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https://www.readbyqxmd.com/read/29452662/pathogenesis-of-follicular-lymphoma
#1
REVIEW
Tracy Lackraj, Rashmi Goswami, Robert Kridel
Follicular lymphoma (FL) is presented as a germinal centre B cell lymphoma that is characterized by an indolent clinical course, but remains - paradoxically - largely incurable to date. The last years have seen significant progress in our understanding of FL lymphomagenesis, which is a multi-step process beginning in the bone marrow with the hallmark t(14;18)(q32;q21) translocation. The pathobiology of FL is complex and combines broad somatic changes at the level of both the genome and the epigenome, the latter evidenced by highly recurrent mutations in chromatin-modifying genes such as KMT2D and CREBBP...
March 2018: Best Practice & Research. Clinical Haematology
https://www.readbyqxmd.com/read/29449436/mixed-species-rnaseq-analysis-of-human-lymphoma-cells-adhering-to-mouse-stromal-cells-identifies-a-core-gene-set-that-is-also-differentially-expressed-in-the-lymph-node-microenvironment-of-mantle-cell-lymphoma-and-chronic-lymphocytic-leukemia-patients
#2
Gustav Arvidsson, Johan Henriksson, Birgitta Sander, Anthony P Wright
A subset of hematological cancer patients is refractory to treatment or suffers relapse, due in part to minimal residual disease, whereby some cancer cells survive treatment. Cell-adhesion mediated drug resistance is an important mechanism, whereby cancer cells receive survival signals via interaction with e.g. stromal cells. No genome-wide studies of in vitro systems have yet been performed to compare gene expression in different cell subsets within a co-culture and cells grown separately. Using RNA sequencing and species-specific read mapping, we compared transcript levels in human Jeko-1 mantle cell lymphoma cells stably adhered to mouse MS-5 stromal cells or in suspension within a co-culture or cultured separately as well as in stromal cells in co-culture or in separate culture...
February 15, 2018: Haematologica
https://www.readbyqxmd.com/read/29449275/circulating-tumor-dna-reveals-genetics-clonal-evolution-and-residual-disease-in-classical-hodgkin-lymphoma
#3
Valeria Spina, Alessio Bruscaggin, Annarosa Cuccaro, Maurizio Martini, Martina Di Trani, Gabriela Forestieri, Martina Manzoni, Adalgisa Condoluci, Alberto Arribas, Lodovico Terzi-Di-Bergamo, Silvia Laura Locatelli, Elisa Cupelli, Luca Ceriani, Alden A Moccia, Anastasios Stathis, Luca Nassi, Clara Deambrogi, Fary Diop, Francesca Guidetti, Alessandra Cocomazzi, Salvatore Annunziata, Vittoria Rufini, Alessandro Giordano, Antonino Neri, Renzo Boldorini, Bernhard Gerber, Francesco Bertoni, Michele Ghielmini, Georg Stüssi, Armando Santoro, Franco Cavalli, Emanuele Zucca, Luigi Maria Larocca, Gianluca Gaidano, Stefan Hohaus, Carmelo Carlo-Stella, Davide Rossi
The rarity of neoplastic cells in the biopsy imposes major technical hurdles that have so far limited genomic studies in classical Hodgkin lymphoma (cHL). By using a highly sensitive and robust deep-next-generation-sequencing approach for circulating tumor DNA (ctDNA), here we aimed at tracking the genetics of cHL in different clinical phases, and its modifications upon treatment. The analysis was based on specimens collected from 80 newly diagnosed and 32 refractory cHL patients, including longitudinal samples collected under ABVD chemotherapy and longitudinal samples from relapsing patients treated with chemotherapy and immunotherapy...
February 15, 2018: Blood
https://www.readbyqxmd.com/read/29446487/tm2d3-rs675436-or-fgfr2-rs755793-polymorphisms-and-susceptibility-to-epstein-barr-virus-associated-tumors-in-chinese-han-population
#4
Qianqian Zhang, Wen Liu, Yang Yang, Zhenzhen Zhao, Bing Luo
BACKGROUND: Epstein-Barr virus (EBV) is etiologically linked to nasopharyngeal carcinoma, lymphoma and gastric carcinoma. The aim of this study was to assess the association of TM2 domain containing 3 (TM2D3) and fibroblast growth factor receptor 2 (FGFR2) SNPs rs675436 and rs755793 with susceptibility to EBV-associated tumors in Chinese Han population. MATERIALS AND METHODS: Genomic DNA of 415 patients with cancer and 99 healthy controls was assessed using a MALDI-TOF mass spectrometer, and was genotyped in EBV-associated/-negative gastric cancer (EBVa/nGC), EBV-associated/-negative nasopharyngeal carcinoma (EBVa/nNPC), EBV-associated/ -negative lymphoma (EBVa/nL) and normal controls (NC)...
