Cancer genetics articles within Nature Communications

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  • Article
    | Open Access

    DNA circulating in the plasma of cancer patients carries features of the primary tumour, however such DNA is found in low levels in brain cancer patients. Here, the authors show that circulating tumour DNA can be detected in the cerebral spinal fluid of cancer patients and that this better recapitulates the primary tumour compared to DNA from the plasma.

    • Leticia De Mattos-Arruda
    • , Regina Mayor
    •  & Joan Seoane

  • Article
    | Open Access

    Individual tumours are heterogeneous with regards to genetic mutations. In this study, the authors use sequencing to follow multiple tumour and plasma samples over 3 years from a breast cancer patient and show mutations detected in the plasma samples could partially reproduce the clonal nature of the primary tumour.

    • Muhammed Murtaza
    • , Sarah-Jane Dawson
    •  & Carlos Caldas

  • Article
    | Open Access

    BAG3 is found in the serum of pancreatic cancer patients and can be used as a marker of disease, but its role in cancer is unclear. Here, the authors show that BAG3 secreted from tumour cells binds to and activates macrophages, which in turn promotes cell growth, and an antibody blocking BAG3 binding reduces tumour formation in mice.

    • Alessandra Rosati
    • , Anna Basile
    •  & Maria Caterina Turco

  • Article
    | Open Access

    Cancer genome analysis has demonstrated that some breast and ovarian tumours show reduced homologous recombination, a feature that can be therapeutically exploited. Here, Alexandrov et al.search for this mutational signature in 36 different cancer types and find that some gastric tumours also harbour this mutational spectrum.

    • Ludmil B. Alexandrov
    • , Serena Nik-Zainal
    •  & Michael R Stratton

  • Article
    | Open Access

    This genome-wide association study identifies four novel risk loci for testicular germ cell tumour, and provides functional correlation between a disease-associated variant and gene expression in patient samples for one of the identified loci.

    • Kevin Litchfield
    • , Amy Holroyd
    •  & Clare Turnbull

  • Article
    | Open Access

    Genome-wide association studies have identified regions which confer risk of high-grade serous epithelial ovarian cancer. Here the authors use expression quantitative train locus analysis to identify candidate genes and functionally characterise them, identifying a role for HOXD9 in ovarian cancer.

    • Kate Lawrenson
    • , Qiyuan Li
    •  & Matthew L. Freedman

  • Article
    | Open Access

    Atypical adenomatous hyperplasia is thought to be a precursor lesion for lung adenocarcinoma. Here, using targeted deep sequencing, the authors demonstrate that hyperplastic lesions contain somatic mutations associated with malignant disease and that these can be detected in circulating tumour cells.

    • Evgeny Izumchenko
    • , Xiaofei Chang
    •  & David Sidransky

  • Article
    | Open Access

    Some colon carcinomas with microsatellite instability carry a frameshift mutation in a tumour suppressor UVRAG. Here the authors show that mutant UVRAG triggers colorectal cancer by antagonizing the activity of normal UVRAG in autophagy and chromosomal stability, but also sensitizes the cancer to DNA damage-inducing chemotherapeutic drugs.

    • Shanshan He
    • , Zhen Zhao
    •  & Chengyu Liang

  • Article
    | Open Access

    Mutations in the serine/threonine kinase ataxia teleangiectasia mutated (ATM) have been linked to pancreatic ductal adenocarcinoma (PDAC) cohorts. Here Russellet al. show that loss of ATM induces a greater number of proliferative precursor lesions in a mouse model, recapitulating many features of human PDAC subtypes.

    • Ronan Russell
    • , Lukas Perkhofer
    •  & Alexander Kleger

  • Article |

    Previous studies have shown that both rare pathogenic mutations and common genetic variants contribute to the familial risk of developing colorectal cancer. Here, the authors carry out a two-stage genome-wide association study and identify six new loci associated with colorectal cancer.

    • Fredrick R. Schumacher
    • , Stephanie L. Schmit
    •  & Ulrike Peters

  • Article
    | Open Access

    Anaplastic oligodendrogliomas are rare and incurable primary brain tumours with few treatment options. Here Labrecheet al. perform whole-exome sequencing and identify recurring mutations in transcription factor TCF12, which are associated with aggressive tumours.

