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Fang J, Wood AM, Chen Y, Yue J, Ming R. Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset. BMC Genomics 2020; 21:398. [PMID: 32532215 PMCID: PMC7291442 DOI: 10.1186/s12864-020-06804-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 06/05/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. RESULTS In this study, a total of more than 74 million Illumina reads for progenitor 'Sunset' were mapped onto transgenic papaya 'SunUp' reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between 'Sunset' and 'SunUp'. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10- 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in 'SunUp', which is proportionally higher than the predicted total NUPT and NUMT junction sites in 'Sunset' (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by 'SunUp' and 'Sunset'. The average identity between 'SunUp' specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by 'SunUp' and 'Sunset'. Six 'SunUp' organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped 'Sunset' reads were elongated by any 'SunUp' transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. CONCLUSIONS Comparative whole-genome analyses between 'SunUp' and 'Sunset' provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.
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Affiliation(s)
- Jingping Fang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China.,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew Michael Wood
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Mezquita L, Jové M, Nadal E, Kfoury M, Morán T, Ricordel C, Dhooge M, Tlemsani C, Léna H, Teulé A, Álvarez JV, Raimbourg J, Hiret S, Lacroix L, Menéndez M, Saldaña J, Brunet J, Lianes P, Coupier I, Auclin E, Recondo G, Friboulet L, Adam J, Green E, Planchard D, Frébourg T, Capellà G, Rouleau E, Lázaro C, Caron O, Besse B. High Prevalence of Somatic Oncogenic Driver Alterations in Patients With NSCLC and Li-Fraumeni Syndrome. J Thorac Oncol 2020; 15:1232-1239. [PMID: 32179180 DOI: 10.1016/j.jtho.2020.03.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 11/15/2022]
Abstract
INTRODUCTION Actionable somatic molecular alterations are found in 15% to 20% of NSCLC in Europe. NSCLC is a tumor observed in patients with germline TP53 variants causing Li-Fraumeni syndrome (LFS), but its somatic molecular profile is unknown. METHODS Retrospective study of clinical and molecular profiles of patients with NSCLC and germline TP53 variants. RESULTS Among 22 patients with NSCLC and LFS (n = 23 lung tumors), 64% were women, median age was 51 years, 84% were nonsmokers, 73% had adenocarcinoma histological subtype, and 84% were diagnosed with advanced-stage disease. These patients harbored 16 distinct germline TP53 variants; the most common was p.R158H (5/22; three in the same family). Personal and family histories of cancer were reported in 71% and 90% of patients, respectively. In most cases (87%, 13/15), lung cancer was diagnosed with a late onset. Of the 21 tumors analyzed, somatic oncogenic driver mutations were found in 19 of 21 (90%), EGFR mutations in 18 (exon 19 deletion in 12 cases, L858R in three cases, and G719A, exon 20 insertion, and missing mutation subtype, each with one case), and ROS1 fusion in one case. A PI3KCA mutation was concurrently detected at diagnosis in three EGFR exon 19-deleted tumors (3/12). The median overall survival was 37.3 months in 14 patients treated with EGFR inhibitors; seven developed resistance, five (71%) acquired EGFR-T790M mutation, and one had SCLC transformation. CONCLUSIONS Driver oncogenic alterations were observed in 90% of the LFS tumors, mainly EGFR mutations; one ROS1 fusion was also observed. The germline TP53 variants and lung cancer carcinogenesis driven by oncogenic processes need further evaluation.
