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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
#1
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
#2
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/29439670/phase-i-study-of-an-active-immunotherapy-for-asymptomatic-phase-lymphoplasmacytic-lymphoma-with-dna-vaccines-encoding-antigen-chemokine-fusion-study-protocol
#3
Sheeba K Thomas, Soung-Chul Cha, D Lynne Smith, Kun Hwa Kim, Sapna R Parshottam, Sheetal Rao, Michael Popescu, Vincent Y Lee, Sattva S Neelapu, Larry W Kwak
BACKGROUND: There is now a renewed interest in cancer vaccines. Patients responding to immune checkpoint blockade usually bear tumors that are heavily infiltrated by T cells and express a high load of neoantigens, indicating that the immune system is involved in the therapeutic effect of these agents; this finding strongly supports the use of cancer vaccine strategies. Lymphoplasmacytic lymphoma (LPL) is a low grade, incurable disease featuring an abnormal proliferation of Immunoglobulin (Ig)-producing malignant cells...
February 13, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29439385/alv-integration-associated-hypomethylation-at-the-tert-promoter-locus
#4
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/29432597/identification-of-novel-recurrent-etv6-igh-fusions-in-primary-central-nervous-system-lymphoma
#5
Aurélie Bruno, Karim Labreche, Maïlys Daniau, Blandine Boisselier, Guillaume Gauchotte, Louis Royer-Perron, Amithys Rahimian, Frédéric Lemoine, Pierre de la Grange, Justine Guégan, Franck Bielle, Marc Polivka, Clovis Adam, David Meyronet, Dominique Figarella-Branger, Chiara Villa, Fabrice Chrétien, Sandrine Eimer, Frédéric Davi, Audrey Rousseau, Caroline Houillier, Carole Soussain, Karima Mokhtari, Khê Hoang-Xuan, Agusti Alentorn
Background: Primary central nervous system lymphoma (PCNSL) represents a particular entity within non-Hodgkin lymphomas and is associated with poor outcome. The present study addresses the potential clinical relevance of chimeric transcripts in PCSNL discovered by using RNA-sequencing (RNA-Seq). Methods: Seventy-two immunocompetent and newly diagnosed PCNSL cases were included in the present study. Among them, six were analyzed by RNA-seq to detect new potential fusion transcripts...
February 8, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29432186/adaptive-antibody-diversification-through-n-linked-glycosylation-of-the-immunoglobulin-variable-region
#6
Fleur S van de Bovenkamp, Ninotska I L Derksen, Pleuni Ooijevaar-de Heer, Karin A van Schie, Simone Kruithof, Magdalena A Berkowska, C Ellen van der Schoot, Hanna IJspeert, Mirjam van der Burg, Ann Gils, Lise Hafkenscheid, René E M Toes, Yoann Rombouts, Rosina Plomp, Manfred Wuhrer, S Marieke van Ham, Gestur Vidarsson, Theo Rispens
A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N -linked glycans, a process conditional on the introduction of consensus amino acid motifs ( N -glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
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/29427587/highly-sensitive-virome-capture-sequencing-technique-vircapseq-vert-identifies-partial-non-coding-sequences-but-no-active-viral-infection-in-cutaneous-t-cell-lymphoma
#9
Mary E Anderson, Dorottya Nagy-Szakal, Komal Jain, Christina C Patrone, Mark G Frattini, W Ian Lipkin, Larisa J Geskin
No abstract text is available yet for this article.
February 7, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29422597/from-genetics-to-the-clinic-a-translational-perspective-on-follicular-lymphoma
#10
REVIEW
Sarah Huet, Pierre Sujobert, Gilles Salles
Follicular lymphoma (FL) is the most frequent indolent B cell lymphoma and is still considered to be incurable. In recent years, whole-exome sequencing studies of large cohorts of patients have greatly improved our knowledge of the FL mutational landscape. Moreover, the prolonged evolution of this disease has enabled some insights regarding the early pre-lymphoma lesions as well as the clonal evolution after treatment, allowing an evolutionary perspective on lymphomagenesis. Deciphering the earliest initiating lesions and identifying the molecular alterations leading to disease progression currently represent important goals; accomplishing these could help identify the most relevant targets for precision therapy...
