Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2022-05-07

AUTHORS

Hari Sankaran, Simarjeet Negi, Lisa M. McShane, Yingdong Zhao, Julia Krushkal

ABSTRACT

BackgroundIndian natural products have been anecdotally used for cancer treatment but with limited efficacy. To better understand their mechanism, we examined the publicly available data for the activity of Indian natural products in the NCI-60 cell line panel.MethodsWe examined associations of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 75 compounds derived from Indian plant-based natural products. We analyzed expression measures for annotated transcripts, lncRNAs, and miRNAs, and protein-changing single nucleotide variants in cancer-related genes. We also examined the similarities between cancer cell line response to Indian natural products and response to reference anti-tumor compounds recorded in a U.S. National Cancer Institute (NCI) Developmental Therapeutics Program database.ResultsHierarchical clustering based on cell line response measures identified clustering of Phyllanthus and cucurbitacin products with known anti-tumor agents with anti-mitotic mechanisms of action. Curcumin and curcuminoids mostly clustered together. We found associations of response to Indian natural products with expression of multiple genes, notably including SLC7A11 involved in solute transport and ATAD3A and ATAD3B encoding mitochondrial ATPase proteins, as well as significant associations with functional single nucleotide variants, including BRAF V600E.ConclusionThese findings suggest potential mechanisms of action and novel associations of in vitro response with gene expression and some cancer-related mutations that increase our understanding of these Indian natural products. More... »

PAGES

512

References to SciGraph publications

  • 2010-04. Translational control in cancer in NATURE REVIEWS CANCER
  • 2016-01-25. Nimbolide inhibits pancreatic cancer growth and metastasis through ROS-mediated apoptosis and inhibition of epithelial-to-mesenchymal transition in SCIENTIFIC REPORTS
  • 2021-05-12. DHODH-mediated ferroptosis defence is a targetable vulnerability in cancer in NATURE
  • 2008-07. MYB function in normal and cancer cells in NATURE REVIEWS CANCER
  • 2000-03. A gene expression database for the molecular pharmacology of cancer in NATURE GENETICS
  • 2006-10-01. The NCI60 human tumour cell line anticancer drug screen in NATURE REVIEWS CANCER
  • 2013-07-29. Tylophorine, a phenanthraindolizidine alkaloid isolated from Tylophora indica exerts antiangiogenic and antitumor activity by targeting vascular endothelial growth factor receptor 2–mediated angiogenesis in MOLECULAR CANCER
  • 2013-07-06. Patients with advanced cancer and their usage of complementary and alternative medicine in JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
  • 2017-03-28. Inhibiting the system xC−/glutathione axis selectively targets cancers with mutant-p53 accumulation in NATURE COMMUNICATIONS
  • 2012-10-12. Cucurbitacin B inhibits human breast cancer cell proliferation through disruption of microtubule polymerization and nucleophosmin/B23 translocation in BMC COMPLEMENTARY MEDICINE AND THERAPIES
  • 2020-04-03. Review on natural products databases: where to find data in 2020 in JOURNAL OF CHEMINFORMATICS
  • 2014-12-01. Apoptosis induction by an analog of curcumin (BDMC-A) in human laryngeal carcinoma cells through intrinsic and extrinsic pathways in CELLULAR ONCOLOGY
  • 2011-02-07. Curcumin: A review of anti-cancer properties and therapeutic activity in head and neck squamous cell carcinoma in MOLECULAR CANCER
  • 2008-03-18. Merger of Ayurveda and Tissue Culture-Based Functional Genomics: Inspirations from Systems Biology in JOURNAL OF TRANSLATIONAL MEDICINE
  • 2018-03-12. IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics in SCIENTIFIC REPORTS
  • 2004-05. Profile identification of disease-associated humoral antigens using AMIDA, a novel proteomics-based technology in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2018-01-16. Plumbagin inhibits the proliferation and survival of esophageal cancer cells by blocking STAT3-PLK1-AKT signaling in CELL DEATH & DISEASE
  • 2020-10-01. Cystine transporter SLC7A11/xCT in cancer: ferroptosis, nutrient dependency, and cancer therapy in PROTEIN & CELL
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s12885-022-09580-7

    DOI

    http://dx.doi.org/10.1186/s12885-022-09580-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1147717461

