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Subcloning

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https://www.readbyqxmd.com/read/28924241/clinical-impact-of-the-subclonal-architecture-and-mutational-complexity-in-chronic-lymphocytic-leukemia
#1
F Nadeu, G Clot, J Delgado, D Martín-García, T Baumann, I Salaverria, S Beà, M Pinyol, P Jares, A Navarro, H Suárez-Cisneros, M Aymerich, M Rozman, N Villamor, D Colomer, M González, M Alcoceba, M J Terol, B Navarro, E Colado, Á R Payer, X S Puente, C López-Otín, A López-Guillermo, A Enjuanes, E Campo
Genome studies of chronic lymphocytic leukemia (CLL) have revealed the remarkable subclonal heterogeneity of the tumors, but the clinical implications of this phenomenon are not well known. We assessed the mutational status of 28 CLL driver genes by deep-targeted next-generation sequencing and copy number alterations (CNA) in 406 previously untreated patients and 48 sequential samples. We detected small subclonal mutations (0.6-25% of cells) in nearly all genes (26/28), and they were the sole alteration in 22% of the mutated cases...
September 19, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28921816/comprehensive-genetic-analysis-of-donor-cell-derived-leukemia-with-kmt2a-rearrangement
#2
Rieko Taniguchi, Hideki Muramatsu, Yusuke Okuno, Kyogo Suzuki, Satoshi Obu, Masahiro Nakatochi, Teppei Shimamura, Yoshiyuki Takahashi, Yasuo Horikoshi, Kenichiro Watanabe, Seiji Kojima
BACKGROUND: Donor cell leukemia (DCL) occurs after allogeneic hematopoietic stem cell transplantation. Several mechanisms, including occult leukemic/preleukemic subclones in the donor graft and germline predisposition to leukemia, are proposed to be associated with DCL's molecular pathogenesis. We report a comprehensive genetic analysis of a patient with KMT2A-rearranged DCL after allogeneic bone marrow transplantation for refractory cytopenia of childhood. PROCEDURE: We performed a whole-exome sequencing of the recipient's peripheral blood before transplant and the donor's peripheral blood and the recipient's bone marrow at the time of DCL diagnosis...
September 17, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28916750/comprehensive-multiregional-analysis-of-molecular-heterogeneity-in-bladder-cancer
#3
Mathilde Borg Houlberg Thomsen, Iver Nordentoft, Philippe Lamy, Søren Vang, Line Reinert, Christophe Kamungu Mapendano, Søren Høyer, Torben F Ørntoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt
Genetic alterations identified in adjacent normal appearing tissue in bladder cancer patients are indicative of a field disease. Here we assessed normal urothelium transformation and intra-tumour heterogeneity (ITH) in four patients with bladder cancer. Exome sequencing identified private acquired mutations in a lymph node metastasis and local recurrences. Deep re-sequencing revealed presence of at least three and four subclones in two patients with multifocal disease, while no demarcation of subclones was identified in the two patients with unifocal disease...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911083/multiregion-whole-exome-sequencing-of-matched-primary-and-metastatic-tumors-revealed-genomic-heterogeneity-and-suggested-polyclonal-seeding-in-colorectal-cancer-metastasis
#4
Q Wei, Z Ye, X Zhong, L Li, C Wang, R E Myers, J P Palazzo, D Fortuna, A Yan, S A Waldman, X Chen, J A Posey, A Basu-Mallick, B H Jiang, L Hou, J Shu, Y Sun, J Xing, B Li, H Yang
Background: Distant metastasis accounts for 90% of deaths from colorectal cancer (CRC). Genomic heterogeneity has been reported in various solid malignancies, but remains largely under-explored in metastatic CRC tumors, especially in primary to metastatic tumor evolution. Patients and methods: We conducted high-depth whole-exome sequencing in multiple regions of matched primary and metastatic CRC tumors. Using a total of 28 tumor, normal, and lymph node tissues, we analyzed inter- and intra-individual heterogeneity, inferred the tumor subclonal architectures, and depicted the subclonal evolutionary routes from primary to metastatic tumors...