February 9, 2018: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29421668/first-report-of-sporadic-cases-of-candida-auris-in-colombia
#11
Claudia M Parra-Giraldo, Sandra L Valderrama, Gloria Cortes-Fraile, Javier R Garzón, Beatriz E Ariza, Florent Morio, Melva Y Linares-Linares, Andrés Ceballos-Garzón, Alejandro de la Hoz, Catalina Hernandez, Carlos Alvarez-Moreno, Patrice Le Pape
BACKGROUND: Candida auris is a recently reported Candida species which is phenotypically similar to Candida haemulonii and related to hospital outbreaks. This organism can be misidentified as C. haemulonii, C. famata, C. catenulata or Rhodotorula glutinis by phenotypic approaches. MALDI-TOF MS and DNA sequence analysis using ITS rDNA barcoding provide an accurate identification. CASE PRESENTATIONS: Three cases of C. auris infection in patients with risk factors for fungal infection (Admitted to the intensive care unit, lymphoma and HIV respectively, all three with previous antibiotic use) and not epidemiologically related...
February 5, 2018: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29400604/capture-based-ultra-deep-sequencing-in-plasma-ctdna-reveals-the-resistance-mechanism-of-alk-inhibitors-in-a-patient-with-advanced-alk-positive-nsclc
#12
Jing Guo, Lihong Guo, Li Sun, Zhenzhen Wu, Junyi Ye, Jing Liu, Qiang Zuo
BACKGROUND: Anaplastic lymphoma kinase (ALK) is a validated molecular target in non-small-cell lung cancer (NSCLC). However, the clinical benefits of ALK inhibitors are almost universally limited by the emergence of drug resistance. METHODS: We monitored the plasma circulating tumor DNA (ctDNA) using captured-based ultra-deep sequencing analysis of one patient with metastatic ALK-positive NSCLC who had received therapies including first-, second- and third-generation ALK inhibitors...
February 5, 2018: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/29398045/-management-of-orbital-inflammation-in-internal-medicine-proposal-for-a-diagnostic-work-up
#13
S Abad, F Héran, C Terrada, P Bielefeld, D Sène, S Trad, D Saadoun, P Sève
Inflammatory orbitopathies relate to an inflammatory state originating within the orbit and its adnexes, except the inner ocular globe. Orbital inflammation (OI) may be either localized manifestation of a proven or like autoimmune disease, or local response from immune system against infectious, structural or tumoral antigens. We review the clinical manifestations of OI, which provide helpful clues to the diagnosis and describe the inflammatory, infectious and neoplastic conditions classically associated with OI...
February 1, 2018: La Revue de Médecine Interne
https://www.readbyqxmd.com/read/29396094/r-chop-radioimmunotherapy-and-maintenance-rituximab-in-untreated-follicular-lymphoma-swog-s0801-a-single-arm-phase-2-multicentre-study
#14
Paul M Barr, Hongli Li, W Richard Burack, Michael LeBlanc, Sonali M Smith, Ajay K Gopal, Justin D Floyd, Daniel O Persky, Oliver W Press, Richard I Fisher, Jonathan W Friedberg
BACKGROUND: Despite an abundance of therapeutic options, advanced-stage follicular lymphoma remains incurable. Furthermore, the ideal sequence and absolute benefit of post-induction therapy is unclear. We designed SWOG S0801 to assess the efficacy and safety of consolidative radioimmunotherapy and sequential maintenance rituximab following chemoimmunotherapy. METHODS: For this single-arm, phase 2, multicentre study, we enrolled patients aged 18 years and older with a diagnosis of stage III, IV, or bulky stage II follicular lymphoma, grades 1, 2, or 3a, who had not received previous therapy, from from 20 institutions within the United States National Cancer Institute Clinical Trials Network...
January 25, 2018: Lancet Haematology
https://www.readbyqxmd.com/read/29386283/modified-cross-linking-ligation-and-sequencing-of-hybrids-qclash-identifies-kshv-microrna-targets-in-endothelial-cells
#15
Lauren A Gay, Sunantha Sethuraman, Merin Thomas, Peter C Turner, Rolf Renne
KS tumors are derived from endothelial cells and express KHSV microRNAs (miRNAs). Although miRNA targets have been identified in B cell lymphoma-derived cells and in epithelial cells, little has been done to characterize the KSHV miRNA targetome in endothelial cells. A recent innovation in the identification of miRNA targetomes, Cross-linking, Ligation, and Sequencing of Hybrids (CLASH), unambiguously identifies miRNAs and their targets by ligating the two species while both are still bound within the RNA-Induced Silencing Complex (RISC)...