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35525914


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/11", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Medical and Health Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1112", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Oncology and Carcinogenesis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "ATPases Associated with Diverse Cellular Activities", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Antineoplastic Agents", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Biological Products", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Cell Line, Tumor", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Membrane Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mitochondrial Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "National Cancer Institute (U.S.)", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Neoplasms", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Nucleotides", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Pharmacogenetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "United States", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sankaran", 
            "givenName": "Hari", 
            "id": "sg:person.014637111012.05", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014637111012.05"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Negi", 
            "givenName": "Simarjeet", 
            "id": "sg:person.01302247036.73", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01302247036.73"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "McShane", 
            "givenName": "Lisa M.", 
            "id": "sg:person.01111206713.59", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01111206713.59"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zhao", 
            "givenName": "Yingdong", 
            "id": "sg:person.010430056017.20", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010430056017.20"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.48336.3a", 
              "name": [
                "Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Krushkal", 
            "givenName": "Julia", 
            "id": "sg:person.01110513472.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110513472.52"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/s13321-020-00424-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1126125760", 
              "https://doi.org/10.1186/s13321-020-00424-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41419-017-0068-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1100423673", 
              "https://doi.org/10.1038/s41419-017-0068-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1479-5876-6-14", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024807464", 
              "https://doi.org/10.1186/1479-5876-6-14"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41598-018-22631-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101436531", 
              "https://doi.org/10.1038/s41598-018-22631-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00018-004-4045-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007150241", 
              "https://doi.org/10.1007/s00018-004-4045-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1476-4598-12-82", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034170601", 
              "https://doi.org/10.1186/1476-4598-12-82"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc2439", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049875030", 
              "https://doi.org/10.1038/nrc2439"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep19819", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024238151", 
              "https://doi.org/10.1038/srep19819"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s13402-014-0207-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038776177", 
              "https://doi.org/10.1007/s13402-014-0207-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc1951", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053488336", 
              "https://doi.org/10.1038/nrc1951"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1472-6882-12-185", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017427268", 
              "https://doi.org/10.1186/1472-6882-12-185"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms14844", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084129032", 
              "https://doi.org/10.1038/ncomms14844"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s13238-020-00789-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1131331578", 
              "https://doi.org/10.1007/s13238-020-00789-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrc2824", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027786679", 
              "https://doi.org/10.1038/nrc2824"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/73439", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017120232", 
              "https://doi.org/10.1038/73439"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00432-013-1460-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002500108", 
              "https://doi.org/10.1007/s00432-013-1460-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-021-03539-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1137958722", 
              "https://doi.org/10.1038/s41586-021-03539-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1476-4598-10-12", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011423539", 
              "https://doi.org/10.1186/1476-4598-10-12"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2022-05-07", 
        "datePublishedReg": "2022-05-07", 
        "description": "BackgroundIndian natural products have been anecdotally used for cancer treatment but with limited efficacy. To better understand their mechanism, we examined the publicly available data for the activity of Indian natural products in the NCI-60 cell line panel.MethodsWe examined associations of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 75 compounds derived from Indian plant-based natural products. We analyzed expression measures for annotated transcripts, lncRNAs, and miRNAs, and protein-changing single nucleotide variants in cancer-related genes. We also examined the similarities between cancer cell line response to Indian natural products and response to reference anti-tumor compounds recorded in a U.S. National Cancer Institute (NCI) Developmental Therapeutics Program database.ResultsHierarchical clustering based on cell line response measures identified clustering of Phyllanthus and cucurbitacin products with known anti-tumor agents with anti-mitotic mechanisms of action. Curcumin and curcuminoids mostly clustered together. We found associations of response to Indian natural products with expression of multiple genes, notably including SLC7A11 involved in solute transport and ATAD3A and ATAD3B encoding mitochondrial ATPase proteins, as well as significant associations with functional single nucleotide variants, including BRAF V600E.ConclusionThese findings suggest potential mechanisms of action and novel associations of in vitro response with gene expression and some cancer-related mutations that increase our understanding of these Indian natural products.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s12885-022-09580-7", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1024632", 
            "issn": [
              "1471-2407"
            ], 
            "name": "BMC Cancer", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "22"
          }
        ], 
        "keywords": [
          "single nucleotide variants", 
          "cell line panel", 
          "NCI-60 cancer cell line panel", 
          "nucleotide variants", 
          "cancer cell line panel", 
          "line panel", 
          "cancer cell line response", 
          "functional single nucleotide variants", 
          "cancer-related mutations", 
          "natural products", 
          "cancer-related genes", 
          "genomic features", 
          "multiple genes", 
          "gene expression", 
          "plant-based natural products", 
          "cell line response", 
          "ATPase protein", 
          "NCI-60 cell line panel", 
          "anti-tumor compounds", 
          "expression measures", 
          "novel associations", 
          "genes", 
          "anti-tumor agents", 
          "potential mechanisms", 
          "expression", 
          "ATAD3B", 
          "ATAD3A", 
          "miRNAs", 
          "lncRNAs", 
          "transcripts", 
          "variants", 
          "mechanism", 
          "protein", 
          "SLC7A11", 
          "mutations", 
          "line response", 
          "response", 
          "cancer treatment", 
          "similarity", 
          "Phyllanthus", 
          "pharmacogenomics", 
          "association", 
          "products", 
          "compounds", 
          "clustering", 
          "panel", 
          "activity", 
          "action", 
          "transport", 
          "understanding", 
          "available data", 
          "solute transport", 
          "significant association", 
          "curcumin", 
          "agents", 
          "limited efficacy", 
          "treatment", 
          "findings", 
          "database", 
          "curcuminoids", 
          "data", 
          "features", 
          "MethodsWe", 
          "association of response", 
          "efficacy", 
          "measures", 
          "response measures", 
          "Program database"
        ], 
        "name": "Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products", 
        "pagination": "512", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1147717461"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s12885-022-09580-7"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "35525914"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s12885-022-09580-7", 
          "https://app.dimensions.ai/details/publication/pub.1147717461"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-06-01T22:25", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_943.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s12885-022-09580-7"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s12885-022-09580-7'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12885-022-09580-7'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12885-022-09580-7'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12885-022-09580-7'


