title: Pathway-centric integrative analysis identifies RRM2 as a prognostic marker in breast cancer associated with poor survival and tamoxifen resistance.
abstract: Breast cancer (BCa) molecular subtypes include luminal A, luminal B, normal-like, HER-2-enriched, and basal-like tumors, among which luminal B and basal-like cancers are highly aggressive. Biochemical pathways associated with patient survival or treatment response in these more aggressive subtypes are not well understood. With the limited availability of pathologically verified clinical specimens, cell line models are routinely used for pathway-centric studies. We measured the metabolome of luminal and basal-like BCa cell lines using mass spectrometry, linked metabolites to biochemical pathways using Gene Set Analysis, and developed a novel rank-based method to select pathways on the basis of their enrichment in patient-derived omics data sets and prognostic relevance. Key mediators of the pathway were then characterized for their role in disease progression. Pyrimidine metabolism was altered in luminal versus basal BCa, whereas the combined expression of its associated genes or expression of one key gene, ribonucleotide reductase subunit M2 (RRM2) alone, associated significantly with decreased survival across all BCa subtypes, as well as in luminal patients resistant to tamoxifen. Increased RRM2 expression in tamoxifen-resistant patients was verified using tissue microarrays, whereas the metabolic products of RRM2 were higher in tamoxifen-resistant cells and in xenograft tumors. Both genetic and pharmacological inhibition of this key enzyme in tamoxifen-resistant cells significantly decreased proliferation, reduced expression of cell cycle genes, and sensitized the cells to tamoxifen treatment. Our study suggests for evaluating RRM2-associated metabolites as noninvasive markers for tamoxifen resistance and its pharmacological inhibition as a novel approach to overcome tamoxifen resistance in BCa.
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA; Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Nagireddy
authors.initials: N
authors.lastname: Putluri
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA; Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Suman
authors.initials: S
authors.lastname: Maity
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Ramakrishna
authors.initials: R
authors.lastname: Kommagani
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Ramakrishna
authors.initials: R
authors.lastname: Kommangani
authors.affiliation: Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Chad J
authors.initials: CJ
authors.lastname: Creighton
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA; Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Vasanta
authors.initials: V
authors.lastname: Putluri
authors.affiliation: Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Fengju
authors.initials: F
authors.lastname: Chen
authors.affiliation: Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Sarmishta
authors.initials: S
authors.lastname: Nanda
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA; Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Salil Kumar
authors.initials: SK
authors.lastname: Bhowmik
authors.affiliation: Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Terunuma
authors.affiliation: Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Tiffany
authors.initials: T
authors.lastname: Dorsey
authors.affiliation: Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Agostina
authors.initials: A
authors.lastname: Nardone
authors.affiliation: Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Fu
authors.affiliation: Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Chad
authors.initials: C
authors.lastname: Shaw
authors.affiliation: Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Tapasree Roy
authors.initials: TR
authors.lastname: Sarkar
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA; Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Schiff
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Lydon
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Bert W
authors.initials: BW
authors.lastname: O'Malley
authors.affiliation: Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Ambs
authors.affiliation: Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors.forename: Gokul M
authors.initials: GM
authors.lastname: Das
authors.affiliation: Department of Statistics, University of Michigan, Ann Arbor, MI, USA. Electronic address: gmichail@umich.edu.
authors.forename: George
authors.initials: G
authors.lastname: Michailidis
authors.affiliation: Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA; Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, TX, USA; Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA. Electronic address: arun.sreekumar@bcm.edu.
authors.forename: Arun
authors.initials: A
authors.lastname: Sreekumar
mesh_terms: D018931:Antineoplastic Agents, Hormonal; D014408:Biomarkers, Tumor / Q000032:analysis*; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000401:mortality; D045744:Cell Line, Tumor; D019008:Drug Resistance, Neoplasm / Q000502:physiology*; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted; D007150:Immunohistochemistry; D066298:In Vitro Techniques; D053208:Kaplan-Meier Estimate; D013058:Mass Spectrometry / Q000379:methods; D055442:Metabolome; D055432:Metabolomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D012262:Ribonucleoside Diphosphate Reductase / Q000235:genetics / Q000378:metabolism*; D013629:Tamoxifen; D046888:Tissue Array Analysis
chemical_list: D018931:Antineoplastic Agents, Hormonal; D014408:Biomarkers, Tumor; D013629:Tamoxifen; C093713:ribonucleotide reductase M2; D012262:Ribonucleoside Diphosphate Reductase