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Clonal evolution

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https://www.readbyqxmd.com/read/28810325/-heterogeneity-and-clonal-evolution-in-pediatric-etv6-runx1-acute-lymphoblastic-leukemia-by-quantitative-multigene-fluorescence-in-situ-hybridization
#1
L Zhang, L P Hu, X M Liu, Y Guo, W Y Yang, J Y Zhang, F Liu, T F Liu, S C Wang, X J Chen, M Ruan, B Q Qi, L X Chang, Y M Chen, Y Zou, X F Zhu
Objective: To evaluate heterogeneity and clonal evolution in pediatric ETV6-RUNX1(+) acute lymphoblastic leukemia (ALL) in China. Methods: Totally 48 children (<14 years) with newly diagnosed ETV6-RUNX1(+) ALL in Institute of Hematology and Blood Disease Hospital, CAMS and PUMC, from February 2006 to June 2011 were included. The copy number variations were analyzed by quantitative multigene fluorescence in situ hybridization (QM-FISH) in 48 patients. Non-normal distribution of measurement data were shown with Median (range) , count data were shown with percent (%) ...
July 14, 2017: Zhonghua Xue Ye Xue za Zhi, Zhonghua Xueyexue Zazhi
https://www.readbyqxmd.com/read/28808044/germline-mutation-contribution-to-chromosomal-instability
#2
REVIEW
Sock Hoai Chan, Joanne Ngeow
Genomic instability is a feature of cancer that fuels oncogenesis through increased frequency of genetic disruption, leading to loss of genomic integrity and promoting clonal evolution as well as tumor transformation. A form of genomic instability prevalent across cancer types is chromosomal instability, which involves karyotypic changes including chromosome copy number alterations as well as gross structural abnormalities such as transversions and translocations. Defects in cellular mechanisms that are in place to govern fidelity of chromosomal segregation, DNA repair and ultimately genomic integrity are known to contribute to chromosomal instability...
September 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28790994/insight-into-the-origin-and-evolution-of-the-vibrio-parahaemolyticus-pandemic-strain
#3
REVIEW
Romilio T Espejo, Katherine García, Nicolas Plaza
A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28790201/division-of-labor-bet-hedging-and-the-evolution-of-mixed-biofilm-investment-strategies
#4
Nick Vallespir Lowery, Luke McNally, William C Ratcliff, Sam P Brown
Bacterial cells, like many other organisms, face a tradeoff between longevity and fecundity. Planktonic cells are fast growing and fragile, while biofilm cells are often slower growing but stress resistant. Here we ask why bacterial lineages invest simultaneously in both fast- and slow-growing types. We develop a population dynamic model of lineage expansion across a patchy environment and find that mixed investment is favored across a broad range of environmental conditions, even when transmission is entirely via biofilm cells...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28781850/t315i-clone-selection-in-a-ph-all-patient-under-low-dose-ponatinib-maintenance
#5
Jasmine Noetzli, Mathilde Gavillet, Stavroula Masouridi-Levrat, Michel Duchosal, Olivier Spertini
We report here the clinical course of a Ph+ ALL patient who was treated with ponatinib 15 mg/day, as maintenance therapy, and developed a BCR-ABL T315I mutation leading to ALL relapse. This clonal evolution was reversed, without adverse effects, by increasing ponatinib to 45 mg/day. To our knowledge, we have been confronted with the first clinical case of a T315I clonal selection of ALL caused by subeffective therapeutic level of the drug. This single patient experience highlights the risk of T315I clone selection in Ph+ ALL treated with reduced dose ponatinib...
August 2017: Clinical Case Reports
https://www.readbyqxmd.com/read/28780131/commentary-on-clonal-evolution-of-chemotherapy-resistant-urothelial-carcinoma-faltas-bm-prandi-d-tagawa-st-molina-am-nanus-dm-sternberg-c-rosenberg-j-mosquera-jm-robinson-b-elemento-o-sboner-a-beltran-h-demichelis-f-rubin-ma-nat-genet-2016-oct-17-http-dx-doi
#6
Byron H Lee
Chemotherapy-resistant urothelial carcinoma has no uniformly curative therapy. Understanding how selective pressure from chemotherapy directs the evolution of urothelial carcinoma and shapes its clonal architecture is a central biological question with clinical implications. To address this question, we performed whole-exome sequencing and clonality analysis of 72 urothelial carcinoma samples, including 16 matched sets of primary and advanced tumors prospectively collected before and after chemotherapy. Our analysis provided several insights that are as follows: (1) chemotherapy-treated urothelial carcinoma is characterized by intrapatient mutational heterogeneity, and most mutations are not shared; (2) both branching evolution and metastatic spread are very early events in the natural history of urothelial carcinoma; (3) chemotherapy-treated urothelial carcinoma is enriched with clonal mutations involving L1 cell-adhesion molecule and integrin signaling pathways; and (4) APOBEC-induced mutagenesis is clonally enriched in chemotherapy-treated urothelial carcinoma and continues to shape the evolution of urothelial carcinoma throughout its lifetime...