     

    This table displays all metadata directly associated to this object as RDF triples.

    277 TRIPLES      22 PREDICATES      124 URIs      98 LITERALS      19 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s12885-022-09580-7 schema:about N250cbfc3763547f3a9983218854ef92e
    2 N36f56f3fbbe442cc8d6a9be8088fa333
    3 N5b2fb92cc2684620a4dfe4ceafd800b4
    4 N679bcc37075d419e9fc626a5d7fcb869
    5 N74b4bf773fc94cb1872bc31ea6706bbf
    6 N7c0fb9f87b814fe3a8b1cc3c45a3a6c3
    7 N8c56e8d56ce5483f95c234c5d13e6988
    8 Na77c9dc1f3834141bd83e66c97b00a49
    9 Nacd74f4f34bf4821a7f27c3cab0134a8
    10 Ncf9f8bb0d3dc429ab13553d6c47e9872
    11 Ndaf5ff611c7944ef95de8cd4b8d29769
    12 Ne62d6b535cf64a39acb80ddc4e7bfefc
    13 anzsrc-for:11
    14 anzsrc-for:1112
    15 schema:author Nafa59fd227564fa1943554390c27913d
    16 schema:citation sg:pub.10.1007/s00018-004-4045-8
    17 sg:pub.10.1007/s00432-013-1460-y
    18 sg:pub.10.1007/s13238-020-00789-5
    19 sg:pub.10.1007/s13402-014-0207-3
    20 sg:pub.10.1038/73439
    21 sg:pub.10.1038/ncomms14844
    22 sg:pub.10.1038/nrc1951
    23 sg:pub.10.1038/nrc2439
    24 sg:pub.10.1038/nrc2824
    25 sg:pub.10.1038/s41419-017-0068-6
    26 sg:pub.10.1038/s41586-021-03539-7
    27 sg:pub.10.1038/s41598-018-22631-z
    28 sg:pub.10.1038/srep19819
    29 sg:pub.10.1186/1472-6882-12-185
    30 sg:pub.10.1186/1476-4598-10-12
    31 sg:pub.10.1186/1476-4598-12-82
    32 sg:pub.10.1186/1479-5876-6-14
    33 sg:pub.10.1186/s13321-020-00424-9
    34 schema:datePublished 2022-05-07
    35 schema:datePublishedReg 2022-05-07
    36 schema:description BackgroundIndian natural products have been anecdotally used for cancer treatment but with limited efficacy. To better understand their mechanism, we examined the publicly available data for the activity of Indian natural products in the NCI-60 cell line panel.MethodsWe examined associations of molecular genomic features in the well-characterized NCI-60 cancer cell line panel with in vitro response to treatment with 75 compounds derived from Indian plant-based natural products. We analyzed expression measures for annotated transcripts, lncRNAs, and miRNAs, and protein-changing single nucleotide variants in cancer-related genes. We also examined the similarities between cancer cell line response to Indian natural products and response to reference anti-tumor compounds recorded in a U.S. National Cancer Institute (NCI) Developmental Therapeutics Program database.ResultsHierarchical clustering based on cell line response measures identified clustering of Phyllanthus and cucurbitacin products with known anti-tumor agents with anti-mitotic mechanisms of action. Curcumin and curcuminoids mostly clustered together. We found associations of response to Indian natural products with expression of multiple genes, notably including SLC7A11 involved in solute transport and ATAD3A and ATAD3B encoding mitochondrial ATPase proteins, as well as significant associations with functional single nucleotide variants, including BRAF V600E.ConclusionThese findings suggest potential mechanisms of action and novel associations of in vitro response with gene expression and some cancer-related mutations that increase our understanding of these Indian natural products.
    37 schema:genre article
    38 schema:inLanguage en
    39 schema:isAccessibleForFree true
    40 schema:isPartOf N4c60789a4d064b568306af58dedcc02b
    41 Nd6dd10cf6d0a44fe8acde92438ae9c24
    42 sg:journal.1024632
    43 schema:keywords ATAD3A
    44 ATAD3B
    45 ATPase protein
    46 MethodsWe
    47 NCI-60 cancer cell line panel