January 31, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29385200/preferential-use-of-unmutated-immunoglobulin-heavy-variable-region-genes-in-boxer-dogs-with-chronic-lymphocytic-leukemia
#16
Emily D Rout, Robert C Burnett, Julia D Labadie, Janna A Yoshimoto, Anne C Avery
Human chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease, and immunoglobulin heavy variable region (IGHV) gene mutational status is an important prognostic marker. IGHV mutational status has not been previously examined in canine CLL. We sequenced the IGHV-D-J rearrangements from 55 canine patients with CLL, including 36 non-Boxer and 19 Boxer dogs. The majority of non-Boxers (75%) had mutated IGHV genes, whereas the majority of Boxers (79%) had unmutated IGHV genes. IGHV3-41 and IGHV3-67 gene usage was significantly higher in Boxers with CLL compared to non-Boxers...
2018: PloS One
https://www.readbyqxmd.com/read/29372844/molecular-testing-of-non-small-cell-lung-carcinoma-diagnosed-by-endobronchial-ultrasound-guided-transbronchial-fine-needle-aspiration
#17
Erika E Doxtader, Yu-Wei Cheng, Yaxia Zhang
CONTEXT: - Given the increasing demand for molecular testing of non-small cell lung carcinoma specimens to guide therapeutic decision-making, and the trend toward minimally invasive techniques for obtaining diagnostic tissue, cytopathology laboratories must devise strategies to maximize DNA yield for necessary molecular testing. OBJECTIVE: - To describe our experience at Cleveland Clinic with epidermal growth factor receptor ( EGFR) mutation testing by next-generation sequencing and anaplastic lymphoma kinase ( ALK) gene rearrangement testing by fluorescence in situ hybridization of non-small cell lung carcinomas diagnosed by cytology, with an emphasis on specimens obtained by endobronchial ultrasound-guided transbronchial fine-needle aspiration...
January 26, 2018: Archives of Pathology & Laboratory Medicine
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
#18
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/29363235/e7777-in-japanese-patients-with-relapsed-refractory-peripheral-and-cutaneous-t-cell-lymphoma-a-phase-1-study
#19
Ken Ohmachi, Kiyoshi Ando, Michinori Ogura, Toshiki Uchida, Kensei Tobinai, Dai Maruyama, Masayuki Namiki, Tadashi Nakanishi
E7777, a recombinant cytotoxic fusion protein comprising diphtheria toxin fragments A and B and human interleukin-2, shares an amino acid sequence with denileukin diftitox but has improved purity and an increased percentage of active protein monomer species. A phase 1 study was conducted to evaluate the tolerability, safety, pharmacokinetics and anti-tumour activity of E7777 in Japanese patients with relapsed/refractory peripheral and cutaneous T-cell lymphoma. E7777 (6, 12 and expanded 9 μg/kg/day) was administered to 13 patients via intravenous infusion on 5 consecutive days per 21-day cycle...
January 24, 2018: Cancer Science
https://www.readbyqxmd.com/read/29363116/eml4-alk-fusion-variant-v3-is-a-high-risk-feature-conferring-accelerated-metastatic-spread-early-treatment-failure-and-worse-overall-survival-in-alk-nsclc
#20
Petros Christopoulos, Volker Endris, Farastuk Bozorgmehr, Mei Elsayed, Martina Kirchner, Jonas Ristau, Ivo Buchhalter, Roland Penzel, Felix J Herth, Claus P Heussel, Martin Eichhorn, Thomas Muley, Michael Meister, Jürgen R Fischer, Stefan Rieken, Arne Warth, Helge Bischoff, Peter Schirmacher, Albrecht Stenzinger, Michael Thomas
In order to identify anaplastic lymphoma kinase-driven non-small cell lung cancer (ALK+ NSCLC) patients with a worse outcome, who might require novel therapeutic approaches, we retrospectively analyzed all stage IV cases treated at our institutions with one of the main echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion variants V1, V2, V3 as detected by next-generation sequencing (NGS) or RT-PCR (n=67). Progression under tyrosine kinase inhibitor (TKI) treatment was evaluated both according to Response Evaluation Criteria in Solid Tumors (RECIST) and by the need to change systemic therapy...
January 24, 2018: International Journal of Cancer. Journal International du Cancer
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