1. Mutational History of a Human Cell Lineage from Somatic to Induced Pluripotent Stem Cells.

    PLoS Genetics 12(4):e1005932 (2016) PMID 27054363 PMCID PMC4824386

    The accuracy of replicating the genetic code is fundamental. DNA repair mechanisms protect the fidelity of the genome ensuring a low error rate between generations. This sustains the similarity of individuals whilst providing a repertoire of variants for evolution. The mutation rate in the human...
  2. Chromosome engineering in zygotes with CRISPR/Cas9.

    Genesis 54(2):78 (2016) PMID 26742453 PMCID PMC4819711

    Deletions, duplications, and inversions of large genomic regions covering several genes are an important class of disease causing variants in humans. Modeling these structural variants in mice requires multistep processes in ES cells, which has limited their availability. Mutant mice containing ...
  3. Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice.

    Nature Communications 7:10770 (2016) PMID 26916719 PMCID PMC4773438

    Mouse transgenesis has provided fundamental insights into pancreatic cancer, but is limited by the long duration of allele/model generation. Here we show transfection-based multiplexed delivery of CRISPR/Cas9 to the pancreas of adult mice, allowing simultaneous editing of multiple gene sets in i...
  4. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies.

    Genome Biology 17(1):115 (2016) PMID 27246460 PMCID PMC4888588

    Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes aff...
  5. CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice.

    PNAS 112(45):13982 (2015) PMID 26508638 PMCID PMC4653208

    Here, we show CRISPR/Cas9-based targeted somatic multiplex-mutagenesis and its application for high-throughput analysis of gene function in mice. Using hepatic single guide RNA (sgRNA) delivery, we targeted large gene sets to induce hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcin...
  6. A Synergistic Interaction between Chk1- and MK2 Inhibitors in KRAS-Mutant Cancer

    Cell 162(5):1169 (2015)

  7. A Synergistic Interaction between Chk1- and MK2 Inhibitors in KRAS-Mutant Cancer.

    Cell 162(1):146 (2015) PMID 26140595

    KRAS is one of the most frequently mutated oncogenes in human cancer. Despite substantial efforts, no clinically applicable strategy has yet been developed to effectively treat KRAS-mutant tumors. Here, we perform a cell-line-based screen and identify strong synergistic interactions between cell...
  8. Off-target assessment of CRISPR-Cas9 guiding RNAs in human iPS and mouse ES cells.

    Genesis 53(2):225 (2015) PMID 25378133

    The CRISPR-Cas9 system consists of a site-specific, targetable DNA nuclease that holds great potential in gene editing and genome-wide screening applications. To apply the CRISPR-Cas9 system to these assays successfully, the rate at which Cas9 induces DNA breaks at undesired loci must be underst...
  9. High-density P300 enhancers control cell state transitions.

    BMC Genomics 16(1):903 (2015) PMID 26546038 PMCID PMC4636788

    Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise extended clusters dubbed stretch- or super-enhancers (SEs). These SEs are located near ...
  10. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.

    Nature Genetics 47(1):47 (2015) PMID 25485836

    Here we describe a conditional piggyBac transposition system in mice and report the discovery of large sets of new cancer genes through a pancreatic insertional mutagenesis screen. We identify Foxp1 as an oncogenic transcription factor that drives pancreatic cancer invasion and spread in a mouse...
  11. A next-generation dual-recombinase system for time- and host-specific targeting of pancreatic cancer.

    Nature Medicine 20(11):1340 (2014) PMID 25326799 PMCID PMC4270133

    Genetically engineered mouse models (GEMMs) have dramatically improved our understanding of tumor evolution and therapeutic resistance. However, sequential genetic manipulation of gene expression and targeting of the host is almost impossible using conventional Cre-loxP-based models. We have dev...
  12. Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse.

    PLoS Genetics 10(10):e1004705 (2014) PMID 25340873 PMCID PMC4207618

    The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have...
  13. Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress.

    PNAS 111(37):13427 (2014) PMID 25197064 PMCID PMC4169945

    Aneuploidy is a hallmark of human solid cancers that arises from errors in mitosis and results in gain and loss of oncogenes and tumor suppressors. Aneuploidy poses a growth disadvantage for cells grown in vitro, suggesting that cancer cells adapt to this burden. To understand better the consequ...
  14. Genetic background drives transcriptional variation in human induced pluripotent stem cells.

    PLoS Genetics 10(6):e1004432 (2014) PMID 24901476 PMCID PMC4046971

    Human iPS cells have been generated using a diverse range of tissues from a variety of donors using different reprogramming vectors. However, these cell lines are heterogeneous, which presents a limitation for their use in disease modeling and personalized medicine. To explore the basis of this ...
  15. Complete humanization of the mouse immunoglobulin loci enables efficient therapeutic antibody discovery.

    Nature Biotechnology 32(4):356 (2014) PMID 24633243

    If immunized with an antigen of interest, transgenic mice with large portions of unrearranged human immunoglobulin loci can produce fully human antigen-specific antibodies; several such antibodies are in clinical use. However, technical limitations inherent to conventional transgenic technology ...
  16. MiR-210 is induced by Oct-2, regulates B cells, and inhibits autoantibody production.

    Journal of Immunology 191(6):3037 (2013) PMID 23960236 PMCID PMC4162006

    MicroRNAs (MiRs) are small, noncoding RNAs that regulate gene expression posttranscriptionally. In this study, we show that MiR-210 is induced by Oct-2, a key transcriptional mediator of B cell activation. Germline deletion of MiR-210 results in the development of autoantibodies from 5 mo of age...
  17. Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

    Cell 154(2):452 (2013) PMID 23870131 PMCID PMC3717207

    Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found th...
  18. A genetic progression model of Braf(V600E)-induced intestinal tumorigenesis reveals targets for therapeutic intervention.

    Cancer Cell 24(1):15 (2013) PMID 23845441 PMCID PMC3706745

    We show that BRAF(V600E) initiates an alternative pathway to colorectal cancer (CRC), which progresses through a hyperplasia/adenoma/carcinoma sequence. This pathway underlies significant subsets of CRCs with distinctive pathomorphologic/genetic/epidemiologic/clinical characteristics. Genetic an...
  19. ATR acts stage specifically to regulate multiple aspects of mammalian meiotic silencing.

    Genes & Development 27(13):1484 (2013) PMID 23824539 PMCID PMC3713429

    In mammals, homologs that fail to synapse during meiosis are transcriptionally inactivated. This process, meiotic silencing, drives inactivation of the heterologous XY bivalent in male germ cells (meiotic sex chromosome inactivation [MSCI]) and is thought to act as a meiotic surveillance mechani...
  20. The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.

    Molecular and Cellular Biology 33(7):1317 (2013) PMID 23358416 PMCID PMC3624274

    The DNA transposon piggyBac is widely used as a tool in mammalian experimental systems for transgenesis, mutagenesis, and genome engineering. We have characterized genome-wide insertion site preferences of piggyBac by sequencing a large set of integration sites arising from transposition from tw...