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Affiliation(s)
- Laura Mezquita
- Thoracic Oncology Group, Cancer Medicine Department, Gustave Roussy, Villejuif, France; Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain; Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Maria Jové
- Medical Oncology Department, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ernest Nadal
- Medical Oncology Department, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Maria Kfoury
- Thoracic Oncology Group, Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Teresa Morán
- Medical Oncology Department, Catalan Institute of Oncology-Badalona (ICO-Badalona), Institut Germans Trias i Pujol (IGTP), Badalona Applied Research Group in Oncology (B-ARGO), Universitat Autònoma de Barcelona (UAB), Medicine Department, Badalona, Spain
| | - Charles Ricordel
- Department of Respiratory Medicine, Pontchaillou Hospital, Rennes, France; University of Rennes, Rennes, France; Chemistry, Oncogenesis, and Stress Signaling, INSERM, Centre Eugène Marquis, Rennes, France
| | - Marion Dhooge
- Gastroenterology Department, Cochin University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Camille Tlemsani
- Medical Oncology Department, Cochin University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Cancer Research for PErsonalized Medicine (CARPEM), Paris, France; Paris Descartes University, USPC, Paris, France
| | - Hervé Léna
- Department of Respiratory Medicine, Pontchaillou Hospital, Rennes, France; University of Rennes, Rennes, France; Chemistry, Oncogenesis, and Stress Signaling, INSERM, Centre Eugène Marquis, Rennes, France
| | - Alex Teulé
- Medical Oncology Department, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose-Valero Álvarez
- Medical Oncology Department, Complejo Hospitalario de Zamora, Hospital Provincial, Zamora, Spain
| | - Judith Raimbourg
- Medical Oncology Department, Institute de Cancerologie de l'Ouest, Nantes, France
| | - Sandrine Hiret
- Medical Oncology Department, Institute de Cancerologie de l'Ouest, Nantes, France
| | - Ludovic Lacroix
- Medical Biology and Pathology Department, Translational Research Laboratory and BioBank, Gustave Roussy, Villejuif, France
| | - Mireia Menéndez
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL-CIBERONC), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Juana Saldaña
- Medical Oncology Department, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Brunet
- Medical Oncology Department, Catalan Institute of Oncology-Badalona (ICO-Badalona), Institut Germans Trias i Pujol (IGTP), Badalona Applied Research Group in Oncology (B-ARGO), Universitat Autònoma de Barcelona (UAB), Medicine Department, Badalona, Spain
| | - Pilar Lianes
- Medical Oncology Department, Hospital de Mataró, Mataró, Spain
| | - Isabelle Coupier
- Clinical Genetic Unit, Montpeiller Cancer Institut, CHU Montpellier, Montpeiller, France
| | - Edouard Auclin
- Gastrointestinal and Medical Oncology Department, Hôpital Européen Georges Pompidou, Paris, France
| | - Gonzalo Recondo
- INSERM, Gustave Roussy Cancer Campus, Université Paris Saclay, Saint-Aubin, France
| | - Luc Friboulet
- INSERM, Gustave Roussy Cancer Campus, Université Paris Saclay, Saint-Aubin, France
| | - Julien Adam
- Pathology Department, Gustave Roussy, Villejuif, France
| | | | - David Planchard
- Thoracic Oncology Group, Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Thierry Frébourg
- Normandie Univ, UNIROUEN, INSERM, and Rouen University Hospital, Department of Genetics, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Gabriel Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL-CIBERONC), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Etienne Rouleau
- Medical Biology and Pathology Department, Translational Research Laboratory and BioBank, Gustave Roussy, Villejuif, France
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL-ONCOBELL-CIBERONC), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Olivier Caron
- Clinical Genetic Unit, Cancer Medicine Department, Gustave Roussy, Villejuif, France.
| | - Benjamin Besse
- Thoracic Oncology Group, Cancer Medicine Department, Gustave Roussy, Villejuif, France; INSERM, Gustave Roussy Cancer Campus, Université Paris Saclay, Saint-Aubin, France
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Ma Z, Kim YM, Howard EW, Feng X, Kosanke SD, Yang S, Jiang Y, Parris AB, Cao X, Li S, Yang X. DMBA promotes ErbB2‑mediated carcinogenesis via ErbB2 and estrogen receptor pathway activation and genomic instability. Oncol Rep 2018; 40:1632-1640. [PMID: 30015966 PMCID: PMC6072406 DOI: 10.3892/or.2018.6545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/21/2018] [Indexed: 01/03/2023] Open
Abstract
Environmental factors, including 7,12‑dimethylbenz[a]anthracene (DMBA) exposure, and genetic predisposition, including ErbB2 overexpression/amplification, have been demonstrated to increase breast cancer susceptibility. Although DMBA‑ and ErbB2‑mediated breast cancers are well‑studied in their respective models, key interactions between environmental and genetic factors on breast cancer risk remain unclear. Therefore, the present study aimed to investigate the effect of DMBA exposure on ErbB2‑mediated mammary tumorigenesis. MMTV‑ErbB2 transgenic mice exposed to DMBA (1 mg) via weekly oral gavage for 6 weeks exhibited significantly enhanced mammary tumor development, as indicated by reduced tumor latency and increased tumor multiplicity compared with control mice. Whole mount analysis of premalignant mammary tissues from 15‑week‑old mice revealed increased ductal elongation and proliferative index in DMBA‑exposed mice. Molecular analyses of premalignant mammary tissues further indicated that DMBA exposure enhanced epidermal growth factor receptor (EGFR)/ErbB2 and estrogen receptor (ER) signaling, which was associated with increased mRNA levels of EGFR/ErbB2 family members and ER‑targeted genes. Furthermore, analysis of tumor karyotypes revealed that DMBA‑exposed tumors displayed more chromosomal alterations compared with control tumors, implicating DMBA‑induced chromosomal instability in tumor promotion in this model. Together, the data suggested that DMBA‑induced deregulation of EGFR/ErbB2‑ER pathways plays a critical role in the enhanced chromosomal instability and promotion of ErbB2‑mediated mammary tumorigenesis. The study highlighted gene‑environment interactions that may increase risk of breast cancer, which is a critical clinical issue.
