• Associations of statins and diabetes with diagnosis of ulcerated cutaneous melanoma.

      von Schuckmann, L; Smith, D; Hughes, M; Malt, M; van der Pols, J; Khosrotehrani, K; Smithers, B; Green, Adèle C; Population Health Department, QIMR Berghofer Medical Research Institute, Australia; (2017-08-22)
      Ulcerated primary melanomas are associated with an inflammatory tumor micro-environment. We hypothesised that systemic pro-inflammatory states and anti-inflammatory medications are also associated with a diagnosis of ulcerated melanoma. In a cross-sectional study of 787 patients with newly-diagnosed clinical stage IB or II melanoma, we estimated odds ratios (ORs) for the association of pro-inflammatory factors (high body mass index (BMI), diabetes, cardiovascular disease, hypertension and smoking) or use of anti-inflammatory medications (statins, aspirin, corticosteroids and non-steroidal anti-inflammatory drugs), with ulcerated primary melanoma using regression models and subgroup analyses to control for melanoma thickness and mitotic rate. Based on information from 194 patients with ulcerated and 593 patients with non-ulcerated primary melanomas, regular statin users had lower likelihood of a diagnosis of ulcerated primary melanoma (OR 0.67, 95% CI 0.45-0.99) and this association remained after adjusting for age, sex, thickness and mitosis. When analysis was limited to melanomas that were ≤2mm thick and had ≤2 mitoses/mm(2) (40 ulcerated; 289 without ulceration), patients with diabetes had significantly raised odds of diagnosis of ulcerated melanoma (OR 2.90, 95% CI 1.07-7.90), adjusted for age, sex, BMI and statin use. These findings support our hypotheses that statin use is inversely associated, and diabetes is positively associated, with ulcerated melanoma.
    • Asymmetric inheritance of cell fate determinants: focus on RNA

      Shlyakhtina, Yelyzaveta; Moran, Katherine L; Portal, Maximiliano M; Cell Plasticity & Epigenetics Lab, Cancer Research UK(-)Manchester Institute, The University of Manchester, SK10 4TG Manchester, UK. (2019)
      During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.
    • An ataxia-telangiectasia-mutated (ATM) kinase mediated response to DNA damage down-regulates the mRNA-binding potential of THOC5.

      Ramachandran, S; Tran, D; Klebba-Faerber, S; Kardinal, C; Whetton, Anthony D; Tamura, T; Institut für Biochemie, OE4310, Medizinische Hochschule Hannover, D-30623 Hannover, Germany. (2011-11)
      In response to DNA damage, transcription is blocked by inhibition of RNA polymerase II activity. The regulation of a preexisting pool of mRNAs, therefore, plays a key role in DNA repair, cell cycle arrest, or inhibition of differentiation. THOC5 is a member of the THO complex and plays a role in the export of a subset of mRNA, which plays an important role in hematopoiesis and maintaining primitive cells. Since three serine residues in the PEST domain of THOC5 have been shown to be directly phosphorylated by ataxia-telangiectasia-mutated (ATM) kinase, we examined the THOC5-dependent mRNA export under DNA damage. We show here that DNA damage drastically decreased the cytoplasmic pool of a set of THOC5-dependent mRNAs and impaired the THOC5/mRNA complex formation. The mRNP complex formed with nonphosphorylation mutant (S307/312/314A) THOC5, but not with a C-terminal deletion mutant after DNA damage, suggesting that the C-terminal domain of THOC5, but not its phosphorylation in the PEST domain, is necessary for the regulation of the mRNA-binding potency of THOC5. The cytoplasmic THOC5-dependent mRNAs were recovered by treatment with ATM kinase-specific or p53-specific siRNA, as well as by treatment with ATM kinase inhibitor, KU55933, under DNA damage conditions, suggesting that the ATM-kinase-p53 pathway is involved in this response to the DNA damage. Furthermore, the treatment with KU55933 blocked DNA damage-induced THOC5mRNP complex dissociation, indicating that activation of ATM kinase suppresses the ability of THOC5 to bind to its target mRNAs.
    • ATF2 and ATF7 are critical mediators of intestinal epithelial repair