    • Karim Labreche
    • , Iva Simeonova
    •  & Michel Wager

  • Article |

    Mutations in the tumour suppressor p53 can produce a protein that has additional functions. Here, the authors describe gain of function mutants of p53 that induce the expression of genes involved in nucleotide metabolism, which increases the activity of GTPases and results in invasion and metastasis.

    • Madhusudhan Kollareddy
    • , Elizabeth Dimitrova
    •  & Luis A. Martinez

  • Article |

    Several oncogenic mutations have been identified in melanoma; however, despite exhaustive sequencing, in a subset of melanomas no oncogenic mutation has been identified. Here, the authors identify new genomic rearrangements causing oncogenic fusions between the kinase domain of MET and several N-terminal partners in Spitzoid tumours.

    • Iwei Yeh
    • , Thomas Botton
    •  & Boris C. Bastian

  • Article |

    Chronic myeloid leukaemia is characterized by the genetic translocation t(9;22) encoding for BCR-ABL oncogene; however, the molecular mechanisms of disease progression are poorly understood. Here Amabile et al. show that aberrant methylation is promoted by BCR-ABL, driving the evolution of the disease.

    • Giovanni Amabile
    • , Annalisa Di Ruscio
    •  & Daniel G. Tenen

  • Article |

    BRAF inhibitors have shown encouraging clinical effects in melanoma patients; however, patients rapidly develop resistance via different mechanisms including alternative splicing. Here the authors find a specific mutation affecting BRAF splicing and highlight the therapeutic potential of splicing interference.

    • Maayan Salton
    • , Wojciech K. Kasprzak
    •  & Tom Misteli

  • Article |

    Aberrant oncogene expression can cause replication stress leading to chromosomal breaks. Here the authors map the chromosomal break loci induced by two different oncogenes and by a replication inhibitor, and show that each treatment induces a unique pattern of breaks in the same cell type.

    • Karin Miron
    • , Tamar Golan-Lev
    •  & Batsheva Kerem

  • Article |

    Prostate cancer often does not progress to invasive disease and thus markers predicting the course of the disease progression are critical for optimal treatment choices. Here the authors show that variants at two genetic loci correlate with the aggressiveness of prostate cancer.

    • Sonja I. Berndt
    • , Zhaoming Wang
    •  & Stephen J. Chanock

  • Article
    | Open Access

    Estrogen-receptor-positive breast cancer cells undergo hormone-independent proliferation after long-term oestrogen deprivation and become resistant to endocrine therapies. Here, the authors report a cluster of noncoding RNAs important for this adaptation process.

    • Saori Tomita
    • , Mohamed Osama Ali Abdalla
    •  & Mitsuyoshi Nakao

  • Article
    | Open Access

    Diagnosis of pancreatic ductal adenocarcinoma (PDA) has poor long-term survival rates with limited therapy options. Here Witkiewicz et al.use microdissection and whole-exome sequencing to identify novel recurrent PDA mutations, highlighting the genetic diversity of this aggressive cancer.

    • Agnieszka K. Witkiewicz
    • , Elizabeth A. McMillan
    •  & Erik S. Knudsen

  • Article
    | Open Access

    Basal cell carcinoma is a common cancer among people of European ancestry, with associated high economic costs to monitor and treat. Here Stacey et al.conduct a genome-wide association study on Icelandic and other European populations, identifying four novel loci associated with cancer susceptibility.

    • Simon N. Stacey
    • , Hannes Helgason
    •  & Kari Stefansson

  • Article
    | Open Access

    Primary prostate tumours are known to be genetically heterogeneous and clonal selection has the potential to drive metastasis. Here Hong et al. show that the acquisition of TP53 mutations is linked to clonal expansion and metastatic progression to lethality.

    • Matthew K.H. Hong
    • , Geoff Macintyre
    •  & Christopher M. Hovens

  • Article |

    Triple-negative breast cancers (TNBCs) are a heterogeneous group of cancers with varying prognoses. Here, the authors carry out whole-genome methylation capture sequencing from TNBC samples and matched normal samples, and identify differentially methylated regions that define a potentially novel TNBC signature.