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Affiliation(s)
- Zhikun Ma
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Young Mi Kim
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Erin W Howard
- Julius L. Chambers Biomedical/Biotechnology Research Institute, Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Xiaoshan Feng
- Department of Oncology, First Affiliated Hospital of Henan University of Sciences and Technology, Luoyang, Henan 471500, P.R. China
| | - Stanley D Kosanke
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Shihe Yang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Yunbo Jiang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Amanda B Parris
- Julius L. Chambers Biomedical/Biotechnology Research Institute, Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Xia Cao
- Julius L. Chambers Biomedical/Biotechnology Research Institute, Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Xiaohe Yang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Gulluni F, Martini M, De Santis MC, Campa CC, Ghigo A, Margaria JP, Ciraolo E, Franco I, Ala U, Annaratone L, Disalvatore D, Bertalot G, Viale G, Noatynska A, Compagno M, Sigismund S, Montemurro F, Thelen M, Fan F, Meraldi P, Marchiò C, Pece S, Sapino A, Chiarle R, Di Fiore PP, Hirsch E. Mitotic Spindle Assembly and Genomic Stability in Breast Cancer Require PI3K-C2α Scaffolding Function. Cancer Cell 2017; 32:444-459.e7. [PMID: 29017056 DOI: 10.1016/j.ccell.2017.09.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/25/2017] [Accepted: 09/05/2017] [Indexed: 12/11/2022]
Abstract
Proper organization of the mitotic spindle is key to genetic stability, but molecular components of inter-microtubule bridges that crosslink kinetochore fibers (K-fibers) are still largely unknown. Here we identify a kinase-independent function of class II phosphoinositide 3-OH kinase α (PI3K-C2α) acting as limiting scaffold protein organizing clathrin and TACC3 complex crosslinking K-fibers. Downregulation of PI3K-C2α causes spindle alterations, delayed anaphase onset, and aneuploidy, indicating that PI3K-C2α expression is required for genomic stability. Reduced abundance of PI3K-C2α in breast cancer models initially impairs tumor growth but later leads to the convergent evolution of fast-growing clones with mitotic checkpoint defects. As a consequence of altered spindle, loss of PI3K-C2α increases sensitivity to taxane-based therapy in pre-clinical models and in neoadjuvant settings.
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Affiliation(s)
- Federico Gulluni
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Miriam Martini
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy.
| | - Maria Chiara De Santis
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Carlo Cosimo Campa
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Alessandra Ghigo
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Jean Piero Margaria
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Elisa Ciraolo
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Irene Franco
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Ugo Ala
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Torino, Turin, Italy; Pathology Unit, Department of Laboratory Medicine, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Davide Disalvatore
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Giovanni Bertalot
- Program of Molecular Medicine, IEO, European Institute of Oncology, Milan, Italy
| | - Giuseppe Viale
- Division of Pathology, European Institute of Oncology, Milan, Italy; Department of Oncology and Hemato-oncology (DIPO), University of Milan, Milan, Italy
| | - Anna Noatynska
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Mara Compagno
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy; Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara Sigismund
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy
| | - Filippo Montemurro
- Unit of Investigative Oncology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo (TO), Italy
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Fan Fan
- Department of Biological Science and Bioengineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Patrick Meraldi
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Caterina Marchiò
- Department of Medical Sciences, University of Torino, Turin, Italy; Pathology Unit, Department of Laboratory Medicine, Azienda Ospedaliera Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Salvatore Pece
- Program of Molecular Medicine, IEO, European Institute of Oncology, Milan, Italy; Department of Oncology and Hemato-oncology (DIPO), University of Milan, Milan, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Torino, Turin, Italy; Unit of Pathology, Candiolo Cancer Institute - FPO, IRCCS, Candiolo (TO), Italy
| | - Roberto Chiarle
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy; Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pier Paolo Di Fiore
- IFOM, The FIRC Institute for Molecular Oncology Foundation, Milan, Italy; Program of Molecular Medicine, IEO, European Institute of Oncology, Milan, Italy; Department of Oncology and Hemato-oncology (DIPO), University of Milan, Milan, Italy
| | - Emilio Hirsch
- Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin 10126, Italy.
