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  • br Our study has several limitations This is a

    2020-07-28


    Our study has several limitations. This is a retrospective analysis of publicly available data. The sequencing depth of the primary and metastatic samples was on average 77× [6], thus we cannot rule out that subclonal mutations were missed. In addition, we could per-form mutational signature analysis separately only in the subset of the matched primary and metastatic ECs with sufficient shared and private mutations. More comprehensive analyses including whole-genome sequencing may better define the mutational processes that are driving the progression from primary to metastatic disease in EC.
    Despite these limitations, our study demonstrated that EC is a het-erogeneous disease with multiple mutational processes shaping the mutational spectra of these lesions. Although the molecular subtype classification proposed by TCGA for endometrioid and serous carcino-mas captures some of this heterogeneity, our mutational signature anal-ysis identified examples that would result in their reclassification. We also observed a shift from aging- or POLE- to MSI-related mutational processes in the progression from primary to metastatic ECs in a subset of cases. With the decreasing costs of genomic sequencing, routine whole-genome or even multiple-site sequencing of tumors is rapidly becoming reality in the clinical setting. In the era of precision medicine, information on the mutational processes shaping the GW311616 of a given EC may provide important information in addition to the specific muta-tions and gene copy number alteration.
    Supplementary data to this article can be found online at https://doi.
    Author contributions
    Conflict of interest
    N. Riaz reports research support from Pfizer and Bristol-Myers Squibb, and personal fees from the Illumina Speakers' Bureau, outside the submitted work. J.S. Reis-Filho reports personal/consultancy fees from VolitionRx, Page.AI and Goldman Sachs, outside the submitted work. The remaining authors have no conflicts of interest to declare.
    Funding support
    J.S. Reis-Filho is funded in part by the Breast Cancer Research Foun-dation. Research reported in this publication was supported in part by a Cancer Center Support Grant of the National Institutes of Health/Na-tional Cancer Institute (Grant No. P30CA008748).
    Acknowledgements
    We thank S.H. Kim and L.A. Moukarzel for critical reading of the manuscript.
    References
    [16] Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours, Nature 490 (2012) 61–70. [17] R. Rosenthal, N. McGranahan, J. Herrero, B.S. Taylor, C. Swanton, DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair defi-ciencies and patterns of carcinoma evolution, Genome Biol. 17 (2016) 31.
    [30] N.J. Haradhvala, J. Kim, Y.E. Maruvka, P. Polak, D. Rosebrock, D. Livitz, et al., Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair, Nat. Commun. 9 (2018) 1746. [31] F. Bellido, M. Pineda, G. Aiza, R. Valdes-Mas, M. Navarro, D.A. Puente, et al., POLE and POLD1 mutations in 529 kindred with familial colorectal cancer and/or polyposis: review of reported cases and recommendations for genetic testing and surveillance, Genet. Med. 18 (2016) 325–332. [32] C.C. Billingsley, D.E. Cohn, D.G. Mutch, J.A. Stephens, A.A. Suarez, P.J. Goodfellow, Po-lymerase varepsilon (POLE) mutations in endometrial cancer: clinical outcomes and implications for Lynch syndrome testing, Cancer 121 (2015) 386–394.
    [38] M.K. McConechy, A. Talhouk, H.H. Li-Chang, S. Leung, D.G. Huntsman, C.B. Gilks, et al., Detection of DNA mismatch repair (MMR) deficiencies by immunohistochem-istry can effectively diagnose the microsatellite instability (MSI) phenotype in endo-metrial carcinomas, Gynecol. Oncol. 137 (2015) 306–310. [39] S. Mylavarapu, A. Das, M. Roy, Role of BRCA mutations in the modulation of response to platinum therapy, Front. Oncol. 8 (2018) 16.
    Contents lists available at ScienceDirect
    Journal of Oral Biosciences
    Original Article
    Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing
    Yasuharu Takahashi a, e, 1, Jonguk Park b, 1, Koji Hosomi c, Tomonori Yamada d, Ayaka Kobayashi d, Yuji Yamaguchi d, Susumu Iketani d, Jun Kunisawa c, Kenji Mizuguchi b, Nobuko Maeda e, Tomoko Ohshima e, *
    a Department of Oral Microbiology, Doctor of Philosophy in Dental Science, Graduate School of Dental Medicine, Tsurumi University, 2-1-3 Tsurumi, Tsurumi-ku, Yokohama-shi, Kanagawa, 230-8501, Japan b Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Asagi, Saito, Ibaraki-shi, Osaka, 567-0085, Japan