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lymphoma sequencing

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https://www.readbyqxmd.com/read/29036679/human-recombinant-fab-fragment-from-combinatorial-libraries-of-a-b-cell-lymphoma-patient-recognizes-core-protein-of-chondroitin-sulfate-proteoglycan-4
#1
Yoko Egami, Yuta Narushima, Motohiro Ohshima, Akira Yoshida, Naruki Yoneta, Yasufumi Masaki, Kunihiko Itoh
CD antigens are well known as therapeutic targets of B-cell lymphoma. To isolate therapeutic antibodies that recognize novel targets other than CD antigens, we constructed a phage display combinatorial antibody Fab library from bone marrow lymphocytes of B-cell lymphoma patient. To eliminate antibodies reactive with known B-cell lymphoma antigen, non-hematopoietic and patient's sera reactive HeLaS3 cells was selected as a target of whole cell panning. Five rounds of panning against live HeLaS3 cells retrieved single Fab clone, termed AHSA (Antibody to HeLa Surface Antigen)...
September 28, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29029457/prognostic-relevance-of-protein-expression-clinical-factors-and-myd88-mutation-in-primary-bone-lymphoma
#2
Yong Xu, Jian Li, Jian Ouyang, Juan Li, Jingyan Xu, Qiguo Zhang, Yonggong Yang, Min Zhou, Jing Wang, Cuiling Zhang, Yueyi Xu, Ping Li, Rongfu Zhou, Bing Chen
Primary bone lymphomas (PBLs) are composed of malignant lymphoid cells presenting in osseous sites, without supra-regional lymph node or extranodal involvement. We systematically characterized the immunophenotype and the myeloid differentiation factor 88 (MYD88)-L265P gene mutation status in PBL. Clinical data from 19 patients with PBL treated at Nanjing Drum Tower Hospital between 2009 and 2015 were analyzed retrospectively. Protein expression patterns were identified immunohistochemically, and MYD88 mutation was assessed using polymerase chain reaction and direct DNA sequencing...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29028854/clinical-insights-and-emerging-strategies-in-managing-cutaneous-t-cell-lymphoma
#3
Christina C Patrone, Larisa J Geskin
<p>Mycosis Fungoides and Sézary Syndrome, the two most common types of Cutaneous T-Cell Lymphoma (CTCL), present many management challenges for dermatologists. Here, we provide a comprehensive review of up-to-date literature, guidelines, and expert clinical insights. We highlight the updates in the World Health Organization Classification of Cutaneous Lymphomas; we summarize the epidemiology, including a recently observed stabilization of increasing incidence of CTCL in the past decade and increased incidence in males, blacks, and veterans; we also provide the most recent updates on prognostic factors for CTCL...
May 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/29025909/histone-deacetylase-inhibitors-downregulate-ccr4-expression-and-decrease-mogamulizumab-efficacy-in-ccr4-positive-mature-t-cell-lymphomas
#4
Akihiro Kitadate, Sho Ikeda, Fumito Abe, Naoto Takahashi, Norio Shimizu, Kosei Matsue, Hiroyuki Tagawa
HDAC inhibitors are promising agents for various T-cell lymphomas, including cutaneous T-cell lymphoma, peripheral T-cell lymphoma, and adult T-cell lymphoma/leukemia. CCR4 is an important therapeutic target molecule because mogamulizumab, an anti-CCR4 antibody, has shown promising efficacy against various T-cell lymphomas. In this study, we examined the in vitro synergistic effects of mogamulizumab and HDAC inhibitors against various T-cell lymphomas. First, we examined the expression of CCR4 mRNA and surface CCR4 in various T-cell lymphoma cell lines and found it was downregulated upon treatment with vorinostat, a pan-HDAC inhibitor...
October 12, 2017: Haematologica
https://www.readbyqxmd.com/read/29018799/truseq-based-gene-expression-analysis-of-formalin-fixed-paraffin-embedded-ffpe-cutaneous-t-cell-lymphoma-samples-subgroup-analysis-results-and-elucidation-of-biases-from-ffpe-sample-processing-on-the-truseq-platform
#5
Philippe Lefrançois, Michael T Tetzlaff, Linda Moreau, Andrew K Watters, Elena Netchiporouk, Nathalie Provost, Martin Gilbert, Xiao Ni, Denis Sasseville, Madeleine Duvic, Ivan V Litvinov
Cutaneous T-cell lymphomas (CTCLs) are a heterogeneous group of malignancies with courses ranging from indolent to potentially lethal. We recently studied in a 157 patient cohort gene expression profiles generated by the TruSeq targeted RNA gene expression sequencing. We observed that the sequencing library quality and depth from formalin-fixed paraffin-embedded (FFPE) skin samples were significantly lower when biopsies were obtained prior to 2009. We also observed that the fresh CTCL samples clustered together, even though they included stage I-IV disease...