September 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28903565/liquid-biopsies-the-clinics-and-the-molecules
#5
V Kubaczková, L Sedlarikova, B Bollová, V Sandecká, M Stork, L Pour, S Sevcikova
Unlike bone marrow biopsies, liquid biopsies represent a gentler, more accessible, less painful, repeatable and more comprehensive approach to get biologically relevant information about the entire tumor but also about treatment response and level of minimal residual disease. This is all possible since peripheral blood contains not only circulating tumor cells but also many circulating molecules of nucleic acids (microRNA, cell-free DNA, long non-coding RNA etc.). Multiple myeloma is a genetically heterogeneous disease characterized by multifocal tumor deposits in the bone marrow but also focal lesions elsewhere...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28902796/carcinosarcoma-of-the-pancreas-case-report-with-comprehensive-literature-review
#6
Dietrich A Ruess, Claudia Kayser, Jakob Neubauer, Stefan Fichtner-Feigl, Ulrich T Hopt, Uwe A Wittel
Carcinosarcomas are rare biphasic neoplasms with distinct malignant epithelial and mesenchymal components. Most commonly, carcinosarcomas arise in the uterus as malignant mixed müllerian tumors, but also infrequently appear in other organs such as the ovaries and breast, the prostate and urinary tract, the lungs, or in the gastrointestinal system, among others. Pancreatic carcinosarcomas are exceedingly rare; only a few cases are reported in the English literature. Their pathogenesis remains to be fully clarified...
October 2017: Pancreas
https://www.readbyqxmd.com/read/28899697/implementation-of-a-human-podocyte-injury-model-of-chronic-kidney-disease-for-profiling-of-renoprotective-compounds
#7
Vivek C Abraham, Loan N Miller, Steve D Pratt, Brent Putman, Laura Kim, Sujatha M Gopalakrishnan, Andrew King
Degradation of podocyte structural integrity and function are hallmarks of proteinuric chronic kidney disease. In vivo, injury of podocytes manifests itself in the form of disruption of foot process morphology and associated cytoskeletal architecture, de-differentiation, and loss of adhesion to the glomerular basement membrane. Given the critical role played by this highly specialized cell type in maintaining glomerular filtration, there is a need for improved physiologically relevant cellular models that enable detection of disease-relevant indicators of podocyte perturbation...
September 9, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28898985/lineage-switch-between-b-lymphoblastic-leukemia-and-acute-myeloid-leukemia-intermediated-by-occult-myelodysplastic-neoplasm-two-cases-of-adult-patients-with-evidence-of-genomic-instability-and-clonal-selection-by-chemotherapy
#8
Bin Wu, Rachel Jug, Catherine Luedke, Pu Su, Catherine Rehder, Chad McCall, Anand S Lagoo, Endi Wang
Objectives: Lineage switch occurs in rare leukemias, and the mechanism is unclear. We report two cases of B-lymphoblastic leukemia (B-ALL) relapsed as acute myeloid leukemia (AML). Methods: Retrospective review of clinical and laboratory data. Results: Complex cytogenetic abnormalities were detected in B-ALL for both cases with subclone heterogeneity. Postchemotherapy marrow biopsies showed trilineage hematopoiesis without detectable B-ALL...
August 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28895245/genetic-evolution-of-glioblastoma-stem-like-cells-from-primary-to-recurrent-tumor
#9
Francesca Orzan, Francesca De Bacco, Giovanni Crisafulli, Serena Pellegatta, Benedetta Mussolin, Giulia Siravegna, Antonio D'Ambrosio, Paolo M Comoglio, Gaetano Finocchiaro, Carla Boccaccio
Glioblastoma (GBM) is a lethal tumor that displays remarkable genetic heterogeneity. It is also known that GBM contains a cell hierarchy driven by stem-like cells (GSCs), responsible for tumor generation, therapeutic resistance and relapse. An important and still open issue is whether phylogenetically related GSCs can be found in matched primary and recurrent GBMs, and reflect tumor genetic evolution under therapeutic pressure. To address this, we analyzed the mutational profile of GSCs isolated from either human primary GBMs (primary GSCs) or their matched tumors recurring after surgery and chemo-radiotherapy (recurrent GSCs)...
