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Clonal evolution

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https://www.readbyqxmd.com/read/28720765/c-ebp%C3%AE-deregulation-as-a-paradigm-for-leukemogenesis
#1
REVIEW
J A Pulikkan, D G Tenen, G Behre
Myeloid master regulator CCAAT enhancer binding protein alpha (C/EBPα) is deregulated by multiple mechanisms in leukemia. Inhibition of C/EBPα function plays pivotal roles in leukemogenesis. While much is known about how C/EBPα orchestrates granulopoiesis, our understanding of molecular transformation events, the role(s) of cooperating mutations and clonal evolution during C/EBPα deregulation in leukemia remains elusive. In this review we will summarize the latest research addressing these topics with special emphasis on CEBPΑ mutations...
July 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28717172/evolution-of-the-pseudomonas-aeruginosa-mutational-resistome-in-an-international-cystic-fibrosis-clone
#2
Carla López-Causapé, Lea Mette Sommer, Gabriel Cabot, Rosa Rubio, Alain A Ocampo-Sosa, Helle Krogh Johansen, Joan Figuerola, Rafael Cantón, Timothy J Kidd, Soeren Molin, Antonio Oliver
Emergence of epidemic clones and antibiotic resistance development compromises the management of Pseudomonas aeruginosa cystic fibrosis (CF) chronic respiratory infections. Whole genome sequencing (WGS) was used to decipher the phylogeny, interpatient dissemination, WGS mutator genotypes (mutome) and resistome of a widespread clone (CC274), in isolates from two highly-distant countries, Australia and Spain, covering an 18-year period. The coexistence of two divergent CC274 clonal lineages was revealed, but without evident geographical barrier; phylogenetic reconstructions and mutational resistome demonstrated the interpatient transmission of mutators...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716556/impact-of-pneumococcal-conjugate-vaccine-pcv7-and-pcv13-on-pneumococcal-invasive-diseases-in-italian-children-and-insight-into-evolution-of-pneumococcal-population-structure
#3
Romina Camilli, Fabio D'Ambrosio, Maria Del Grosso, Fernanda Pimentel de Araujo, Maria Grazia Caporali, Martina Del Manso, Giovanni Gherardi, Fortunato D'Ancona, Annalisa Pantosti
BACKGROUND: The use of PCV7 for children immunization was gradually implemented in the Italian regions starting from 2006 and was replaced by PCV13 in 2010-2011. In this study we aimed to assess the PCV impact on invasive pneumococcal diseases (IPD) incidence, serotype distribution and antibiotic resistance in Italian children under 5years old. METHODS: All IPD cases in children from 5 Italian regions (Emilia-Romagna, Lombardia, A. P. Bolzano, A. P. Trento, and Piemonte) reported through the nationwide surveillance system during 2008-2014 were included in this study...
July 14, 2017: Vaccine
https://www.readbyqxmd.com/read/28716075/the-role-of-tumour-heterogeneity-and-clonal-cooperativity-in-metastasis-immune-evasion-and-clinical-outcome
#4
REVIEW
Deborah R Caswell, Charles Swanton
BACKGROUND: The advent of rapid and inexpensive sequencing technology allows scientists to decipher heterogeneity within primary tumours, between primary and metastatic sites, and between metastases. Charting the evolutionary history of individual tumours has revealed drivers of tumour heterogeneity and highlighted its impact on therapeutic outcomes. DISCUSSION: Scientists are using improved sequencing technologies to characterise and address the challenge of tumour heterogeneity, which is a major cause of resistance to therapy and relapse...
July 18, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28714591/experimental-evolution-with-a-multicellular-host-causes-diversification-within-and-between-microbial-parasite-populations-differences-in-emerging-phenotypes-of-two-different-parasite-strains
#5
Michaela H Kloesener, Joy Bose, Rebecca D Schulte
Host-parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one-sided parasite adaptation)...
July 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28713859/fungus-causing-white-nose-syndrome-in-bats-accumulates-genetic-variability-in-north-america-with-no-sign-of-recombination
#6
Jigar Trivedi, Josianne Lachapelle, Karen J Vanderwolf, Vikram Misra, Craig K R Willis, John M Ratcliffe, Rob W Ness, James B Anderson, Linda M Kohn
Emerging fungal diseases of wildlife are on the rise worldwide, and the white-nose syndrome (WNS) epidemic in North American bats is a catastrophic example. The causal agent of WNS is a single clone of the fungus Pseudogymnoascus destructans. Early evolutionary change in this clonal population has major implications for disease ecology and conservation. Accumulation of variation in the fungus through mutation, and shuffling of variation through recombination, could affect the virulence and transmissibility of the fungus and the durability of what appears to be resistance arising in some bat populations...
