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      Protracted p53-independent stimulation of p21 WAF1/Cip1 fuels genomic instability by deregulating the replication licensing machinery

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          Abstract

          The cyclin-dependent kinase inhibitor p21 WAF1/Cip1 is the prototype downstream effector of the tumor suppressor protein p53. Yet, evidence from human cancer and mice models, imply that p21 WAF1/Cip1, under certain conditions, can exercise oncogenic activity. The mechanism behind this behavior is still obscure. Within this context we unexpectedly noticed, predominantly in p53 mutant human cancers, that a subset of highly atypical cancerous cells expressing strongly p21 WAF1/Cip1 demonstrated also signs of proliferation. This finding suggests either tolerance to high p21 WAF1/Cip1 levels or that p21 WAF1/Cip1 per se guided a selective process that led to more aggressive off-springs. To address the latter scenario we employed p21 WAF1/Cip1-inducible p53-null cellular models and monitored them over a prolonged time period, using high-throughput screening means. After an initial phase characterized by stalled growth, mainly due to senescence, a subpopulation of p21 WAF1/Cip1 cells emerged, demonstrating increased genomic instability, aggressiveness and chemo-resistance. At the mechanistic level unremitted p21 WAF1/Cip1 production “saturates” the CRL4 CDT2 and SCF Skp2 ubiquitin ligase complexes reducing the turn-over of the replication licensing machinery. Deregulation of replication licensing triggered replication stress fuelling genomic instability. Conceptually, the above notion should be considered when anti-tumor strategies are designed, since p21 WAF1/Cip1 responds also to p53-independent signals, including various chemotherapeutic compounds.

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          A faster circular binary segmentation algorithm for the analysis of array CGH data.

          Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number. The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding P-value. The number of computations required for the maximal test statistic is O(N2), where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm. We present a hybrid approach to obtain the P-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analyses of array CGH data from breast cancer cell lines to show the impact of the new approaches on the analysis of real data. An R version of the CBS algorithm has been implemented in the "DNAcopy" package of the Bioconductor project. The proposed hybrid method for the P-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.
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            Mutations in the p53 Tumor Suppressor Gene: Important Milestones at the Various Steps of Tumorigenesis.

            Inactivation of the p53 tumor suppressor is a frequent event in tumorigenesis. In most cases, the p53 gene is mutated, giving rise to a stable mutant protein whose accumulation is regarded as a hallmark of cancer cells. Mutant p53 proteins not only lose their tumor suppressive activities but often gain additional oncogenic functions that endow cells with growth and survival advantages. Interestingly, mutations in the p53 gene were shown to occur at different phases of the multistep process of malignant transformation, thus contributing differentially to tumor initiation, promotion, aggressiveness, and metastasis. Here, the authors review the different studies on the involvement of p53 inactivation at various stages of tumorigenesis and highlight the specific contribution of p53 mutations at each phase of cancer progression.
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              A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

              Chromosome structural changes with nonrecurrent endpoints associated with genomic disorders offer windows into the mechanism of origin of copy number variation (CNV). A recent report of nonrecurrent duplications associated with Pelizaeus-Merzbacher disease identified three distinctive characteristics. First, the majority of events can be seen to be complex, showing discontinuous duplications mixed with deletions, inverted duplications, and triplications. Second, junctions at endpoints show microhomology of 2–5 base pairs (bp). Third, endpoints occur near pre-existing low copy repeats (LCRs). Using these observations and evidence from DNA repair in other organisms, we derive a model of microhomology-mediated break-induced replication (MMBIR) for the origin of CNV and, ultimately, of LCRs. We propose that breakage of replication forks in stressed cells that are deficient in homologous recombination induces an aberrant repair process with features of break-induced replication (BIR). Under these circumstances, single-strand 3′ tails from broken replication forks will anneal with microhomology on any single-stranded DNA nearby, priming low-processivity polymerization with multiple template switches generating complex rearrangements, and eventual re-establishment of processive replication.
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                Author and article information

                Journal
                100890575
                Nat Cell Biol
                Nat. Cell Biol.
                Nature cell biology
                1465-7392
                1476-4679
                1 July 2016
                20 June 2016
                26 May 2019
                : 18
                : 7
                : 777-789
                Affiliations
                [1 ]Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
                [2 ]Biomedical Research Foundation of the Academy of Athens, Athens, Greece
                [3 ]Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
                [4 ]Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
                [5 ]Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, UK
                [6 ]Department of Medical Genetics, Medical School, University of Athens, Athens, Greece
                [7 ]Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
                [8 ]Laboratory of Cell Proliferation and Ageing, Institute of Biology, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
                [9 ]Cancer Center, Ordway Research Institute, Albany, NY, USA
                [10 ]Cancer and Clinical Experimental Science Units, Faculty of Medicine, Institute for Life Sciences, Center for Proteome Research, University of Southampton, Southampton, UK
                [11 ]Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
                [12 ]Manchester Centre for Cellular Metabolism, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
                [13 ]Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
                Author notes
                [** ]To whom correspondence should be addressed: Dr Vassilis G Gorgoulis, Dept Histology-Embryology, Medical School, NKUA, 75 Mikras Asias Str, Goudi, Athens, GR-11146, Greece, Tel.: 0030-2107462352, vgorg@ 123456med.uoa.gr , vgorgoulis@ 123456gmail.com or: Dr. Jiri Bartek, Danish Cancer Society Research Center, Strandboulevarden 49, DK-2100 Copenhagen, Denmark, Tel.: +45 – 35 25 73 57, jb@ 123456cancer.dk
                Article
                PMC6535144 PMC6535144 6535144 ems83002
                10.1038/ncb3378
                6535144
                27323328
                0211c713-57be-4bc3-990e-c11b9b939181
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