    48 NCI-60 cell line panel
    49 Phyllanthus
    50 Program database
    51 SLC7A11
    52 action
    53 activity
    54 agents
    55 anti-tumor agents
    56 anti-tumor compounds
    57 association
    58 association of response
    59 available data
    60 cancer cell line panel
    61 cancer cell line response
    62 cancer treatment
    63 cancer-related genes
    64 cancer-related mutations
    65 cell line panel
    66 cell line response
    67 clustering
    68 compounds
    69 curcumin
    70 curcuminoids
    71 data
    72 database
    73 efficacy
    74 expression
    75 expression measures
    76 features
    77 findings
    78 functional single nucleotide variants
    79 gene expression
    80 genes
    81 genomic features
    82 limited efficacy
    83 line panel
    84 line response
    85 lncRNAs
    86 measures
    87 mechanism
    88 miRNAs
    89 multiple genes
    90 mutations
    91 natural products
    92 novel associations
    93 nucleotide variants
    94 panel
    95 pharmacogenomics
    96 plant-based natural products
    97 potential mechanisms
    98 products
    99 protein
    100 response
    101 response measures
    102 significant association
    103 similarity
    104 single nucleotide variants
    105 solute transport
    106 transcripts
    107 transport
    108 treatment
    109 understanding
    110 variants
    111 schema:name Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products
    112 schema:pagination 512
    113 schema:productId Na2f5a880f1bd49b89c1bda83fcf67dd7
    114 Ne15fb4d97de84919a6863506e710760f
    115 Nfdd039b68f674e0591ee76f11dfdffef
    116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1147717461
    117 https://doi.org/10.1186/s12885-022-09580-7
    118 schema:sdDatePublished 2022-06-01T22:25
    119 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    120 schema:sdPublisher N4f5c40b963af406b8be499453f08a40e
    121 schema:url https://doi.org/10.1186/s12885-022-09580-7
    122 sgo:license sg:explorer/license/
    123 sgo:sdDataset articles
    124 rdf:type schema:ScholarlyArticle
    125 N0daa49896ca942508effae6ce811f1a9 rdf:first sg:person.010430056017.20
    126 rdf:rest Ne35d493a5e8f4054b4b389267628b6dd
    127 N250cbfc3763547f3a9983218854ef92e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    128 schema:name Nucleotides
    129 rdf:type schema:DefinedTerm
    130 N36f56f3fbbe442cc8d6a9be8088fa333 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    131 schema:name Mitochondrial Proteins
    132 rdf:type schema:DefinedTerm
    133 N4c60789a4d064b568306af58dedcc02b schema:volumeNumber 22
    134 rdf:type schema:PublicationVolume
    135 N4f5c40b963af406b8be499453f08a40e schema:name Springer Nature - SN SciGraph project
    136 rdf:type schema:Organization
    137 N5b2fb92cc2684620a4dfe4ceafd800b4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    138 schema:name Antineoplastic Agents
    139 rdf:type schema:DefinedTerm
    140 N679bcc37075d419e9fc626a5d7fcb869 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    141 schema:name ATPases Associated with Diverse Cellular Activities
    142 rdf:type schema:DefinedTerm
    143 N74b4bf773fc94cb1872bc31ea6706bbf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    144 schema:name Humans
    145 rdf:type schema:DefinedTerm
    146 N7c0fb9f87b814fe3a8b1cc3c45a3a6c3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    147 schema:name National Cancer Institute (U.S.)
    148 rdf:type schema:DefinedTerm
    149 N8c56e8d56ce5483f95c234c5d13e6988 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    150 schema:name Neoplasms