February 15, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29440271/phosphorylated-immunoreceptor-tyrosine-based-activation-motifs-and-integrin-cytoplasmic-domains-activate-spleen-tyrosine-kinase-via-distinct-mechanisms
#5
Lina Antenucci, Vesa P Hytönen, Jari Ylänne
Spleen tyrosine kinase (Syk) is involved in cellular adhesion and also in the activation and development of hematopoietic cells. Syk activation induced by genomic rearrangement has been linked to certain T-cell lymphomas, and Syk inhibitors have been shown to prolong survival of patients with B-cell lineage malignancies. Syk is activated either by its interaction with a double-phosphorylated Immunoreceptor Tyrosine-based Activation Motif (pITAM), which induces rearrangements in the Syk structure, or by the phosphorylation of specific tyrosine residues...
February 12, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29439385/alv-integration-associated-hypomethylation-at-the-tert-promoter-locus
#6
Gary Lam, Karen Beemon
Avian leukosis virus (ALV) is a simple retrovirus that can induce B-cell lymphoma in chicken(s) and other birds by insertional mutagenesis. The promoter region of telomerase reverse transcriptase (TERT) has been identified as an important integration site for tumorigenesis. Tumors with TERT promoter integrations are associated with increased TERT expression. The mechanism of this activation is still under investigation. We asked whether insertion of proviral DNA perturbs the epigenome of the integration site and, subsequently, impacts the regulation of neighboring genes...
February 10, 2018: Viruses
https://www.readbyqxmd.com/read/29429887/assessment-of-capture-and-amplicon-based-approaches-for-the-development-of-a-targeted-next-generation-sequencing-pipeline-to-personalize-lymphoma-management
#7
Stacy S Hung, Barbara Meissner, Elizabeth A Chavez, Susana Ben-Neriah, Daisuke Ennishi, Martin R Jones, Hennady P Shulha, Fong Chun Chan, Merrill Boyle, Robert Kridel, Randy D Gascoyne, Andrew J Mungall, Marco A Marra, David W Scott, Joseph M Connors, Christian Steidl
Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients...
February 7, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29429487/dynamic-changes-in-dna-methylation-patterns-in-canine-lymphoma-cell-lines-demonstrated-by-genome-wide-quantitative-dna-methylation-analysis
#8
J Yamazaki, J Jelinek, S Hisamoto, A Tsukamoto, M Inaba
DNA methylation is the conversion of cytosine to 5-methylcytosine, leading to changes in the interactions between DNA and proteins. Methylation of cytosine-guanine (CpG) islands (CGIs) is associated with gene expression silencing of the involved promoter. Although studies focussing on global changes or a few single loci in DNA methylation have been performed in dogs with certain diseases, genome-wide analysis of DNA methylation is required to prospectively identify specific regions with DNA methylation change...
January 2018: Veterinary Journal
https://www.readbyqxmd.com/read/29391350/overcoming-resistance-to-dna-targeted-agents-by-epigenetic-activation-of-schlafen-11-slfn11-expression-with-class-i-histone-deacetylase-inhibitors
#9
Sai Wen Tang, Anish Thomas, Junko Murai, Jane Trepel, Susan E Bates, Vinodh N Rajapakse, Yves Pommier
PURPOSE: Schlafen 11 (SLFN11), a putative DNA/RNA helicase is a dominant genomic determinant of response to DNA damaging agents and is frequently not expressed in cancer cells. Whether histone deacetylase (HDAC) inhibitors can be used to release SLFN11 and sensitize SLFN11-inactivated cancers to DNA-targeted agents is tested here. EXPERIMENTAL DESIGN: SLFN11 expression was examined in The Cancer Genome Atlas (TCGA), in cancer cell line databases and in patients treated with romidepsin...
February 1, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29390075/iw-scoring-an-integrative-weighted-scoring-framework-for-annotating-and-prioritizing-genetic-variations-in-the-noncoding-genome
#10
Jun Wang, Abu Z Dayem Ullah, Claude Chelala
The vast majority of germline and somatic variations occur in the noncoding part of the genome, only a small fraction of which are believed to be functional. From the tens of thousands of noncoding variations detectable in each genome, identifying and prioritizing driver candidates with putative functional significance is challenging. To address this, we implemented IW-Scoring, a new Integrative Weighted Scoring model to annotate and prioritise functionally relevant noncoding variations. We evaluate 11 scoring methods, and apply an unsupervised spectral approach for subsequent selective integration into two linear weighted functional scoring schemas for known and novel variations...