      Meijer, BJ; Giugliano, FP; Baan, B; Van der Meer, JHM; Meisner, S; Van Roest, M; Koelink, PJ; De Boer, RJ; Jones, N; Breitwieser, Wolfgang; et al. (2020)
      BACKGROUND & AIMS: Activation factor-1 transcription factor family members activating transcription factors 2 and 7 (ATF2 and ATF7) have highly redundant functions owing to highly homologous DNA binding sites. Their role in intestinal epithelial homeostasis and repair is unknown. Here, we assessed the role of these proteins in these conditions in an intestine-specific mouse model. METHODS: We performed in vivo and ex vivo experiments using Villin-CreERT2Atf2fl/flAtf7ko/ko mice. We investigated the effects of intestinal epithelium-specific deletion of the Atf2 DNA binding region in Atf7-/- mice on cellular proliferation, differentiation, apoptosis, and epithelial barrier function under homeostatic conditions. Subsequently, we exposed mice to 2% dextran sulfate sodium (DSS) for 7 days and 12 Gy whole-body irradiation and assessed the response to epithelial damage. RESULTS: Activating phosphorylation of ATF2 and ATF7 was detected mainly in the crypts of the small intestine and the lower crypt region of the colonic epithelium. Under homeostatic conditions, no major phenotypic changes were detectable in the intestine of ATF mutant mice. However, on DSS exposure or whole-body irradiation, the intestinal epithelium showed a clearly impaired regenerative response. Mutant mice developed severe ulceration and inflammation associated with increased epithelial apoptosis on DSS exposure and were less able to regenerate colonic crypts on irradiation. In vitro, organoids derived from double-mutant epithelium had a growth disadvantage compared with wild-type organoids, impaired wound healing capacity in scratch assay, and increased sensitivity to tumor necrosis factor-?-induced damage. CONCLUSIONS: ATF2 and ATF7 are dispensable for epithelial homeostasis, but are required to maintain epithelial regenerative capacity and protect against cell death during intestinal epithelial damage and repair.
    • ATF2 is required for amino acid-regulated transcription by orchestrating specific histone acetylation.

      Bruhat, Alain; Chérasse, Yoan; Maurin, Anne-Catherine; Breitwieser, Wolfgang; Parry, Laurent; Deval, Christiane; Jones, Nic; Jousse, Céline; Fafournoux, Pierre; UMR 1019, Unité de Nutrition Humaine, INRA de Theix, 63122 Saint Genès Champanelle, France. bruhat@clermont.inra.fr (2007)
      The transcriptional activation of CHOP (a CCAAT/enhancer-binding protein-related gene) by amino acid deprivation involves the activating transcription factor 2 (ATF2) and the activating transcription factor 4 (ATF4) binding the amino acid response element (AARE) within the promoter. Using a chromatin immunoprecipitation approach, we report that in vivo binding of phospho-ATF2 and ATF4 to CHOP AARE are associated with acetylation of histones H4 and H2B in response to amino acid starvation. A time course analysis reveals that ATF2 phosphorylation precedes histone acetylation, ATF4 binding and the increase in CHOP mRNA. We also show that ATF4 binding and histone acetylation are two independent events that are required for the CHOP induction upon amino acid starvation. Using ATF2-deficient mouse embryonic fibroblasts, we demonstrate that ATF2 is essential in the acetylation of histone H4 and H2B in vivo. The role of ATF2 on histone H4 acetylation is dependent on its binding to the AARE and can be extended to other amino acid regulated genes. Thus, ATF2 is involved in promoting the modification of the chromatin structure to enhance the transcription of a number of amino acid-regulated genes.
    • Atl1 regulates choice between global genome and transcription-coupled repair of O(6)-alkylguanines.

      Latypov, Vitaly F; Tubbs, J L; Watson, Amanda J; Marriott, Andrew S; McGown, Gail; Thorncroft, Mary R; Wilkinson, O J; Senthong, Pattama; Butt, Amna; Arvai, A S; et al. (2012-07-13)
      Nucleotide excision repair (NER) has long been known to remove DNA lesions induced by chemical carcinogens, and the molecular mechanism has been partially elucidated. Here we demonstrate that in Schizosaccharomyces pombe a DNA recognition protein, alkyltransferase-like 1 (Atl1), can play a pivotal role in selecting a specific NER pathway, depending on the nature of the DNA modification. The relative ease of dissociation of Atl1 from DNA containing small O(6)-alkylguanines allows accurate completion of global genome repair (GGR), whereas strong Atl1 binding to bulky O(6)-alkylguanines blocks GGR, stalls the transcription machinery, and diverts the damage to transcription-coupled repair. Our findings redraw the initial stages of the NER process in those organisms that express an alkyltransferase-like gene and raise the question of whether or not O(6)-alkylguanine lesions that are poor substrates for the alkyltransferase proteins in higher eukaryotes might, by analogy, signal such lesions for repair by NER.
    • ATM-dependent phosphorylation of ATF2 is required for the DNA damage response.