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Hiltemann S, Jenster G, Trapman J, van der Spek P, Stubbs A. Discriminating somatic and germline mutations in tumor DNA samples without matching normals. Genome Res 2015. [PMID: 26209359 PMCID: PMC4561496 DOI: 10.1101/gr.183053.114] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tumor analyses commonly employ a correction with a matched normal (MN), a sample from healthy tissue of the same individual, in order to distinguish germline mutations from somatic mutations. Since the majority of variants found in an individual are thought to be common within the population, we constructed a set of 931 samples from healthy, unrelated individuals, originating from two different sequencing platforms, to serve as a virtual normal (VN) in the absence of such an associated normal sample. Our approach removed (1) >96% of the germline variants also removed by the MN sample and (2) a large number (2%–8%) of additional variants not corrected for by the associated normal. The combination of the VN with the MN improved the correction for polymorphisms significantly, with up to ∼30% compared with MN and ∼15% compared with VN only. We determined the number of unrelated genomes needed in order to correct at least as efficiently as the MN is about 200 for structural variations (SVs) and about 400 for single-nucleotide variants (SNVs) and indels. In addition, we propose that the removal of common variants with purely position-based methods is inaccurate and incurs additional false-positive somatic variants, and more sophisticated algorithms, which are capable of leveraging information about the area surrounding variants, are needed for optimal accuracy. Our VN correction method can be used to analyze any list of variants, regardless of sequencing platform of origin. This VN methodology is available for use on our public Galaxy server.
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Affiliation(s)
- Saskia Hiltemann
- Department of Urology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands; Department of Bioinformatics, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Jan Trapman
- Department of Pathology, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Peter van der Spek
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Andrew Stubbs
- Department of Bioinformatics, Erasmus University Medical Center, Rotterdam 3015 CN, The Netherlands
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Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL. A comparative analysis of algorithms for somatic SNV detection in cancer. ACTA ACUST UNITED AC 2013; 29:2223-30. [PMID: 23842810 PMCID: PMC3753564 DOI: 10.1093/bioinformatics/btt375] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm. Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates. Availability: Data accession number SRA081939, code at http://code.google.com/p/snv-caller-review/ Contact:david.adelson@adelaide.edu.au Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicola D Roberts
- School of Molecular and Biomedical Science and School of Mathematical Sciences, University of Adelaide, South Australia, Australia
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7
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Zong C, Lu S, Chapman AR, Xie XS. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 2013; 338:1622-6. [PMID: 23258894 DOI: 10.1126/science.1229164] [Citation(s) in RCA: 790] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Kindred cells can have different genomes because of dynamic changes in DNA. Single-cell sequencing is needed to characterize these genomic differences but has been hindered by whole-genome amplification bias, resulting in low genome coverage. Here, we report on a new amplification method-multiple annealing and looping-based amplification cycles (MALBAC)-that offers high uniformity across the genome. Sequencing MALBAC-amplified DNA achieves 93% genome coverage ≥1x for a single human cell at 25x mean sequencing depth. We detected digitized copy-number variations (CNVs) of a single cancer cell. By sequencing three kindred cells, we were able to identify individual single-nucleotide variations (SNVs), with no false positives detected. We directly measured the genome-wide mutation rate of a cancer cell line and found that purine-pyrimidine exchanges occurred unusually frequently among the newly acquired SNVs.
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Affiliation(s)
- Chenghang Zong
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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8
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Intraductally administered pegylated liposomal doxorubicin reduces mammary stem cell function in the mammary gland but in the long term, induces malignant tumors. Breast Cancer Res Treat 2012; 135:201-8. [PMID: 22752247 DOI: 10.1007/s10549-012-2138-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 06/11/2012] [Indexed: 12/12/2022]
Abstract
Previously, we have shown that the intraductal (i.duc) administration of pegylated liposomal doxorubicin (PLD) to Her2/neu transgenic mice is associated with mammary tumor regression and prevention. Exploring the mechanism underlying the protection afforded by PLD, we studied: the effects of i.duc PLD-treatment with a subsequent pregnancy on outgrowth of tumors in Her2/neu mice; whether the i.duc PLD antitumor effect was mediated partially through changes in normal mammary stem cells (MaSCs); and the long-term safety of i.duc PLD into the normal mouse mammary gland. Her2/neu mice were treated with two i.duc injections of PLD given four weeks apart; pregnancy was induced and mice were followed up for changes in physiology, and tumor formation. We found that all pups born to i.duc PLD-treated Her2/neu mice died without weight gain within 7 days after birth. Despite an additional pregnancy, compared to vehicle control PLD-treated Her2/neu mice had a significantly longer latency and lower frequency of tumor development. Mammary epithelial cells isolated from untreated and i.duc PLD-treated 6-8 months-old multiparous FVB/N mice were analyzed for their repopulating ability in mammary fat pads of naïve recipients. Mice were also monitored for abnormalities in mammary gland morphology and function, including tumor formation. PLD-treated FVB/N mice displayed histomorphologic changes and a significant reduction in the outgrowth potential of cells from the mammary glands. Thus, i.duc PLD administration altered the mammary gland structurally and functionally by reducing the MaSC population, which could compromise milk production. Followed long term, i.duc PLD-treated FVB/N mice developed malignant mammary tumors, confirming similar published findings on doxorubicin injected into the mammary gland of rats. Unless there are fundamental species differences in PLD metabolism in rodents and humans, this finding seriously limits the consideration of i.duc PLD use in the clinic for treatment or prevention of breast cancer.