September 12, 2017: Stem Cells
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#10
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28886708/cancer-heterogeneity-converting-a-limitation-into-a-source-of-biologic-information
#11
REVIEW
Albert Rübben, Arturo Araujo
Analysis of spatial and temporal genetic heterogeneity in human cancers has revealed that somatic cancer evolution in most cancers is not a simple linear process composed of a few sequential steps of mutation acquisitions and clonal expansions. Parallel evolution has been observed in many early human cancers resulting in genetic heterogeneity as well as multilineage progression. Moreover, aneuploidy as well as structural chromosomal aberrations seems to be acquired in a non-linear, punctuated mode where most aberrations occur at early stages of somatic cancer evolution...
September 8, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28881849/advances-in-single-cell-rna-sequencing-and-its-applications-in-cancer-research
#12
REVIEW
Sibo Zhu, Tao Qing, Yuanting Zheng, Li Jin, Leming Shi
Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years' development, single-cell RNA-seq can now achieve massively parallel, full-length mRNA sequencing as well as in situ sequencing and even has potential for multi-omic detection...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28877206/simulation-framework-for-generating-intratumor-heterogeneity-patterns-in-a-cancer-cell-population
#13
Watal M Iwasaki, Hideki Innan
As cancer cell populations evolve, they accumulate a number of somatic mutations, resulting in heterogeneous subclones in the final tumor. Understanding the mechanisms that produce intratumor heterogeneity is important for selecting the best treatment. Although some studies have involved intratumor heterogeneity simulations, their model settings differed substantially. Thus, only limited conditions were explored in each. Herein, we developed a general framework for simulating intratumor heterogeneity patterns and a simulator (tumopp)...
2017: PloS One
https://www.readbyqxmd.com/read/28876040/-secreted-expression-of-japanese-encephalitis-virus-prme-in-pichia-pastoris-and-immunogenicity-evaluation-of-the-virus-like-particles-in-mice
#14
Peng Zhao, Ya Jiang, Jingman Wang, Haojie Fan, Ruibing Cao
The study was to express prME protein of Japanese encephalitis virus (JEV) in Pichia pastoris and then to evaluate the immunological properties of the recombinant protein in mice, so as to explore a new way for subunit vaccine development of JEV. The JEV prME gene was amplified by RT-PCR with genome RNA of JEV vaccine strain SA14-14-2 and subcloned into pPICZa-A vector, designated as pPICZα-prME. pPICZα-SprME was constructed same as pPICZα-prME besides with the additional 19 Aa signal peptides coding gene of the JEV cap protein C terminal...
May 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28875151/molecular-characterization-structural-modeling-and-evaluation-of-antimicrobial-activity-of-basrai-thaumatin-like-protein-against-fungal-infection
#15
Nusrat Yasmin, Mahjabeen Saleem, Mamoona Naz, Roquyya Gul, Hafiz Muzzammel Rehman
A thaumatin-like protein gene from Basrai banana was cloned and expressed in Escherichia coli. Amplified gene product was cloned into pTZ57R/T vector and subcloned into expression vector pET22b(+) and resulting pET22b-basrai TLP construct was introduced into E. coli BL21. Maximum protein expression was obtained at 0.7 mM IPTG concentration after 6 hours at 37°C. Western blot analysis showed the presence of approximately 20 kDa protein in induced cells. Basrai antifungal TLP was tried as pharmacological agent against fungal disease...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28865132/growth-rate-changes-in-cho-host-cells-are-associated-with-karyotypic-heterogeneity
#16
Jong Youn Baik, Kelvin H Lee
Chinese hamster ovary (CHO) cell line instability and clonality issues can affect cell culture phenotypes such as cell growth, productivity, or product quality and remain challenges for biopharmaceutical manufacturing. While there have been efforts for characterizing cell line instability in CHO production cell lines, a pre-existing level of cell line instability in CHO host cells has not been determined. In this study, we report cell line instability and chromosomal heterogeneity of the host, CHO-DUK cell line, by using a karyotyping approach...
