NCI-60 Human Cancer Cell Line Panel (cellline_nci60)

Overview

The NCI-60 is a panel of 60 human cancer cell lines spanning 9 tissue types, maintained by the NCI Developmental Therapeutics Program (DTP). The CellMiner database integrates multi-platform genomic, transcriptomic, and drug activity data from this panel. Transcript data from 5 microarray platforms (Affymetrix HG-U95, HG-U133, HG-U133 Plus 2.0, GeneChip Human Exon 1.0 ST; Agilent Whole Human Genome Oligo Microarray) cover 22,217 genes. Drug activity data includes GI50 values for 18,549 compounds from 47,540 tested, determined by sulforhodamine B assay at 48 hours.

Composition

  • 60 cancer cell lines across 9 tissue types including colon (COAD), lung, breast, ovary, kidney, prostate, CNS, melanoma, and leukemia.
  • MicroRNA data: 360 microRNAs from Agilent Human miRNA Microarray V2.
  • Drug activity: GI50 for 18,549 compounds via NCI DTP.

Assays / panels (linked)

  • cellminer — integrated database and pattern comparison tool for NCI-60 multi-omics and drug activity data.
  • 5 Affymetrix/Agilent microarray platforms — mRNA expression (22,217 genes).
  • Agilent Human miRNA Microarray V2 — 360 microRNAs.
  • Sulforhodamine B (SRB) assay — 48-hour GI50 drug activity.

Papers using this cohort

  • PMID:22802077 — CellMiner: a web-based suite of genomic and pharmacological tools to explore transcript and drug patterns in the NCI-60 cell line set (Reinhold et al., 2012).

Notable findings derived from this cohort

  • ABCB1 overexpression in NCI-ADR-RES and HCT-15 cell lines correlates with doxorubicin resistance via P-glycoprotein-mediated efflux PMID:22802077.
  • Erlotinib drug activity pattern retrieves gefitinib, lapatinib (5th and 6th), and afatinib (3rd) among 18,549 compounds, demonstrating EGFR-class clustering PMID:22802077.
  • Colon-specific expression pattern identifies RNF43, TRIM15, and VIL1 as top correlated colon cancer marker genes PMID:22802077.
  • miR-17-92 oncogenic cluster members show high inter-correlation (r=0.77–0.96) and MYC correlation (r=0.61) consistent with MYC-driven transcription PMID:22802077.
  • selumetinib and sunitinib identified as candidate colorectal cancer therapies via colon-specific drug pattern matching PMID:22802077.

Sources

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