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Cytogenetic analysis of a malignant triton tumour by comparative genomic hybridization (CGH) and review of the literature. Eur Arch Otorhinolaryngol 2011; 268:1391-6. [DOI: 10.1007/s00405-011-1658-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 05/24/2011] [Indexed: 10/18/2022]
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10
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Beer PA, Ortmann CA, Stegelmann F, Guglielmelli P, Reilly JT, Larsen TS, Hasselbalch HC, Vannucchi AM, Möller P, Döhner K, Green AR. Molecular mechanisms associated with leukemic transformation of MPL-mutant myeloproliferative neoplasms. Haematologica 2010; 95:2153-6. [PMID: 20823136 DOI: 10.3324/haematol.2010.029306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Somatic activating mutations in MPL, the thrombopoietin receptor, occur in the myeloproliferative neoplasms, although virtually nothing is known about their role in evolution to acute myeloid leukemia. In this study, the MPL T487A mutation, identified in de novo acute myeloid leukemia, was not detected in 172 patients with a myeloproliferative neoplasm. In patients with a prior MPL W515L-mutant myeloproliferative neoplasm, leukemic transformation was accompanied by MPL-mutant leukemic blasts, was seen in the absence of prior cytoreductive therapy and often involved loss of wild-type MPL by mitotic recombination. Moreover, clonal analysis of progenitor colonies at the time of leukemic transformation revealed the presence of multiple genetically distinct but phylogenetically-related clones bearing different TP53 mutations, implying a mutator-phenotype and indicating that leukemic transformation may be preceded by the parallel expansion of diverse hematopoietic clones.
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Affiliation(s)
- Philip A Beer
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Hills Road, Cambridge, UK
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11
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Abstract
The accumulation of base substitutions (mutations) not subject to natural selection is the neutral mutation rate. Because this rate reflects the in vivo processes involved in maintaining the integrity of genetic information, the factors that affect the neutral mutation rate are of considerable interest. Mammals exhibit two dramatically different neutral mutation rates: the CpG mutation rate, wherein the C of most CpGs (i.e., methyl-CpG) mutate at 10-50 times that of C in any other context or of any other base. The latter mutations constitute the non-CpG rate. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs. Here, we determined the neutral non-CpG mutation rate as a function of CpG content by comparing sequence divergence of thousands of pairs of neutrally evolving chimpanzee and human orthologs that differ primarily in CpG content. Both the mutation rate and the mutational spectrum (transition/transversion ratio) of non-CpG residues change in parallel as sigmoidal (logistic) functions of CpG content. As different mechanisms generate transitions and transversions, these results indicate that both mutation rate and mutational processes are contingent on the local CpG content. We consider several possible mechanisms that might explain how CpG exerts these effects.
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Affiliation(s)
- Jean-Claude Walser
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
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12
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Progression and metastasis in a transgenic mouse breast cancer model: effects of exposure to in vivo hypoxia. Cancer Lett 2009; 282:98-108. [PMID: 19356843 DOI: 10.1016/j.canlet.2009.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/27/2009] [Accepted: 03/02/2009] [Indexed: 11/21/2022]
Abstract
Hypoxia is a predictor of poor patient survival in several cancers, including breast carcinomas. One possible mechanism is genomic instability induced by oxic stress. In this study we examined this possible mechanism by exposing an in vivo breast cancer model to hypoxia/reoxygenation. MMTV-Neu transgenic mice were exposed to cycling acute (AH) or chronic hypoxia (CH) before (early) or after (late) tumour detection to study effects of hypoxia on tumour initiation and progression, respectively. We observed no effect of the hypoxic exposures on times to first tumour detection, but we saw a trend of early AH-exposed mice to develop more tumours and macrometastases than CH-exposed mice. Unexpectedly, but consistent with these findings, we observed significantly reduced 8-oxo-dG lesions levels in the mammary tissue with the greatest difference observed between the air control (AC) and AH-exposed groups. In the late gassing group, there was a similar trend for reduced 8-oxo-dG lesion levels, but interestingly mice that developed macroscopic lung metastases demonstrated significantly increased levels of 8-oxo-dG lesions in their tumours relative to those that did not, irrespective of the gassing exposure. A trend for increased macrophage content was observed in tumours from mice exposed to acute hypoxia. Our results indicate that oxic stress induced by hypoxia/reoxygenation is unlikely to be a major factor driving tumour progression of established MMTV-Neu tumours but suggest that acute and chronic hypoxia may affect tumour incidence and metastasis when applied prior to tumour development.
