna A, Meltzer PS, Khan J, Reinhold WC, Pommier Y (2024 Jun 21). Sarcoma_CellminerCDB: A tool to interrogate the genomic and functional characteristics of a comprehensive collection of sarcoma cell lines. iScience, 27(6), 109781. . PMID: 38868205.
4.) Reinhold WC, Wilson K, Elloumi F, Bradwell KR, Ceribelli M, Varma S, Wang Y, Duveau D, Menon N, Trepel J, Zhang X, Klumpp-Thomas C, Micheal S, Shinn P, Luna A, Thomas C, Pommier Y (2023 Jun 15). CellMinerCDB: NCATS Is a Web-Based Portal Integrating Public Cancer Cell Line Databases for Pharmacogenomic Explorations. Cancer research, 83(12), 1941-1952. . PMID: 37140427.
5.) Pommier Y, Thomas A (2023 Mar 14). New Life of Topoisomerase I Inhibitors as Antibody-Drug Conjugate Warheads. Clinical cancer research : an official journal of the American Association for Cancer Research, 29(6), 991-993. . PMID: 36637483.
6.) Pongor LS, Tlemsani C, Elloumi F, Arakawa Y, Jo U, Gross JM, Mosavarpour S, Varma S, Kollipara RK, Roper N, Teicher BA, Aladjem MI, Reinhold W, Thomas A, Minna JD, Johnson JE, Pommier Y (2022 Nov 18). Integrative epigenomic analyses of small cell lung cancer cells demonstrates the clinical translational relevance of gene body methylation. iScience, 25(11), 105338. . PMID: 36325065.
7.) Luna A, Elloumi F, Varma S, Wang Y, Rajapakse VN, Aladjem MI, Robert J, Sander C, Pommier Y, Reinhold WC (2021 Jan 8). CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. Nucleic acids research, 49(), D1083-D1093. . PMID: 33196823.
8.) Tlemsani C, Pongor L, Elloumi F, Girard L, Huffman KE, Roper N, Varma S, Luna A, Rajapakse VN, Sebastian R, Kohn KW, Krushkal J, Aladjem MI, Teicher BA, Meltzer PS, Reinhold WC, Minna JD, Thomas A, Pommier Y (2020 Oct 20). SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures. Cell reports, 33(3), 108296. . PMID: 33086069.
9.) Reinhold WC, Elloumi F, Varma S, Robert J, Mills GB, Pommier Y (2020 Oct). Candidate biomarker assessment for pharmacological response. Translational oncology, 13(10), 100830. . PMID: 32652468.
10.) Hassan R, Sengupta M, Murai J, Pommier Y (2020 Jun). Response to Letter to the Editor by Yang et al. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer, 15(6), e91. doi: 10.1016/j.jtho.2020.03.033. PMID: 32471568.
11.) Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R (2019 Nov 22). Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. iScience, 21(), 664-680. . PMID: 31733513.
12.) Marzi L, Szabova L, Gordon M, Weaver Ohler Z, Sharan SK, Beshiri ML, Etemadi M, Murai J, Kelly K, Pommier Y (2019 Oct 15). The Indenoisoquinoline TOP1 Inhibitors Selectively Target Homologous Recombination-Deficient and Schlafen 11-Positive Cancer Cells and Synergize with Olaparib. Clinical cancer research : an official journal of the American Association for Cancer Research, 25(20), 6206-6216. . PMID: 31409613.
13.) Reinhold WC, Varma S, Sunshine M, Elloumi F, Ofori-Atta K, Lee S, Trepel JB, Meltzer PS, Doroshow JH, Pommier Y (2019 Jul 1). RNA Sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB. Cancer research, 79(13), 3514-3524. . PMID: 31113817.
14.) Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y (2018 Dec 21). CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines. iScience, 10(), 247-264. . PMID: 30553813.
15.) Marzi L, Agama K, Murai J, Difilippantonio S, James A, Peer CJ, Figg WD, Beck D, Elsayed MSA, Cushman M, Pommier Y (2018 Aug). Novel Fluoroindenoisoquinoline Non-Camptothecin Topoisomerase I Inhibitors. Molecular cancer therapeutics, 17(8), 1694-1704. . PMID: 29748210.
16.) Thomas A, Tanaka M, Trepel J, Reinhold WC, Rajapakse VN, Pommier Y (2017 Feb 15). Temozolomide in the Era of Precision Medicine. Cancer research, 77(4), 823-826. . PMID: 28159862.
17.) Reinhold WC, Varma S, Sunshine M, Rajapakse V, Luna A, Kohn KW, Stevenson H, Wang Y, Heyn H, Nogales V, Moran S, Goldstein DJ, Doroshow JH, Meltzer PS, Esteller M, Pommier Y (2017 Feb 1). The NCI-60 Methylome and Its Integration into CellMiner. Cancer research, 77(3), 601-612. . PMID: 27923837.
18.) Murai J, Feng Y, Yu GK, Ru Y, Tang SW, Shen Y, Pommier Y (2016 Nov 22). Resistance to PARP inhibitors by SLFN11 inactivation can be overcome by ATR inhibition. Oncotarget, 7(47), 76534-76550. . PMID: 27708213.
19.) Quadri M, Olgiati S, Sensi M, Gualandi F, Groppo E, Rispoli V, Graafland J, Breedveld GJ, Fabbrini G, Berardelli A, Bonifati V (2016 May). PRKRA Mutation Causing Early-Onset Generalized Dystonia-Parkinsonism (DYT16) in an Italian Family. Movement disorders : official journal of the Movement Disorder Society, 31(5), 765-7. doi: 10.1002/mds.26583. PMID: 26990861.