      Bhoumik, Anindita; Takahashi, Shoichi; Shiloh, Yosef; Jones, Nic; Ronai, Ze'ev; Breitwieser, Wolfgang; Signal Transduction Program, The Burnham Institute, La Jolla, California 92037, USA. (2005-05-27)
      Activating transcription factor 2 (ATF2) is regulated by JNK/p38 in response to stress. Here, we demonstrate that the protein kinase ATM phosphorylates ATF2 on serines 490 and 498 following ionizing radiation (IR). Phosphoantibodies to ATF2(490/8) reveal dose- and time-dependent phosphorylation of ATF2 by ATM that results in its rapid colocalization with gamma-H2AX and MRN components into IR-induced foci (IRIF). Inhibition of ATF2 expression decreased recruitment of Mre11 to IRIF, abrogated S phase checkpoint, reduced activation of ATM, Chk1, and Chk2, and impaired radioresistance. ATF2 requires neither JNK/p38 nor its DNA binding domain for recruitment to IRIF and the S phase checkpoint. Our findings identify a role for ATF2 in the DNA damage response that is uncoupled from its transcriptional activity.
    • ATP dependent histone phosphorylation and nucleosome assembly in a human cell free extract.

      Banerjee, S; Bennion, Gordon; Goldberg, Martin W; Allen, Terence D; Department of Pathology, Royal Veterinary College, University of London, UK. (1991-11-11)
      Physiologically spaced nucleosome formation in HeLa cell extracts is ATP dependent. ATP hydrolysis is required for chromatin assembly on both linear and covalently closed circular DNA. The link between the phosphorylation state of histones and nucleosome formation has been examined and we demonstrate that in the absence of histone phosphorylation no stable and regularly spaced nucleosomes are formed. Phosphorylated H3 stabilizes the nucleosome core; while phosphorylation of histone H2a is necessary to increase the linker length between nucleosomes from 0 to approximately 45 bp. Histone H1 alone, whether phosphorylated or unphosphorylated, does not increase the nucleosome repeat length in the absence of core histone phosphorylation. Phosphorylations of H1 and H3 correlate with condensation of chromatin. Maximum ATP hydrolysis which is necessary to increase the periodicity of nucleosomes from approximately 150 to approximately 185 bp, not only inhibits H1 and H3 phosphorylation but facilitates their dephosphorylation.
    • Attenuated function of a variant form of the helix-loop-helix protein, Id-3, generated by an alternative splicing mechanism.

      Deed, Richard W; Jasiok, Michelle; Norton, John D; CRC Department of Gene Regulation, Paterson Institute for Cancer Research, Christie Hospital NHS Trust, UK. grgrwd@picr.cr.man.ac.uk (1996-09-09)
      The Id family of helix-loop-helix proteins function as negative regulators of DNA binding, basic helix-loop-helix proteins in the regulation of cell growth and differentiation. We report here on the identification of a 17 kDa variant of the 14 kDa Id-3 protein termed Id-3L (long version) which possesses a unique 60 amino acid carboxy-terminus generated by read through of a 'coding intron' and alternative splicing. Northern analysis revealed expression of a minor 1.1 kb Id-3L transcript together with the predominant 0.95 kb Id-3 transcript in the majority of adult human tissues analysed. The variant Id-3L protein is functionally distinguishable from conventional Id-3 since in in vitro DNA mobility shift assays, it was greatly impaired in its ability to abrogate binding of the basic helix-loop-helix protein, E47, to an E box recognition sequence.
    • Attenuated recombinant vaccinia virus expressing oncofetal antigen (tumor-associated antigen) 5T4 induces active therapy of established tumors.