August 2, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28774726/girardia-dorotocephala-transcriptome-sequence-assembly-and-validation-through-characterization-of-piwi-homologs-and-stem-cell-progeny-markers
#7
Eugene Matthew P Almazan, Sydney L Lesko, Michael P Markey, Labib Rouhana
Planarian flatworms are popular models for the study of regeneration and stem cell biology in vivo. Technical advances and increased availability of genetic information have fueled the discovery of molecules responsible for stem cell pluripotency and regeneration in flatworms. Unfortunately, most of the planarian research performed worldwide utilizes species that are not natural habitants of North America, which limits their availability to newcomer laboratories and impedes their distribution for educational activities...
August 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28770103/subclonal-analysis-in-a-lobular-breast-cancer-with-classical-and-solid-growth-pattern-mimicking-a-solid-papillary-carcinoma
#8
Matthias Christgen, Stephan Bartels, Jana Lisa van Luttikhuizen, Maximilian Schieck, Stefanie Pertschy, Sudip Kundu, Ulrich Lehmann, Bjoern Sander, Enrico Pelz, Florian Länger, Brigitte Schlegelberger, Doris Steinemann, Hans Kreipe
Recently, a new variant of invasive lobular breast cancer (ILBC) with solid-papillary-like growth pattern has been described. We present a case of ILBC with solid-papillary-like growth pattern in the main tumour mass and classical invasive lobular growth pattern in adjacent satellite foci. The two tumour components were subjected to comprehensive molecular analyses. Both components were ER/PR-positive, HER2-negative, and showed a complete loss of E-cadherin and beta-catenin protein expression, as determined by immunohistochemistry...
July 2017: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/28765516/next-generation-sequencing-in-chronic-lymphocytic-leukemia-recent-findings-and-new-horizons
#9
REVIEW
Ana E Rodríguez-Vicente, Vasilis Bikos, María Hernández-Sánchez, Jitka Malcikova, Jesús-María Hernández-Rivas, Sarka Pospisilova
The rapid progress in next-generation sequencing technologies has significantly contributed to our knowledge of the genetic events associated with the development, progression and treatment resistance of chronic lymphocytic leukemia patients. Together with the discovery of new driver mutations, next-generation sequencing has revealed an immense degree of both intra- and inter-tumor heterogeneity and enabled us to describe marked clonal evolution. Advances in immunogenetics may be implemented to detect minimal residual disease more sensitively and to track clonal B cell populations, their dynamics and molecular characteristics...
July 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28762112/targeted-next-generation-sequencing-identifies-clinically-relevant-mutations-in-patients-with-chronic-neutrophilic-leukemia-at-diagnosis-and-blast-crisis
#10
S E Langabeer, K Haslam, J Kelly, J Quinn, R Morrell, E Conneally
PURPOSE: Chronic neutrophilic leukemia is a rare form of myeloproliferative neoplasm characterized by mature neutrophil hyperleukocytosis. The majority of patients harbor somatic mutations of CSF3R gene and are potentially amenable to targeted therapy with JAK inhibitors. The incidence and clinical significance of additional mutations requires clarification. MATERIALS AND METHODS: A next-generation sequencing approach for myeloid malignancy-associated mutations was applied to diagnostic and matched blast crisis samples from four chronic neutrophilic leukemia patients...
July 31, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/28761786/the-bivalve-thyasira-cf-gouldi-hosts-chemoautotrophic-symbiont-populations-with-strain-level-diversity
#11
Bonita McCuaig, France Liboiron, Suzanne C Dufour
Invertebrates from various marine habitats form nutritional symbioses with chemosynthetic bacteria. In chemosynthetic symbioses, both the mode of symbiont transmission and the site of bacterial housing can affect the composition of the symbiont population. Vertically transmitted symbionts, as well as those hosted intracellularly, are more likely to form clonal populations within their host. Conversely, symbiont populations that are environmentally acquired and extracellular may be more likely to be heterogeneous/mixed within host individuals, as observed in some mytilid bivalves...
2017: PeerJ
https://www.readbyqxmd.com/read/28758283/copy-number-profiling-of-adult-relapsed-b-cell-precursor-acute-lymphoblastic-leukemia-reveals-potential-leukemia-progression-mechanisms
#12
Jordi Ribera, Lurdes Zamora, Mireia Morgades, Mar Mallo, Neus Solanes, Montserrat Batlle, Susana Vives, Isabel Granada, Jordi Juncà, Roberto Malinverni, Eulàlia Genescà, Ramon Guàrdia, Santiago Mercadal, Lourdes Escoda, Joaquín Martinez-Lopez, Mar Tormo, Jordi Esteve, Marta Pratcorona, Carmen Martinez-Losada, Francesc Solé, Evarist Feliu, Josep Maria Ribera
The outcome of relapsed adult acute lymphoblastic leukemia (ALL) remains dismal despite new therapeutic approaches. Previous studies analyzing relapse samples have shown a high degree of heterogeneity regarding gene alterations without an evident relapse signature. Bone marrow or peripheral blood samples from 31 adult B-cell precursor ALL patients at first relapse, and 21 paired diagnostic samples were analyzed by multiplex ligation probe-dependent amplification (MLPA). Nineteen paired diagnostic and relapse samples of these 21 patients were also analyzed by SNP arrays...