    151 rdf:type schema:DefinedTerm
    152 Na2f5a880f1bd49b89c1bda83fcf67dd7 schema:name dimensions_id
    153 schema:value pub.1147717461
    154 rdf:type schema:PropertyValue
    155 Na77c9dc1f3834141bd83e66c97b00a49 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    156 schema:name Biological Products
    157 rdf:type schema:DefinedTerm
    158 Nacd74f4f34bf4821a7f27c3cab0134a8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    159 schema:name Pharmacogenetics
    160 rdf:type schema:DefinedTerm
    161 Nafa59fd227564fa1943554390c27913d rdf:first sg:person.014637111012.05
    162 rdf:rest Nb631a163235746bd89bf57a7eb1f7445
    163 Nb631a163235746bd89bf57a7eb1f7445 rdf:first sg:person.01302247036.73
    164 rdf:rest Nec474b4ac482488bb25b7785ec7a302c
    165 Ncf9f8bb0d3dc429ab13553d6c47e9872 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    166 schema:name United States
    167 rdf:type schema:DefinedTerm
    168 Nd6dd10cf6d0a44fe8acde92438ae9c24 schema:issueNumber 1
    169 rdf:type schema:PublicationIssue
    170 Ndaf5ff611c7944ef95de8cd4b8d29769 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    171 schema:name Cell Line, Tumor
    172 rdf:type schema:DefinedTerm
    173 Ne15fb4d97de84919a6863506e710760f schema:name pubmed_id
    174 schema:value 35525914
    175 rdf:type schema:PropertyValue
    176 Ne35d493a5e8f4054b4b389267628b6dd rdf:first sg:person.01110513472.52
    177 rdf:rest rdf:nil
    178 Ne62d6b535cf64a39acb80ddc4e7bfefc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    179 schema:name Membrane Proteins
    180 rdf:type schema:DefinedTerm
    181 Nec474b4ac482488bb25b7785ec7a302c rdf:first sg:person.01111206713.59
    182 rdf:rest N0daa49896ca942508effae6ce811f1a9
    183 Nfdd039b68f674e0591ee76f11dfdffef schema:name doi
    184 schema:value 10.1186/s12885-022-09580-7
    185 rdf:type schema:PropertyValue
    186 anzsrc-for:11 schema:inDefinedTermSet anzsrc-for:
    187 schema:name Medical and Health Sciences
    188 rdf:type schema:DefinedTerm
    189 anzsrc-for:1112 schema:inDefinedTermSet anzsrc-for:
    190 schema:name Oncology and Carcinogenesis
    191 rdf:type schema:DefinedTerm
    192 sg:journal.1024632 schema:issn 1471-2407
    193 schema:name BMC Cancer
    194 schema:publisher Springer Nature
    195 rdf:type schema:Periodical
    196 sg:person.010430056017.20 schema:affiliation grid-institutes:grid.48336.3a
    197 schema:familyName Zhao
    198 schema:givenName Yingdong
    199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010430056017.20
    200 rdf:type schema:Person
    201 sg:person.01110513472.52 schema:affiliation grid-institutes:grid.48336.3a
    202 schema:familyName Krushkal
    203 schema:givenName Julia
    204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110513472.52
    205 rdf:type schema:Person
    206 sg:person.01111206713.59 schema:affiliation grid-institutes:grid.48336.3a
    207 schema:familyName McShane
    208 schema:givenName Lisa M.
    209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01111206713.59
    210 rdf:type schema:Person
    211 sg:person.01302247036.73 schema:affiliation grid-institutes:grid.48336.3a
    212 schema:familyName Negi
    213 schema:givenName Simarjeet
    214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01302247036.73
    215 rdf:type schema:Person
    216 sg:person.014637111012.05 schema:affiliation grid-institutes:grid.48336.3a
    217 schema:familyName Sankaran
    218 schema:givenName Hari
    219 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014637111012.05