    • Clare Stirzaker
    • , Elena Zotenko
    •  & Susan J. Clark

  • Article
    | Open Access

    Pheochromocytomas and paragangliomas (PCCs/PGLs) are rare neuroendocrine tumours with a significant genetic component. Here, the authors carry out a multi-omic integrative characterization of PCC/PGL and reveal potential genomic alterations and regulatory mechanisms involved in the disease.

    • Luis Jaime Castro-Vega
    • , Eric Letouzé
    •  & Anne-Paule Gimenez-Roqueplo

  • Article
    | Open Access

    TAL1 is frequently deregulated in T-cell acute lymphoblastic leukaemias, but the mechanism remains largely unclear. Here the authors show that microinsertions upstream of TAL1 cause its epigenetic reactivation, and that the mode of TAL1activation correlates with prognosis.

    • Jean-Marc Navarro
    • , Aurore Touzart
    •  & Bertrand Nadel

  • Article
    | Open Access

    Marginal zone lymphoma (MZL) is a common subtype of B-cell non-Hodgkin lymphoma. Here the authors carry out a two-stage genome-wide association study in over 8,000 Europeans and identify two new MZL risk loci at chromosome 6p, implicating the major histocompatibility complex in the disease for the first time.

    • Joseph Vijai
    • , Zhaoming Wang
    •  & Alexandra Nieters

  • Article |

    Intrahepatic cholangiocarcinoma (ICC) is a fatal primary liver cancer with a known genetic component. Here the authors sequence the exomes of matched tumour and normal tissue from 103 ICC patients in China, and identify an ICC mutational profile associated with liver inflammation, fibrosis and cirrhosis.

    • Shanshan Zou
    • , Jiarui Li
    •  & Heping Hu

  • Article |

    Cancer can result from mutations in more than one gene and these multiple mutated genes are often functionally dependent on each other; this interaction is known as epistasis. Here, the authors use a combinatorial RNAi screen to identify epistatic genes that are mutated in breast cancer and reveal large numbers of previously unreported gene interactions.

    • Xiaoyue Wang
    • , Audrey Q. Fu
    •  & Kevin P. White

  • Article |

    The accumulation of genetic and epigenetic mutations in cancer cells can drive malignant growth. Here, the authors model the evolution of intratumoral diversity and examine the classification of driver and passenger mutations, heterogeneity within tumours, and the dynamics of tumour response to targeted therapies.

    • R. A. Gatenby
    • , J. J. Cunningham
    •  & J. S. Brown

  • Article |

    Mutations of hCdc73, a component of the PAFc complex that regulates RNA polymerase II-dependent transcription, have been associated with parathyroid carcinoma. Here the authors show that hCdc73 regulates the mRNA stability of p53 through the interaction with eEF1Bγ, a translation elongation complex subunit, and hSki8, a component of mRNA decay complex.

    • Jay-Hyun Jo
    • , Tae-Moon Chung
    •  & Joo-Yeon Yoo

  • Article
    | Open Access

    Genome-wide association studies (GWAS) have revealed gene variants associated with breast cancer, but their association with breast cancer development in Latinas is not clear. Here, the authors carry out a GWAS of breast cancer in Latinas and identify a significant protective variant of Indigenous American origin in the 6q25 region.

    • Laura Fejerman
    • , Nasim Ahmadiyeh
    •  & Elad Ziv

  • Article
    | Open Access

    It is known that hereditary factors contribute to familial colorectal cancer type X. Here, the authors uncover the SEMA4A p.Val78Met germline mutation and show that the protein product is associated with changes in cell cycle progression in colorectal cancer cells.

    • Eduard Schulz
    • , Petra Klampfl
    •  & Heinz Sill

  • Article
    | Open Access

    Previous studies identified genetic variants associated with colorectal cancer (CRC), but the functional consequences of these genetic risk factors remain poorly understood. Here, the authors report that CRC risk variants reside in promoters and enhancers and could increase colon cancer risk through gene expression regulation.

    • Lijing Yao
    • , Yu Gyoung Tak
    •  & Peggy J. Farnham

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