      Mulryan, Kate; Ryan, Matthew G; Myers, Kevin A; Shaw, David M; Wang, Who W; Kingsman, Susan M; Stern, Peter L; Carroll, Miles W; Cancer Research United Kingdom Immunology Group, Paterson Institute for Cancer Research, Christie Hospital, Manchester, M20 9BX, United Kingdom. (2002-10)
      The human oncofetal antigen 5T4 (h5T4) is a transmembrane glycoprotein overexpressed by a wide spectrum of cancers, including colorectal, ovarian, and gastric, but with a limited normal tissue expression. Such properties make 5T4 an excellent putative target for cancer immunotherapy. The murine homologue of 5T4 (m5T4) has been cloned and characterized, which allows for the evaluation of immune intervention strategies in "self-antigen" in vivo tumor models. We have constructed recombinant vaccinia viruses based on the highly attenuated and modified vaccinia virus ankara (MVA strain), expressing h5T4 (MVA-h5T4), m5T4 (MVA-m5T4), and Escherichia coli LacZ (MVA-LacZ). Immunization of BALB/c and C57BL/6 mice with MVA-h5T4 and MVA-m5T4 constructs induced antibody responses to human and mouse 5T4, respectively. C57BL/6 and BALB/c mice vaccinated with MVA-h5T4 were challenged with syngeneic tumor line transfectants, B16 melanoma, and CT26 colorectal cells that express h5T4. MVA-h5T4-vaccinated mice showed significant tumor retardation compared with mice vaccinated with MVA-LacZ or PBS. In active treatment studies, inoculation with MVA-h5T4 was able to treat established CT26-h5T4 lung tumor and to a lesser extent B16.h5T4 s.c. tumors. Additionally, when C57BL/6 mice vaccinated with MVA-m5T4 were challenged with B16 cells expressing m5T4, resulting growth of the tumors was significantly retarded compared with control animals. Furthermore, mice vaccinated with MVA-m5T4 showed no signs of autoimmune toxicity. These data support the use of MVA-5T4 for tumor immunotherapy.
    • Attenuation of O(6)-methylguanine-DNA methyltransferase activity and mRNA levels by cisplatin and temozolomide in jurkat cells.

      D'Atri, Stefania; Graziani, Grazia; Lacal, Pedro M; Nisticò, Vittoria; Gilberti, Sara; Faraoni, Isabella; Watson, Amanda J; Bonmassar, Enzo; Margison, Geoffrey P; Istituto Dermopatico Dell'Immacolata, Rome, Italy. s.datri@idi.it (2000-08)
      The DNA repair protein O(6)-methylguanine-DNA methyltransferase (MGMT) is important in cellular resistance to certain alkylating antitumor agents such as the methylating drug temozolomide (TMZ). To provide a more rational basis for clinical combinations with another commonly used drug, cisplatin, we assessed the modulation of MGMT protein and mRNA levels in the human leukemic cell line Jurkat after treatment with these agents. Cisplatin decreased MGMT activity in a time- and dose-dependent manner, with maximal suppression (50%) observed 24 h after treatment with 25 microM cisplatin. This was probably the result of decreased transcription of the MGMT gene, because there was an earlier nadir of MGMT mRNA levels after cisplatin treatment and neither cisplatin nor DNA reacted with cisplatin in vitro was able to inhibit MGMT activity in an in vitro assay. TMZ alone depleted MGMT activity in a time- and dose-dependent manner with almost complete loss of activity occurring immediately after treatment with 500 microM TMZ. Combinations of cisplatin (12.5 microM) and TMZ (250 microM) caused substantial and prolonged MGMT depletion with recovery to only 30% of pretreatment levels by 48 h. These results suggest that the clinical efficacy of TMZ and cisplatin may be improved by appropriate schedules of combinations of these agents.
    • Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.

      Bitton, Danny A; Wood, V; Scutt, Paul J; Grallert, Agnes; Yates, Tim; Smith, Duncan L; Hagan, Iain M; Miller, Crispin J; Cancer Research UK Applied Computational Biology and Bioinformatics Group, University of Manchester, Christie Hospital Site, Manchester M20 4BX, United Kingdom. (2011-04)
      Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the Schizosaccharomyces pombe genome that ignores thresholds. A complete six-frame translation was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi. Thirty-nine novel loci were identified. RT-PCR and RNA-Seq confirmed transcription at 38 loci; 33 novel gene structures were delineated by 5' and 3' RACE. Expression levels of 14 transcripts fluctuated during meiosis. Translational evidence for 10 genes, evolutionary conservation data supporting 35 predictions, and distinct phenotypes upon ORF deletion (one essential, four slow-growth, two delayed-division phenotypes) suggest that all 39 predictions encode functional proteins. The popularity of S. pombe as a model organism suggests that this augmented annotation will be of interest in diverse areas of molecular and cellular biology, while the generality of the approach suggests widespread applicability to other genomes.
    • The Aurora B specificity switch is required to protect from non-disjunction at the metaphase/anaphase transition

      Kelly James R; Martini, S; Brownlow, N; Joshi, D; Federico, S; Jamshidi, S; Kjaer, S; Lockwood, N; Rahmen, KM; Fraternali, F; et al. (2020)
    • Author correction: Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci.