20.) Tripathi S, Belkacemi L, Cheung MS, Bose RN (2016). Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers. Cancer informatics, 15(), 1-13. . PMID: 26819545.
21.) Reinhold WC, Sunshine M, Liu H, Varma S, Kohn KW, Morris J, Doroshow J, Pommier Y (2012 Jul 15). CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer research, 72(14), 3499-511. . PMID: 22802077.
22.) Zoppoli G, Solier S, Reinhold WC, Liu H, Connelly JW Jr, Monks A, Shoemaker RH, Abaan OD, Davis SR, Meltzer PS, Doroshow JH, Pommier Y (2012 Jan 26). CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute. Oncogene, 31(4), 403-18. . PMID: 21765476.
23.) Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW (2011 Aug 1). PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics (Oxford, England), 27(15), 2165-6. . PMID: 21636591.
24.) Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW (2011 May 17). A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC bioinformatics, 12(), 167. . PMID: 21586134.
25.) Kahn AB, Zeeberg BR, Ryan MC, Jamison DC, Rockoff DM, Pommier Y, Weinstein JN (2010 Aug 15). Ontogenomic study of the relationship between number of gene splice variants and GO categorization. Bioinformatics (Oxford, England), 26(16), 1945-9. . PMID: 20616384.
26.) Reinhold WC, Mergny JL, Liu H, Ryan M, Pfister TD, Kinders R, Parchment R, Doroshow J, Weinstein JN, Pommier Y (2010 Mar 15). Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron. Cancer research, 70(6), 2191-203. . PMID: 20215517.
27.) Shankavaram UT, Varma S, Kane D, Sunshine M, Chary KK, Reinhold WC, Pommier Y, Weinstein JN (2009 Jun 23). CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC genomics, 10(), 277. . PMID: 19549304.
28.) Mikheev AM, Nabekura T, Kaddoumi A, Bammler TK, Govindarajan R, Hebert MF, Unadkat JD (2008 Nov). Profiling gene expression in human placentae of different gestational ages: an OPRU Network and UW SCOR Study. Reproductive sciences (Thousand Oaks, Calif.), 15(9), 866-77. . PMID: 19050320.
29.) Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN (2008 Jul 18). SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC bioinformatics, 9(), 313. . PMID: 18638396.
30.) Liu H, Zeeberg BR, Qu G, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC, Kane DW, Weinstein JN (2007 Sep 15). AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics (Oxford, England), 23(18), 2385-90. . PMID: 17660211.
31.) Shankavaram UT, Reinhold WC, Nishizuka S, Major S, Morita D, Chary KK, Reimers MA, Scherf U, Kahn A, Dolginow D, Cossman J, Kaldjian EP, Scudiero DA, Petricoin E, Liotta L, Lee JK, Weinstein JN (2007 Mar). Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study. Molecular cancer therapeutics, 6(3), 820-32. . PMID: 17339364.
32.) Blum R, Jacob-Hirsch J, Rechavi G, Kloog Y (2006 Sep). Suppression of survivin expression in glioblastoma cells by the Ras inhibitor farnesylthiosalicylic acid promotes caspase-dependent apoptosis. Molecular cancer therapeutics, 5(9), 2337-47. . PMID: 16985068.
33.) Liao Z, Thibaut L, Jobson A, Pommier Y (2006 Jul). Inhibition of human tyrosyl-DNA phosphodiesterase by aminoglycoside antibiotics and ribosome inhibitors. Molecular pharmacology, 70(1), 366-72. . PMID: 16618796.
34.) Stewart JJ, White JT, Yan X, Collins S, Drescher CW, Urban ND, Hood L, Lin B (2006 Mar). Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels. Molecular & cellular proteomics : MCP, 5(3), 433-43. . PMID: 16319398.
35.) Kohn KW, Aladjem MI, Kim S, Weinstein JN, Pommier Y (2006). Depicting combinatorial complexity with the molecular interaction map notation. Molecular systems biology, 2(), 51. . PMID: 17016517.
36.) Reimers M, Weinstein JN (2005 Jul 1). Quality assessment of microarrays: visualization of spatial artifacts and quantitation of regional biases. BMC bioinformatics, 6(), 166. . PMID: 15992406.
37.) Kohn KW, Pommier Y (2005 Jun 10). Molecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage. Biochemical and biophysical research communications, 331(3), 816-27. . PMID: 15865937.
38.) Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, Waltham M, Kouros-Mehr H, Bussey KJ, Lee JK, Espina V, Munson PJ, Petricoin E 3rd, Liotta LA, Weinstein JN (2003 Nov 25). Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proceedings of the National Academy of Sciences of the United States of America, 100(24), 14229-34. . PMID: 14623978.
39.) Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN (2000 Mar). A gene expression database for the molecular pharmacology of cancer. Nature genetics, 24(3), 236-44. . PMID: 10700175.
40.) Weinstein JN, Pommier Y (2003 Oct-Nov). Transcriptomic analysis of the NCI-60 cancer cell lines. Comptes rendus biologies, 326(10), 909-20. . PMID: 14744097.
A pharmacogenomics resource for study of cancer. Multiple tools are available, currently including the CellMiner family with CellMiner, CellMinerCDB (cross data-base), CellMinerCDB: Small Cell Lung Cancer (SCLC), CellMinerCDB: National Center for Advancing Translational Sciences (NCATS) andCellMinerCDB: Sarcoma. These sites include multiple cancerous cell lines sets and data types. In addition there is CIMMiner for cluster image maps and MIMminer, with several scholarly molecular interaction maps.