September 2, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28860343/antigen-receptor-sequencing-of-paired-bone-marrow-samples-shows-homogeneous-distribution-of-acute-lymphoblastic-leukemia-subclones
#17
Prisca M J Theunissen, David van Zessen, Andrew P Stubbs, Malek Faham, Michel Zwaan, Jacques J M van Dongen, Vincent H J Van der Velden
In B-cell precursor acute lymphoblastic leukemia, the initial leukemic cells share the same antigen receptor gene rearrangements. However, due to ongoing rearrangement processes, leukemic cells with different gene rearrangement patterns can develop, resulting in subclone formation. We studied leukemic subclones and their distribution in the bone marrow and peripheral blood at diagnosis. Antigen receptor gene rearrangements (IGH, IGK, TRG, TRD, TRB) were analyzed by next-generation sequencing in seven paired bone marrow samples and five paired bone marrow-blood samples...
August 31, 2017: Haematologica
https://www.readbyqxmd.com/read/28854921/spatial-and-temporal-epithelial-ovarian-cancer-cell-heterogeneity-impacts-maraba-virus-oncolytic-potential
#18
Jessica G Tong, Yudith Ramos Valdes, Milani Sivapragasam, John W Barrett, John C Bell, David Stojdl, Gabriel E DiMattia, Trevor G Shepherd
BACKGROUND: Epithelial ovarian cancer exhibits extensive interpatient and intratumoral heterogeneity, which can hinder successful treatment strategies. Herein, we investigated the efficacy of an emerging oncolytic, Maraba virus (MRBV), in an in vitro model of ovarian tumour heterogeneity. METHODS: Four ovarian high-grade serous cancer (HGSC) cell lines were isolated and established from a single patient at four points during disease progression. Limiting-dilution subcloning generated seven additional subclone lines to assess intratumoral heterogeneity...
August 30, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28845585/intrafocal-heterogeneity-of-erg-protein-expression-and-gene-fusion-pattern-in-prostate-cancer
#19
Ja Hee Suh, Jeong Hwan Park, Cheol Lee, Kyung Chul Moon
BACKGROUND: Prostate cancer is considered to be highly heterogeneous, with various morphologic features and biologic behaviors. The TMPRSS2-ERG gene fusion is the most frequently observed genetic aberration in prostate cancer. The aim of this study was to elucidate the intrafocal heterogeneity of ERG gene fusion status. METHODS: ERG immunohistochemistry (IHC) was performed in samples from 168 prostate cancer patients who had undergone radical prostatectomy, and 40 cases showing ERG-positive IHC staining were selected for tissue microarray (TMA) construction...
August 28, 2017: Prostate
https://www.readbyqxmd.com/read/28844940/subclonal-evolution-of-cancer-related-gene-mutations-in-p53-immunopositive-patches-in-human-skin
#20
Amel A Albibas, Matthew J J Rose-Zerilli, Chester Lai, Reuben J Pengelly, Gabrielle A Lockett, Jeffrey Theaker, Sarah Ennis, John W Holloway, Eugene Healy
Normal sun-exposed skin contains numerous epidermal patches that stain positive for p53 protein (p53 immunopositive patches; PIPs), which are considered potential early precursors of skin cancer. Whilst the TP53 gene is mutated in many PIPs, it is unclear whether PIPs contain any other cancer-related mutations. Here we report that PIPs, predominantly <3,000 p53 immunopositive cells in size, within normal chronically exposed skin contain mutations in multiple genes which are mutated in cutaneous squamous cell cancers...
August 24, 2017: Journal of Investigative Dermatology
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