July 30, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28755443/application-of-liquid-biopsies-in-cancer-targeted-therapy
#13
S Sumanasuriya, M B Lambros, J S de Bono
As a growing body of evidence demonstrates intertumoral and intratumoral heterogeneity and clonal evolution, both during carcinogenesis and also throughout treatment resulting in acquired drug resistance, the utility of blood-based assays or "liquid biopsies" is becoming increasingly recognized in clinical practice and trial design. "Liquid biopsies" provide a less invasive approach to the current gold standard of interrogating tumors by tissue biopsies, which are frequently unfeasible, associated with morbidity, and cannot be performed as often...
July 29, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28752247/breast-cancer-complexity-implications-of-intratumoral-heterogeneity-in-clinical-management
#14
REVIEW
Brittany Haynes, Ashapurna Sarma, Pratima Nangia-Makker, Malathy P Shekhar
Generation of intratumoral phenotypic and genetic heterogeneity has been attributed to clonal evolution and cancer stem cells that together give rise to a tumor with complex ecosystems. Each ecosystem contains various tumor cell subpopulations and stromal entities, which, depending upon their composition, can influence survival, therapy responses, and global growth of the tumor. Despite recent advances in breast cancer management, the disease has not been completely eradicated as tumors recur despite initial response to treatment...
July 27, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28751420/recombination-driven-genome-evolution-and-stability-of-bacterial-species
#15
Purushottam D Dixit, Tin Y Pang, Sergei Maslov
While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift...
July 27, 2017: Genetics
https://www.readbyqxmd.com/read/28750660/remixt-clone-specific-genomic-structure-estimation-in-cancer
#16
Andrew W McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P E de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S Cenk Sahinalp, Sohrab P Shah
Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints...
July 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28750401/a-practical-approach-to-tumor-heterogeneity-in-clinical-research-and-diagnostics
#17
Giorgio Stanta, Serena Bonin
This Pathobiology issue tries to better define the complex phenomenon of intratumor heterogeneity (ITH), mostly from a practical point of view. This topic has been chosen because ITH is a central issue in tumor development and has to be investigated directly in patient tissue and immediately applied in the treatment of the presenting patient. Different types of ITH should be considered: clonal genetic and epigenetic evolution, morphological heterogeneity, and tumor sampling, heterogeneity resulting from microenvironmental autocrine and paracrine interaction, and stochastic plasticity related to different functional cell efficiencies...
July 28, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28746789/cytogenetic-clonal-evolution-in-myelodysplastic-syndromes-is-associated-with-inferior-prognosis
#18
Judith Neukirchen, Michael Lauseker, Barbara Hildebrandt, Ann-Christin Nolting, Jennifer Kaivers, Guido Kobbe, Norbert Gattermann, Rainer Haas, Ulrich Germing
BACKGROUND: The karyotype of bone marrow cells at the time of diagnosis is a strong prognostic parameter for overall survival as well as acute myeloid leukemia (AML) progression in patients with myelodysplastic syndromes (MDS). However, to the authors' knowledge, few data exist regarding the prognostic impact of cytogenetic clonal evolution during the course of MDS. METHODS: The authors evaluated follow-up karyotype analyses in 549 patients from the Dusseldorf MDS Registry...
July 26, 2017: Cancer
https://www.readbyqxmd.com/read/28745003/an-evolutionary-perspective-on-the-systems-of-adaptive-immunity
#19
Viktor Müller, Rob J de Boer, Sebastian Bonhoeffer, Eörs Szathmáry
We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback...
July 26, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28740486/evolution-of-acinetobacter-baumannii-in-vivo-international-clone-ii-more-resistance-to-ceftazidime-mutation-in-ptk
#20
Xiaoting Hua, Zhihui Zhou, Qing Yang, Qiucheng Shi, Qingye Xu, Jianfeng Wang, Keren Shi, Feng Zhao, Long Sun, Zhi Ruan, Yan Jiang, Yunsong Yu
Acinetobacter baumannii is an important nosocomial pathogen worldwide. A more comprehensive understanding of the within-host genomic evolution of A. baumannii would provide a molecule basis for improving treatment of A. baumannii infection. To understand the evolutionary mechanism facilitating A. baumannii survived in human body, we here reported the genomic analysis of A. baumannii isolated sampled from Chinese patients. We used whole-genome sequence of A. baumannii isolates from the same patient to determine single-nucleotide variants, insertion sequence mapping, and gene change...
2017: Frontiers in Microbiology
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