July 2017: MSphere
https://www.readbyqxmd.com/read/28712776/clonal-evolution-in-paired-endometrial-intraepithelial-neoplasia-atypical-hyperplasia-and-endometrioid-adenocarcinoma
#7
Mariano Russo, James Broach, Kathryn Sheldon, Kenneth R Houser, Dajiang J Liu, Joshua Kesterson, Rebecca Phaeton, Carrie Hossler, Nadine Hempel, Maria Baker, Jordan M Newell, Richard Zaino, Joshua I Warrick
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically-defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma...
July 13, 2017: Human Pathology
https://www.readbyqxmd.com/read/28710771/detailed-longitudinal-sampling-of-glioma-stem-cells-in-situ-reveals-chr7-gain-and-chr10-loss-as-repeated-events-in-primary-tumor-formation-and-recurrence
#8
Mehmet Baysan, Kevin Woolard, Margaret C Cam, Wei Zhang, Hua Song, Svetlana Kotliarova, Demosthenes Balamatsias, Amanda Linkous, Susie Ahn, Jennifer Walling, Galina I Belova, Howard A Fine
Intratumoral heterogeneity at the genetic, epigenetic, transcriptomic and morphologic levels is a commonly observed phenomenon in many aggressive cancer types. Clonal evolution during tumor formation as well as in response to therapeutic intervention, can be predicted utilizing reverse engineering approaches on detailed genomic snapshots of heterogeneous patient tumor samples. In this study, we developed an extensive dataset for a GBM case via the generation of polyclonal and monoclonal glioma stem cell lines from initial diagnosis, as well as from multiple sections of distant tumor locations of the deceased patient's brain following tumor recurrence...
July 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28710260/big-bang-tumor-growth-and-clonal-evolution
#9
Ruping Sun, Zheng Hu, Christina Curtis
The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution...
July 14, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28710259/phylogenetic-quantification-of-intratumor-heterogeneity
#10
Thomas B K Watkins, Roland F Schwarz
As sequencing efforts continue to reveal the extent of the intratumor heterogeneity (ITH) present in human cancers, the importance of evolutionary studies attempting to trace its etiology has increased. Sequencing multiple samples or tumor regions from the same patient has become affordable and is an effective way of tracing these evolutionary pathways, understanding selection, and detecting clonal expansions in ways impractical with single samples alone. In this article, we discuss and show the benefits of such multisample studies...
July 14, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28709006/compartmental-hbv-evolution-and-replication-in-liver-and-extrahepatic-sites-after-nucleos-tide-analogue-therapy-in-chronic-hepatitis-b-carriers
#11
Shan Gao, Zhong-Ping Duan, Yu Chen, Frank van der Meer, Samuel S Lee, Carla Osiowy, Guido van Marle, Carla S Coffin
BACKGROUND: Hepatitis B virus (HBV) variants are associated with nucleos/tide analogue (NA) response and liver disease but it is unknown whether NA influences extrahepatic HBV persistence. OBJECTIVES: To investigate HBV replication and genetic evolution in hepatic and extrahepatic sites of chronic hepatitis B (CHB) before and after NA therapy. STUDY DESIGN: A total of 13 paired plasma, peripheral blood mononuclear cells (PBMC), were collected from chronic HBV carriers at baseline and after a median 53 weeks NA therapy as well as liver biopsy (N=7 baseline, N=5 follow-up)...
July 5, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28699658/telomere-length-and-somatic-mutations-in-correlation-with-response-to-immunosuppressive-treatment-in-aplastic-anaemia
#12
Hee S Park, Si N Park, Kyongok Im, Sung-Min Kim, Jung-Ah Kim, Sang M Hwang, Dong S Lee
We investigated the frequencies of cytogenetic aberrations and somatic mutations of prognostic relevance in 393 patients with aplastic anaemia (AA). Clonality was determined by G-banding/fluorescence in situ hybridization (FISH) (n = 245), and targeted capture sequencing was performed for 88 haematopoiesis-related genes (n = 70). The telomere length (TL) of bone marrow nucleated cells was measured at the single cell level by FISH (n = 135). Eighteen (4·6%) patients showed disease progression, and monosomy 7 (50·0%) was the most predominant cytogenetic evolution at disease transformation...
July 12, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28697667/evolutionary-trajectories-to-antibiotic-resistance
#13
Diarmaid Hughes, Dan I Andersson
The ability to predict the evolutionary trajectories of antibiotic resistance would be of great value in tailoring dosing regimens of antibiotics so as to maximize the duration of their usefulness. Useful prediction of resistance evolution requires information about (a) the mutation supply rate, (b) the level of resistance conferred by the resistance mechanism, (c) the fitness of the antibiotic-resistant mutant bacteria as a function of drug concentration, and (d) the strength of selective pressures. In addition, processes including epistatic interactions and compensatory evolution, coselection of drug resistances, and population bottlenecks and clonal interference can strongly influence resistance evolution and thereby complicate attempts at prediction...