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13
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Pannellini T, Spadaro M, Di Carlo E, Ambrosino E, Iezzi M, Amici A, Lollini PL, Forni G, Cavallo F, Musiani P. Timely DNA vaccine combined with systemic IL-12 prevents parotid carcinomas before a dominant-negative p53 makes their growth independent of HER-2/neu expression. THE JOURNAL OF IMMUNOLOGY 2006; 176:7695-703. [PMID: 16751417 DOI: 10.4049/jimmunol.176.12.7695] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Double transgenic mice overexpressing the transforming rat HER-2/neu oncogene and the mutated p53, with both dominant-negative and a gain-of-function properties, display early aggressive and metastasizing parotid tumors. Multiple acinar and ductal hyperplasia foci overexpressing the HER-2/neu gene product are evident at wk 5 and progress to poorly differentiated carcinoma by wk 7. Mice die before wk 18 with invasive carcinomas and multiple metastases that no longer express HER-2/neu. A combination of repeated electroporations of plasmids coding for the extracellular and transmembrane domains of the rat HER-2/neu receptor with systemic IL-12 administrations started when the parotids that present diffuse hyperplasia protected all female and 50% of the male mice until the close of the experiment at wk 40. This combined treatment began when multifocal in situ carcinomas that were already present cured 33% of the females and 25% of the males. The most prominent immunologic features associated with the antitumor protection were the production of high titers of anti-HER-2/neu Abs and the nonappearance of cell-mediated cytotoxic reactivity. In conclusion, anti-HER-2/neu vaccination combined with systemic IL-12 control parotid carcinomas as far as p53 mutation makes their growth independent of HER-2/neu expression.
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Affiliation(s)
- Tania Pannellini
- Aging Research Center, CeSi, G. d'Annunzio University Foundation, Chieti, Italy
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14
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Crowe JP, Patrick RJ, Rybicki LA, Escobar PF, Weng D, Thomas Budd G, Tubbs RR, Procop GW, Hicks DG. A data model to predict HER2 status in breast cancer based on the clinical and pathologic profiles of a large patient population at a single institution. Breast 2006; 15:728-35. [PMID: 16716590 DOI: 10.1016/j.breast.2006.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 03/07/2006] [Accepted: 03/08/2006] [Indexed: 11/21/2022] Open
Abstract
Recently published clinical trial data have produced compelling evidence for increased survival when Herceptin is administered to patients whose tumors are HER2 amplified. Therefore, the accuracy of HER2 status is essential to determine which patients should or should not receive Herceptin. Although HER2 results obtained by FISH and IHC are often in agreement, there is a persistent group of cases in which results are discordant, particularly among tumors with intermediate results. A multivariable analysis was undertaken to determine relative significance of various clinical and pathologic findings for patients diagnosed with infiltrating ductal carcinoma, and a data model was produced that predicts which patients are most likely to have HER2 amplified tumors. Correlates of HER2 amplification were higher Scarff-Bloom-Richardson grade, younger age at diagnosis, and a comedo ductal carcinoma in situ component.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Female
- Gene Amplification/physiology
- Genes, erbB-2/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Middle Aged
- Models, Statistical
- Multivariate Analysis
- Predictive Value of Tests
- Receptor, ErbB-2/metabolism
- Registries
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Affiliation(s)
- Joseph P Crowe
- Department of General Surgery-Breast Center, The Cleveland Clinic Foundation, 9500 Euclid Avenue, Desk A-80, Cleveland, OH 44195, USA.
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15
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Stringer JR, Larson JS, Fischer JM, Medvedovic M, Hersh MN, Boivin GP, Stringer SL. Modeling variation in tumors in vivo. Proc Natl Acad Sci U S A 2005; 102:2408-13. [PMID: 15695337 PMCID: PMC548963 DOI: 10.1073/pnas.0401340102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transgenic mice that allow mutant cells to be visualized in situ were used to study variation in tumors. These mice carry the G11 placental alkaline phosphatase (PLAP) transgene, a mutant allele rendered incapable of producing its enzyme product by a frameshift caused by insertion of a tract of G:C base pairs in a coding region. Spontaneous deletion of one G:C base pair from this tract restores gene function, and cells with PLAP activity can be detected histochemically. To study tumors, the G11 PLAP transgene was introduced into the polyoma virus middle T antigen mammary tumor model. Tumors in these mice exhibited up to 300 times more PLAP+ cells than normal tissues. PLAP+ cells were located throughout each tumor. Many of the PLAP+ cells were singlets, but clusters also were common, with one cluster containing >30,000 cells. Comparison of these data to simulations produced by computer models suggested that multiple factors were involved in generating mutant cells in tumors. Although genetic instability appeared to have occurred in most tumors, large clusters were much more common than expected based on instability alone.