January 30, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29364576/simultaneous-detection-of-single-nucleotide-variant-deletion-insertion-and-fusion-in-lung-and-thyroid-carcinoma-using-cytology-specimen-and-an-rna-based-next-generation-sequencing-assay
#11
Natalya V Guseva, Omar Jaber, Aaron A Stence, Krishnaveni Sompallae, Amani Bashir, Ramakrishna Sompallae, Aaron D Bossler, Chris S Jensen, Deqin Ma
BACKGROUND: Molecular testing for epidermal growth factor receptor (EGFR) mutation and anaplastic lymphoma kinase (ALK) and ROS proto-oncogene 1, receptor tyrosine kinase (ROS1) fusion is routinely performed in patients with stage IV lung adenocarcinoma to assess their eligibility for targeted therapy. Fine-needle aspiration (FNA)-derived material frequently is the only pathologic material available. The identification of genomic aberrations in thyroid nodules from FNA smears may help stratify cancer risk and spare patients from a second surgery...
January 24, 2018: Cancer Cytopathology
https://www.readbyqxmd.com/read/29359812/novel-insights-into-the-disease-dynamics-of-b-cell-lymphomas-in-the-genomics-era
#12
REVIEW
Fong Chun Chan, Emilia Lim, Robert Kridel, Christian Steidl
High-throughput sequencing has significantly contributed to revealing the molecular underpinnings of B-cell lymphomagenesis and disease progression. It is now a widely accepted concept that the diversity of clinical responses to front-line therapy and the development of relapsed/refractory disease are in part explained by "interpatient" genetic heterogeneity measurable by individual sets of somatic gene alterations in tumor genomes. Moreover, extensive "intratumor" heterogeneity on the genotypic and phenotypic levels is the product of ongoing tumor evolution and adaptation to various selective pressures during cancer initiation, progression and therapeutic intervention...
January 23, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29351194/involvement-of-bax-and-bcl-2-in-induction-of-apoptosis-by-essential-oils-of-three-lebanese-salvia-species-in-human-prostate-cancer-cells
#13
Alessandra Russo, Venera Cardile, Adriana C E Graziano, Rosanna Avola, Maurizio Bruno, Daniela Rigano
Prostate cancer is one of the most common forms of cancer in men, and research to find more effective and less toxic drugs has become necessary. In the frame of our ongoing program on traditionally used Salvia species from the Mediterranean Area, here we report the biological activities of Salvia aurea, S. judaica and S. viscosa essential oils against human prostate cancer cells (DU-145). The cell viability was measured by 3(4,5-dimethyl-thiazol-2-yl)2,5-diphenyl-tetrazolium bromide (MTT) test and lactate dehydrogenase (LDH) release was used to quantify necrosis cell death...
January 19, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29340061/analysis-of-the-mutational-landscape-of-classic-hodgkin-lymphoma-identifies-disease-heterogeneity-and-potential-therapeutic-targets
#14
Elena Mata, Antonio Díaz-López, Ana M Martín-Moreno, Margarita Sánchez-Beato, Ignacio Varela, María J Mestre, Carlos Santonja, Fernando Burgos, Javier Menárguez, Mónica Estévez, Mariano Provencio, Beatriz Sánchez-Espiridión, Eva Díaz, Carlos Montalbán, Miguel A Piris, Juan F García
Defining the mutational landscape of classic Hodgkin lymphoma is still a major research goal. New targeted next-generation sequencing (NGS) techniques may identify pathogenic mechanisms and new therapeutic opportunities related to this disease. We describe the mutational profile of a series of 57 cHL cases, enriched in Hodgkin and Reed-Sternberg (HRS) cells. Overall, the results confirm the presence of strong genomic heterogeneity. However, several variants were consistently detected in genes related to relevant signaling pathways, such as GM-CSF/IL-3, CBP/EP300, JAK/STAT, NF-kappaB, and numerous variants of genes affecting the B-cell receptor (BCR) pathway, such as BTK, CARD11, BCL10, among others...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29337376/crispr-cas9-mediated-genome-editing-in-epstein-barr-virus-transformed-lymphoblastoid-b-cell-lines
#15
Sizun Jiang, Liang Wei Wang, Michael J Walsh, Stephen J Trudeau, Catherine Gerdt, Bo Zhao, Benjamin E Gewurz
Epstein-Barr virus (EBV) efficiently transforms primary human B cells into immortalized lymphoblastoid cell lines (LCLs), which are extensively used in human genetic, immunological and virological studies. LCLs provide unlimited sources of DNA for genetic investigation, but can be difficult to manipulate, for instance because low retroviral or lentiviral transduction frequencies hinder experiments that require co-expression of multiple components. This unit details Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 engineering for robust LCL genome editing...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29325248/-survival-of-patients-with-primary-central-nervous-system-diffuse-large-b-cell-lymphoma-impact-of-gene-aberrations-and-protein-overexpression-of-bcl-2-and-c-myc-and-selection-of-chemotherapy-regimens
#16
W J Yin, X Zhu, H Y Yang, W Y Sun, M J Wu
Objective: To investigate the impact of clinicopathological features, gene rearrangements and protein expression of bcl-6, bcl-2, C-MYC and chemotherapy regime on the prognosis of patients with primary central nervous system diffuse large B-cell lymphoma (PCNS-DLBCL). Methods: Thirty-three cases of PCNS-DLBCL diagnosed from January 2006 to December 2016 at Zhejiang Cancer Hospital were collected. The expression of CD10, bcl-6, bcl-2, MUM1 and MYC were detected by immunohistochemical staining (IHC). The presence of EB virus was detected by in situ hybridization(EBER)...