July 11, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28695208/population-genomics-of-picophytoplankton-unveils-novel-chromosome-hypervariability
#14
Romain Blanc-Mathieu, Marc Krasovec, Maxime Hebrard, Sheree Yau, Elodie Desgranges, Joel Martin, Wendy Schackwitz, Alan Kuo, Gerald Salin, Cecile Donnadieu, Yves Desdevises, Sophie Sanchez-Ferandin, Hervé Moreau, Eric Rivals, Igor V Grigoriev, Nigel Grimsley, Adam Eyre-Walker, Gwenael Piganeau
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28690319/interbacterial-predation-as-a-strategy-for-dna-acquisition-in-naturally-competent-bacteria
#15
REVIEW
Jan-Willem Veening, Melanie Blokesch
Natural competence enables bacteria to take up exogenous DNA. The evolutionary function of natural competence remains controversial, as imported DNA can act as a source of substrates or can be integrated into the genome. Exogenous homologous DNA can also be used for genome repair. In this Opinion article, we propose that predation of non-related neighbouring bacteria coupled with competence regulation might function as an active strategy for DNA acquisition. Competence-dependent kin-discriminated killing has been observed in the unrelated bacteria Vibrio cholerae and Streptococcus pneumoniae...
July 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28687650/parallel-evolution-of-two-clades-of-a-major-atlantic-endemic-vibrio-parahaemolyticus-pathogen-lineage-by-independent-acquisition-of-related-pathogenicity-islands
#16
Feng Xu, Narjol Gonzalez-Escalona, Kevin P Drees, Robert P Sebra, Vaughn S Cooper, Stephen H Jones, Cheryl A Whistler
Shellfish-transmitted Vibrio parahaemolyticus infections have recently increased from locations with historically low disease incidence, such as the Northeast United States (US). This change coincided with a bacterial population shift towards human pathogenic variants occurring in part through the introduction of several Pacific native lineages (ST36, ST43 and ST636) to near-shore areas off the Atlantic coast of the Northeast US. Concomitantly, ST631 emerged as a major endemic pathogen. Phylogenetic trees of clinical and environmental isolates indicated that two clades diverged from a common ST631 ancestor, and in each of these clades, a human pathogenic variant evolved independently through acquisition of distinct Vibrio pathogenicity islands (VPaI)...
July 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28674026/clonal-evolution-and-outcomes-in-myelofibrosis-after-ruxolitinib-discontinuation
#17
Kate J Newberry, Keyur Patel, Lucia Masarova, Rajyalakshmi Luthra, Taghi Manshouri, Elias Jabbour, Prithviraj Bose, Naval Daver, Jorge Cortes, Hagop Kantarjian, Srdan Verstovsek
Despite significant improvements in the signs and symptoms of myelofibrosis (MF), and possible prolongation of patients' survival, some have disease that is refractory to ruxolitinib and many lose their response over time. Furthermore, patients with ≥3 mutations are less likely to respond to ruxolitinib. Here we describe outcomes after ruxolitinib discontinuation in MF patients enrolled in a phase 1/2 study at our center. After a median follow-up of 79 months, 86 patients had discontinued ruxolitinib (30 of whom died while on therapy)...
July 3, 2017: Blood
https://www.readbyqxmd.com/read/28671999/speciation-trajectories-in-recombining-bacterial-species
#18
Pekka Marttinen, William P Hanage
It is generally agreed that bacterial diversity can be classified into genetically and ecologically cohesive units, but what produces such variation is a topic of intensive research. Recombination may maintain coherent species of frequently recombining bacteria, but the emergence of distinct clusters within a recombining species, and the impact of habitat structure in this process are not well described, limiting our understanding of how new species are created. Here we present a model of bacterial evolution in overlapping habitat space...
July 3, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28670320/evidence-and-consequence-of-a-highly-adapted-clonal-haplotype-within-the-australian-ascochyta-rabiei-population
#19
Yasir Mehmood, Prabhakaran Sambasivam, Sukhjiwan Kaur, Jenny Davidson, Audrey E Leo, Kristy Hobson, Celeste C Linde, Kevin Moore, Jeremy Brownlie, Rebecca Ford
The Australian Ascochyta rabiei (Pass.) Labr. (syn. Phoma rabiei) population has low genotypic diversity with only one mating type detected to date, potentially precluding substantial evolution through recombination. However, a large diversity in aggressiveness exists. In an effort to better understand the risk from selective adaptation to currently used resistance sources and chemical control strategies, the population was examined in detail. For this, a total of 598 isolates were quasi-hierarchically sampled between 2013 and 2015 across all major Australian chickpea growing regions and commonly grown host genotypes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28669404/ultra-sensitive-sequencing-identifies-high-prevalence-of-clonal-hematopoiesis-associated-mutations-throughout-adult-life
#20
Rocio Acuna-Hidalgo, Hilal Sengul, Marloes Steehouwer, Maartje van de Vorst, Sita H Vermeulen, Lambertus A L M Kiemeney, Joris A Veltman, Christian Gilissen, Alexander Hoischen
Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals ≥65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs)...
July 6, 2017: American Journal of Human Genetics
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