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Affiliation(s)
- James R Stringer
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, Cincinnati, OH 45267-0524, USA.
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16
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Xu W, Yuan X, Xiang Z, Mimnaugh E, Marcu M, Neckers L. Surface charge and hydrophobicity determine ErbB2 binding to the Hsp90 chaperone complex. Nat Struct Mol Biol 2005; 12:120-6. [PMID: 15643424 DOI: 10.1038/nsmb885] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 11/24/2004] [Indexed: 11/09/2022]
Abstract
The molecular chaperone Hsp90 modulates the function of specific cell signaling proteins. Although targeting Hsp90 with the antibiotic inhibitor geldanamycin (GA) may be a promising approach for cancer treatment, little is known about the determinants of Hsp90 interaction with its client proteins. Here we identify a loop within the N lobe of the kinase domain of ErbB2 that determines Hsp90 binding. The amino acid sequence of the loop determines the electrostatic and hydrophobic character of the protein's surface, which in turn govern interaction with Hsp90. A point mutation within the loop that alters ErbB2 surface properties disrupts Hsp90 association and confers GA resistance. Notably, the immature ErbB2 point mutant remains sensitive to GA, suggesting that mature and nascent client kinases may use distinct motifs to interact with the Hsp90 chaperone complex.
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Affiliation(s)
- Wanping Xu
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Rockville, Maryland 20850, USA
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17
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Amann J, Kalyankrishna S, Massion PP, Ohm JE, Girard L, Shigematsu H, Peyton M, Juroske D, Huang Y, Stuart Salmon J, Kim YH, Pollack JR, Yanagisawa K, Gazdar A, Minna JD, Kurie JM, Carbone DP. Aberrant Epidermal Growth Factor Receptor Signaling and Enhanced Sensitivity to EGFR Inhibitors in Lung Cancer. Cancer Res 2005. [DOI: 10.1158/0008-5472.226.65.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epidermal growth factor receptor (EGFR) is occasionally amplified and/or mutated in non–small cell lung cancer (NSCLC) and can be coexpressed with other members of the HER receptor family to form functional heterodimers. We therefore investigated lung cancer cell lines for alterations in EGFR gene copy number, enhanced expression of EGFR and other HER family members, and EGFR coding sequence mutations and correlated these findings with response to treatment with the EGFR inhibitors and the kinetics of ligand-induced signaling. We show here that somatic deletions in the tyrosine kinase domain of EGFR were associated with increased EGFR gene copy number in NSCLC. Treatment with the specific EGFR tyrosine kinase inhibitors (TKI) gefitinib or erlotinib or the EGFR inhibitory antibody cetuximab induced apoptosis of HCC827, a NSCLC cell line with EGFR gene amplification and an exon 19 deletion. H1819, a NSCLC cell line that expresses high levels of EGFR, ErbB2, and ErbB3 but has wild-type EGFR, showed intermediate sensitivity to TKIs. In both cell lines, ligand-induced receptor tyrosine phosphorylation was delayed and prolonged and AKT was constitutively phosphorylated (but remained inhibitable by EGFR TKI). Thus, in addition to EGFR mutations, other factors in NSCLC cells, such as high expression of ErbB family members, may constitutively activate AKT and sensitize cells to EGFR inhibitors.
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Affiliation(s)
- Joseph Amann
- 1Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Shailaja Kalyankrishna
- 2Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Joyce E. Ohm
- 1Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Luc Girard
- 3Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hisayuki Shigematsu
- 3Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Michael Peyton
- 3Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Denise Juroske
- 2Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Yuhui Huang
- 1Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | | | - Young H. Kim
- 4Department of Pathology, Stanford University School of Medicine, Stanford, California; and
| | - Jonathan R. Pollack
- 4Department of Pathology, Stanford University School of Medicine, Stanford, California; and
| | | | - Adi Gazdar
- 3Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - John D. Minna
- 3Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jonathan M. Kurie
- 2Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
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18
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Leung DW, Tompkins C, Brewer J, Ball A, Coon M, Morris V, Waggoner D, Singer JW. Phospholipase C delta-4 overexpression upregulates ErbB1/2 expression, Erk signaling pathway, and proliferation in MCF-7 cells. Mol Cancer 2004; 3:15. [PMID: 15140260 PMCID: PMC420486 DOI: 10.1186/1476-4598-3-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 05/13/2004] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The expression of the rodent phosphoinositide-specific phospholipase C delta-4 (PLCdelta4) has been found to be elevated upon mitogenic stimulation and expression analysis have linked the upregulation of PLCdelta4 expression with rapid proliferation in certain rat transformed cell lines. The human homologue of PLCdelta4 has not been extensively characterized. Accordingly, we investigate the effects of overexpression of human PLCdelta4 on cell signaling and proliferation in this study. RESULTS The cDNA for human PLCdelta4 has been isolated and expressed ectopically in breast cancer MCF-7 cells. Overexpression of PLCdelta4 selectively activates protein kinase C-phi and upregulates the expression of epidermal growth factor receptors EGFR/erbB1 and HER2/erbB2, leading to constitutive activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) pathway in MCF-7 cells. MCF-7 cells stably expressing PLCdelta4 demonstrates several phenotypes of transformation, such as rapid proliferation in low serum, formation of colonies in soft agar, and capacity to form densely packed spheroids in low-attachment plates. The growth signaling responses induced by PLCdelta4 are not reversible by siRNA. CONCLUSION Overexpression or dysregulated expression of PLCdelta4 may initiate oncogenesis in certain tissues through upregulation of ErbB expression and activation of ERK pathway. Since the growth responses induced by PLCdelta4 are not reversible, PLCdelta4 itself is not a suitable drug target, but enzymes in pathways activated by PLCdelta4 are potential therapeutic targets for oncogenic intervention.
