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Cancer Cell Line Panels Empower Genomics-Based Discovery of Precision Cancer Medicine.

Kim HS, Sung YJ, Paik S - Yonsei Med. J. (2015)

Bottom Line: Cancer cell lines have made significant contributions to the development of various chemotherapeutic agents.Different types of statistical and machine learning algorithms have been developed to analyze the large-scale data sets that have been produced.However, much work remains to address the discrepancies in drug assay results from different platforms and the frequent failures to translate discoveries from cell line models to the clinic.

View Article: PubMed Central - PubMed

Affiliation: Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.

ABSTRACT
Since the first human cancer cell line, HeLa, was established in the early 1950s, there has been a steady increase in the number and tumor type of available cancer cell line models. Cancer cell lines have made significant contributions to the development of various chemotherapeutic agents. Recent advances in multi-omics technologies have facilitated detailed characterizations of the genomic, transcriptomic, proteomic, and epigenomic profiles of these cancer cell lines. An increasing number of studies employ the power of a cancer cell line panel to provide predictive biomarkers for targeted and cytotoxic agents, including those that are already used in clinical practice. Different types of statistical and machine learning algorithms have been developed to analyze the large-scale data sets that have been produced. However, much work remains to address the discrepancies in drug assay results from different platforms and the frequent failures to translate discoveries from cell line models to the clinic. Nevertheless, continuous expansion of cancer cell line panels should provide unprecedented opportunities to identify new candidate targeted therapies, particularly for the so-called "dark matter" group of cancers, for which pharmacologically tractable driver mutations have not been identified.

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Related in: MedlinePlus

A compendium of established cancer cell line models and the number of associated multi-omics data sets are represented as heatmaps for each of the 12 major tumor types. See Table 1 for the list of relevant studies that were used to generate this figure.
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Figure 1: A compendium of established cancer cell line models and the number of associated multi-omics data sets are represented as heatmaps for each of the 12 major tumor types. See Table 1 for the list of relevant studies that were used to generate this figure.

Mentions: To identify the factors underlying tumor diversity, initial efforts focused on targeted sequencing of commonly mutated genes.154546 Identified somatic DNA alterations from primary and metastatic tumors as well as from established cancer cell lines have been deposited in the Catalog of Somatic Mutations in Cancer database. The information in this database is professionally curated with published literature regardless of the discovery platform.47 Recently innovated platforms in microarray and NGS technology have allowed more in-depth and high-resolution profiling of cancer variations, including gene expression changes in various cancer cell lines4849 and genome and exome level deciphering of DNA variations at relatively low cost. In addition, epigenomic50 and proteomic profiles are also beginning to be employed for such analyses.51 These multi-omics characterizations of cancer cell lines have been pursued for various lineages of tumors, including breast,46525354 lung,45555657 gastric,58 melanoma,12 pancreatic,1459 colorectal,1360 glioblastoma,61 ovarian,1130 prostate,1516 and pan-cancer lines.19212223254962 The annotated established cancer cell lines for 12 major solid tumor types have been surveyed and summarized with respect to the type of assay and depth of corresponding orthogonal data sets (Fig. 1).


Cancer Cell Line Panels Empower Genomics-Based Discovery of Precision Cancer Medicine.

Kim HS, Sung YJ, Paik S - Yonsei Med. J. (2015)

A compendium of established cancer cell line models and the number of associated multi-omics data sets are represented as heatmaps for each of the 12 major tumor types. See Table 1 for the list of relevant studies that were used to generate this figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4541646&req=5

Figure 1: A compendium of established cancer cell line models and the number of associated multi-omics data sets are represented as heatmaps for each of the 12 major tumor types. See Table 1 for the list of relevant studies that were used to generate this figure.
Mentions: To identify the factors underlying tumor diversity, initial efforts focused on targeted sequencing of commonly mutated genes.154546 Identified somatic DNA alterations from primary and metastatic tumors as well as from established cancer cell lines have been deposited in the Catalog of Somatic Mutations in Cancer database. The information in this database is professionally curated with published literature regardless of the discovery platform.47 Recently innovated platforms in microarray and NGS technology have allowed more in-depth and high-resolution profiling of cancer variations, including gene expression changes in various cancer cell lines4849 and genome and exome level deciphering of DNA variations at relatively low cost. In addition, epigenomic50 and proteomic profiles are also beginning to be employed for such analyses.51 These multi-omics characterizations of cancer cell lines have been pursued for various lineages of tumors, including breast,46525354 lung,45555657 gastric,58 melanoma,12 pancreatic,1459 colorectal,1360 glioblastoma,61 ovarian,1130 prostate,1516 and pan-cancer lines.19212223254962 The annotated established cancer cell lines for 12 major solid tumor types have been surveyed and summarized with respect to the type of assay and depth of corresponding orthogonal data sets (Fig. 1).

Bottom Line: Cancer cell lines have made significant contributions to the development of various chemotherapeutic agents.Different types of statistical and machine learning algorithms have been developed to analyze the large-scale data sets that have been produced.However, much work remains to address the discrepancies in drug assay results from different platforms and the frequent failures to translate discoveries from cell line models to the clinic.

View Article: PubMed Central - PubMed

Affiliation: Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.

ABSTRACT
Since the first human cancer cell line, HeLa, was established in the early 1950s, there has been a steady increase in the number and tumor type of available cancer cell line models. Cancer cell lines have made significant contributions to the development of various chemotherapeutic agents. Recent advances in multi-omics technologies have facilitated detailed characterizations of the genomic, transcriptomic, proteomic, and epigenomic profiles of these cancer cell lines. An increasing number of studies employ the power of a cancer cell line panel to provide predictive biomarkers for targeted and cytotoxic agents, including those that are already used in clinical practice. Different types of statistical and machine learning algorithms have been developed to analyze the large-scale data sets that have been produced. However, much work remains to address the discrepancies in drug assay results from different platforms and the frequent failures to translate discoveries from cell line models to the clinic. Nevertheless, continuous expansion of cancer cell line panels should provide unprecedented opportunities to identify new candidate targeted therapies, particularly for the so-called "dark matter" group of cancers, for which pharmacologically tractable driver mutations have not been identified.

Show MeSH
Related in: MedlinePlus