January 8, 2018: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29311308/dna-double-strand-break-response-factors-influence-end-joining-features-of-igh-class-switch-and-general-translocation-junctions
#17
Rohit A Panchakshari, Xuefei Zhang, Vipul Kumar, Zhou Du, Pei-Chi Wei, Jennifer Kao, Junchao Dong, Frederick W Alt
Ig heavy chain (IgH) class switch recombination (CSR) in B lymphocytes switches IgH constant regions to change antibody functions. CSR is initiated by DNA double-strand breaks (DSBs) within a donor IgH switch (S) region and a downstream acceptor S region. CSR is completed by fusing donor and acceptor S region DSB ends by classical nonhomologous end-joining (C-NHEJ) and, in its absence, by alternative end-joining that is more biased to use longer junctional microhomologies (MHs). Deficiency for DSB response (DSBR) factors, including ataxia telangiectasia-mutated (ATM) and 53BP1, variably impair CSR end-joining, with 53BP1 deficiency having the greatest impact...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29305299/identification-of-oaf-and-pvrl1-as-candidate-genes-for-an-ocular-anomaly-characterized-by-keratolenticular-dysgenesis-and-ectopia-lentis
#18
Dezső David, Deepti Anand, Carlos Araújo, Brian Gloss, Joana Fino, Marcel Dinger, Päivi Lindahl, Minna Pöyhönen, Laivuori Hannele, João Lavinha
Keratolenticular dysgenesis (KLD) and ectopia lentis are congenital eye defects. The aim of this study is the identification of molecular genetic alterations responsible for those ocular anomalies with neurologic impairment in an individual with a de novo balanced chromosome translocation t(11;18)(q23.3;q11.2)dn. Disruption of OAF, the human orthologue of the Drosophila oaf, by the 11q23.3 breakpoint results in reduced expression of this transcriptional regulator. Furthermore, four most likely nonfunctional chimeric transcripts comprising up to OAF exon 3, derived from the der(11) allele, have also been identified...
January 2, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29301886/complete-genome-sequence-of-elizabethkingia-miricola-strain-em798-26-isolated-from-the-blood-of-a-cancer-patient
#19
Jiun-Nong Lin, Chung-Hsu Lai, Chih-Hui Yang, Yi-Han Huang, Hsi-Hsun Lin
Elizabethkingia miricola EM798-26 was isolated from the blood of a patient with diffuse large B-cell lymphoma in Taiwan. We report here the complete genome sequence of EM798-26, which contains a G+C content of 35.7% and 3,877 candidate protein-coding genes.
January 4, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29296973/high-throughput-sequencing-of-the-b-cell-receptor-in-african-burkitt-lymphoma-reveals-clues-to-pathogenesis
#20
Katharine A Lombardo, David G Coffey, Alicia J Morales, Christopher S Carlson, Andrea M H Towlerton, Sarah E Gerdts, Francis K Nkrumah, Janet Neequaye, Robert J Biggar, Jackson Orem, Corey Casper, Sam M Mbulaiteye, Kishor G Bhatia, Edus H Warren
Burkitt lymphoma (BL), the most common pediatric cancer in sub-Saharan Africa, is a malignancy of antigen-experienced B lymphocytes. High-throughput sequencing (HTS) of the immunoglobulin heavy (IGH) and light chain (IGK/IGL) loci was performed on genomic DNA from 51 primary BL tumors: 19 from Uganda and 32 from Ghana. Reverse transcription polymerase chain reaction analysis and tumor RNA sequencing (RNAseq) was performed on the Ugandan tumors to confirm and extend the findings from the HTS of tumor DNA. Clonal IGH and IGK/IGL rearrangements were identified in 41 and 46 tumors, respectively...
March 28, 2017: Blood Advances
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