    220 rdf:type schema:Person
    221 sg:pub.10.1007/s00018-004-4045-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007150241
    222 https://doi.org/10.1007/s00018-004-4045-8
    223 rdf:type schema:CreativeWork
    224 sg:pub.10.1007/s00432-013-1460-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1002500108
    225 https://doi.org/10.1007/s00432-013-1460-y
    226 rdf:type schema:CreativeWork
    227 sg:pub.10.1007/s13238-020-00789-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1131331578
    228 https://doi.org/10.1007/s13238-020-00789-5
    229 rdf:type schema:CreativeWork
    230 sg:pub.10.1007/s13402-014-0207-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038776177
    231 https://doi.org/10.1007/s13402-014-0207-3
    232 rdf:type schema:CreativeWork
    233 sg:pub.10.1038/73439 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017120232
    234 https://doi.org/10.1038/73439
    235 rdf:type schema:CreativeWork
    236 sg:pub.10.1038/ncomms14844 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084129032
    237 https://doi.org/10.1038/ncomms14844
    238 rdf:type schema:CreativeWork
    239 sg:pub.10.1038/nrc1951 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053488336
    240 https://doi.org/10.1038/nrc1951
    241 rdf:type schema:CreativeWork
    242 sg:pub.10.1038/nrc2439 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049875030
    243 https://doi.org/10.1038/nrc2439
    244 rdf:type schema:CreativeWork
    245 sg:pub.10.1038/nrc2824 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027786679
    246 https://doi.org/10.1038/nrc2824
    247 rdf:type schema:CreativeWork
    248 sg:pub.10.1038/s41419-017-0068-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100423673
    249 https://doi.org/10.1038/s41419-017-0068-6
    250 rdf:type schema:CreativeWork
    251 sg:pub.10.1038/s41586-021-03539-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1137958722
    252 https://doi.org/10.1038/s41586-021-03539-7
    253 rdf:type schema:CreativeWork
    254 sg:pub.10.1038/s41598-018-22631-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1101436531
    255 https://doi.org/10.1038/s41598-018-22631-z
    256 rdf:type schema:CreativeWork
    257 sg:pub.10.1038/srep19819 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024238151
    258 https://doi.org/10.1038/srep19819
    259 rdf:type schema:CreativeWork
    260 sg:pub.10.1186/1472-6882-12-185 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017427268
    261 https://doi.org/10.1186/1472-6882-12-185
    262 rdf:type schema:CreativeWork
    263 sg:pub.10.1186/1476-4598-10-12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011423539
    264 https://doi.org/10.1186/1476-4598-10-12
    265 rdf:type schema:CreativeWork
    266 sg:pub.10.1186/1476-4598-12-82 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034170601
    267 https://doi.org/10.1186/1476-4598-12-82
    268 rdf:type schema:CreativeWork
    269 sg:pub.10.1186/1479-5876-6-14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024807464
    270 https://doi.org/10.1186/1479-5876-6-14
    271 rdf:type schema:CreativeWork
    272 sg:pub.10.1186/s13321-020-00424-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1126125760
    273 https://doi.org/10.1186/s13321-020-00424-9
    274 rdf:type schema:CreativeWork
    275 grid-institutes:grid.48336.3a schema:alternateName Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA
    276 schema:name Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, 20850, Rockville, MD, USA
    277 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...