      Schumacher, FR; Olama, AAA; Berndt, SI; Benlloch, S; Ahmed, M; Saunders, EJ; Dadaev, T; Leongamornlert, D; Anokian, E; Cieza-Borrella, C; et al. (2019)
      In the version of this article initially published, the name of author Manuela Gago-Dominguez was misspelled as Manuela Gago Dominguez. The error has been corrected in the HTML and PDF version of the article.
    • Author Correction: Lysyl oxidase drives tumour progression by trapping EGF receptors at the cell surface

      Tang, Haoran; Leung, L; Saturno, G; Viros, Amaya; Smith, Duncan L; Di Leva, Gianpiero; Morrison, Eamonn; Niculescu-Duvaz, D; Lopes, F; Johnson, L; et al. (2019)
      An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    • Author correction: Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data

      Rudin, CM; Poirier, JT; Byers, LA; Dive, Caroline; Dowlati, A; George, J; Heymach, JV; Johnson, JE; Lehman, JM; MacPherson, D; et al. (2019)
      An amendment to this paper has been published and can be accessed via a link at the top of the paper. Erratum for Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. [Nat Rev Cancer. 2019]
    • Author Correction: The Aurora B specificity switch is required to protect from non-disjunction at the metaphase/anaphase transition

      Kelly, Joanna; Martini, S; Brownlow, N; Joshi, D; Federico, S; Jamshidi, S; Kjaer, S; Lockwood, N; Rahman, KM; Fraternali, F; et al. (2020)
      The original version of this article contained an error in the spelling of the author Khondaker Miraz Rahman, which was incorrectly given as Khondaker Miraz Rahmen. This has now been corrected in the PDF and HTML versions of the article.
    • The authors reply.

      Ghiasvand, R; Rueegg, C; Weiderpass, E; Green, Adèle C; Lund, E; Veierød, M; Oslo Center for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway (2017)
    • Auto-tumor immunity in patients with solid tumors: participation of CD3 complex and MHC class I antigens in the lytic interaction.

      Vánky, F; Roberts, Trudie; Klein, E; Willems, J; Department of Tumor Biology, Karolinska Institute, Stockholm, Sweden. (1987-10)
      In a number of experiments performed with blood lymphocytes of patients, the high density subset lysed autologous tumor cells separated from the surgical specimens. The lysis was abrogated by pretreatment of the effector cells with antibodies (OKT3) directed against the T3 molecule associated with the T cell receptor and by pretreatment of the target cells with antibodies (W6/32) directed against the monomorphic part of the MHC class I antigens. This subset lyses only autologous tumor cells. The selectivity and the characteristics shared with antigen specific cytotoxic T lymphocytes (CTL) suggest that the auto-tumor lysis by the effectors reflects an immune response against the tumor cells. The low density lymphocytes, separated from the blood, can lyse both auto- and allogeneic tumor cell. In the autologous system, incubation of the effectors with the mAb OKT3 had no inhibitory effect and incubation of the targets with the anti W6/32 mAb inhibited their lysis only in some experiments. The nature of the reactivity of the LD lymphocytes remains to be defined. Whether it is similar to the indiscriminative natural killing or whether part of these lymphocytes are antigen(s) specific and exhibit a high avidity interaction with the target remains to be seen. It is possible that both types of target recognition occur since the LD lymphocyte population is heterogeneous.
    • Autocrine TGF-{beta} and stromal cell-derived factor-1 (SDF-1) signaling drives the evolution of tumor-promoting mammary stromal myofibroblasts.

      Kojima, Yasushi; Acar, Ahmet; Eaton, E N; Mellody, Kieran T; Scheel, C; Ben-Porath, I; Onder, T T; Wang, Z C; Richardson, A L; Weinberg, R A; et al. (2010-11-01)
      Much interest is currently focused on the emerging role of tumor-stroma interactions essential for supporting tumor progression. Carcinoma-associated fibroblasts (CAFs), frequently present in the stroma of human breast carcinomas, include a large number of myofibroblasts, a hallmark of activated fibroblasts. These fibroblasts have an ability to substantially promote tumorigenesis. However, the precise cellular origins of CAFs and the molecular mechanisms by which these cells evolve into tumor-promoting myofibroblasts remain unclear. Using a coimplantation breast tumor xenograft model, we show that resident human mammary fibroblasts progressively convert into CAF myofibroblasts during the course of tumor progression. These cells increasingly acquire two autocrine signaling loops, mediated by TGF-β and SDF-1 cytokines, which both act in autostimulatory and cross-communicating fashions. These autocrine-signaling loops initiate and maintain the differentiation of fibroblasts into myofibroblasts and the concurrent tumor-promoting phenotype. Collectively, these findings indicate that the establishment of the self-sustaining TGF-β and SDF-1 autocrine signaling gives rise to tumor-promoting CAF myofibroblasts during tumor progression. This autocrine-signaling mechanism may prove to be an attractive therapeutic target to block the evolution of tumor-promoting CAFs.