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Affiliation(s)
- David W Leung
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - Chris Tompkins
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - Jim Brewer
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - Alexey Ball
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - Mike Coon
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - Valerie Morris
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - David Waggoner
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
| | - Jack W Singer
- Cell Therapeutics, Inc., 201 Elliott Ave., W., Seattle, WA 98119, U.S.A
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19
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Felix K, Polack A, Pretsch W, Jackson SH, Feigenbaum L, Bornkamm GW, Janz S. Moderate Hypermutability of a TransgeniclacZReporter Gene inMyc-Dependent Inflammation-Induced Plasma Cell Tumors in Mice. Cancer Res 2004; 64:530-7. [PMID: 14744766 DOI: 10.1158/0008-5472.can-03-2602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutator phenotypes, a common and largely unexplained attribute of human cancer, might be better understood in mouse tumors containing reporter genes for accurate mutation enumeration and analysis. Previous work on peritoneal plasmacytomas (PCTs) in mice suggested that PCTs have a mutator phenotype caused by Myc-deregulating chromosomal translocations and/or phagocyte-induced mutagenesis due to chronic inflammation. To investigate this hypothesis, we generated PCTs that harbored the transgenic shuttle vector, pUR288, with a lacZ reporter gene for the assessment of mutations in vivo. PCTs exhibited a 5.5 times higher mutant frequency in lacZ (40.3 +/- 5.1 x 10(-5)) than in normal B cells (7.36 +/- 0.77 x 10(-5)), demonstrating that the tumors exhibit the phenotype of increased mutability. Studies on lacZ mutant frequency in serially transplanted PCTs and phagocyte-induced lacZ mutations in B cells in vitro indicated that mutant levels in tumors are not determined by exogenous damage inflicted by inflammatory cells. In vitro studies with a newly developed transgenic model of inducible Myc expression (Tet-off/MYC) showed that deregulated Myc sensitizes B cells to chemically induced mutations, but does not cause, on its own, mutations in lacZ. These findings suggested that the hypermutability of PCT is governed mainly by intrinsic features of tumor cells, not by deregulated Myc or chronic inflammation.
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Affiliation(s)
- Klaus Felix
- Laboratory of Genetics, Center for Cancer Research, National Cancer Institute, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
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20
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Yen HCS, Gordon C, Chang EC. Schizosaccharomyces pombe Int6 and Ras homologs regulate cell division and mitotic fidelity via the proteasome. Cell 2003; 112:207-17. [PMID: 12553909 DOI: 10.1016/s0092-8674(03)00043-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Yin6 is a yeast homolog of Int6, which is implicated in tumorigenesis. We show that Yin6 binds to and regulates proteasome activity. Overexpression of Yin6 strengthens proteasome function while inactivation weakens and causes the accumulation of polyubiquitinated proteins including securin/Cut2 and cyclin/Cdc13. Yin6 regulates the proteasome by preferentially interacting with Rpn5, a conserved proteasome subunit, and affecting its localization/assembly. We showed previously that Yin6 cooperates with Ras1 to mediate chromosome segregation; here, we demonstrate that Ras1 similarly regulates the proteasome via Rpn5. In yeast, human Int6 binds Rpn5 and regulates its localization. We propose that human Int6, either alone or cooperatively with Ras, influences proteasome activities via Rpn5. Inactivating Int6 can lead to accumulation of mitotic regulators affecting cell division and mitotic fidelity.
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Affiliation(s)
- Hsueh-Chi S Yen
- Department of Molecular and Cellular Biology, Breast Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
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21
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Affiliation(s)
- Johan G de Boer
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC, Canada
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