2017: Frontiers in Medicine
https://www.readbyqxmd.com/read/29017070/conducting-electrospun-fibres-with-polyanionic-grafts-as-highly-selective-label-free-electrochemical-biosensor-with-a-low-detection-limit-for-non-hodgkin-lymphoma-gene
#6
Thomas E Kerr-Phillips, Nihan Aydemir, Eddie Wai Chi Chan, David Barker, Jenny Malmstro M, Cedric Plesse, Jadranka Travas-Sejdic
A highly selective, label-free sensor for the non-Hodgkin lymphoma gene, with an aM detection limit, utilizing electrochemical impedance spectroscopy (EIS) is presented. The sensor consists of a conducting electrospun fibre mat, surface-grafted with poly(acrylic acid) (PAA) brushes and a conducting polymer sensing element with covalently attached oligonucleotide probes. The sensor was fabricated from electrospun NBR rubber, embedded with poly(3,4-ethylenedioxythiophene) (PEDOT), followed by grafting poly(acrylic acid) brushes and then electrochemically polymerizing a conducting polymer monomer with ssDNA probe sequence pre-attached...
September 28, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28993566/fecal-microbiome-in-dogs-with-inflammatory-bowel-disease-and-intestinal-lymphoma
#7
Marie Omori, Shingo Maeda, Hirotaka Igarashi, Koichi Ohno, Kosei Sakai, Tomohiro Yonezawa, Ayako Horigome, Toshitaka Odamaki, Naoaki Matsuki
Although alteration of commensal microbiota is associated with chronic gastrointestinal (GI) diseases such as inflammatory bowel disease (IBD) in dogs, the microbiota composition in intestinal lymphoma, an important differential diagnosis of canine IBD, has not been investigated. The objective of this study was to compare the fecal microbiota in dogs with IBD, dogs with intestinal lymphoma, and healthy dogs. Eight dogs with IBD, eight dogs with intestinal lymphoma, and fifteen healthy dogs were included in the study...
October 6, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28989285/unintended-target-effect-of-anti-bcl-2-dnai
#8
Abdul Shukkur Ebrahim, Mustapha Kandouz, Nada Emara, Amara B Sugalski, Leonard Lipovich, Ayad M Al-Katib
INTRODUCTION: Previous research suggested that a novel compound PNT2258 inhibits B-cell lymphoma 2 (BCL-2) transcription by DNA interference (DNAi) and demonstrated its activity in preclinical xenograft models and in a pilot Phase II clinical trial in non-Hodgkin's lymphoma (NHL). While the drug downregulates BCL-2 at the promoter, mRNA, and protein levels, there is a significant homology (13-16 bases) between PNT100 and a number of promoters of genes involved in cell cycle regulation and survival...
2017: Cancer Management and Research
https://www.readbyqxmd.com/read/28988412/cognitive-outcomes-among-latino-survivors-of-childhood-acute-lymphoblastic-leukemia-and-lymphoma-a-cross-sectional-cohort-study-using-culturally-competent-performance-based-assessment
#9
Laura Bava, Alexis Johns, Kimberly Kayser, David R Freyer
BACKGROUND: This study sought to characterize cognitive outcomes among Latino survivors of childhood acute lymphoblastic leukemia (ALL) and lymphoblastic lymphoma (LL). PROCEDURE: In this cross-sectional cohort study, Latino survivors of ALL (n = 57) and LL (n = 5) aged 6-16 years were pooled and evaluated using validated measures of cognitive, academic, and behavioral function and English language proficiency. Performance was compared with norms using single-sample t-tests...
October 8, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28985567/genetic-and-functional-drivers-of-diffuse-large-b%C3%A2-cell-lymphoma
#10
Anupama Reddy, Jenny Zhang, Nicholas S Davis, Andrea B Moffitt, Cassandra L Love, Alexander Waldrop, Sirpa Leppa, Annika Pasanen, Leo Meriranta, Marja-Liisa Karjalainen-Lindsberg, Peter Nørgaard, Mette Pedersen, Anne O Gang, Estrid Høgdall, Tayla B Heavican, Waseem Lone, Javeed Iqbal, Qiu Qin, Guojie Li, So Young Kim, Jane Healy, Kristy L Richards, Yuri Fedoriw, Leon Bernal-Mizrachi, Jean L Koff, Ashley D Staton, Christopher R Flowers, Ora Paltiel, Neta Goldschmidt, Maria Calaminici, Andrew Clear, John Gribben, Evelyn Nguyen, Magdalena B Czader, Sarah L Ondrejka, Angela Collie, Eric D Hsi, Eric Tse, Rex K H Au-Yeung, Yok-Lam Kwong, Gopesh Srivastava, William W L Choi, Andrew M Evens, Monika Pilichowska, Manju Sengar, Nishitha Reddy, Shaoying Li, Amy Chadburn, Leo I Gordon, Elaine S Jaffe, Shawn Levy, Rachel Rempel, Tiffany Tzeng, Lanie E Happ, Tushar Dave, Deepthi Rajagopalan, Jyotishka Datta, David B Dunson, Sandeep S Dave
Diffuse large B cell lymphoma (DLBCL) is the most common form of blood cancer and is characterized by a striking degree of genetic and clinical heterogeneity. This heterogeneity poses a major barrier to understanding the genetic basis of the disease and its response to therapy. Here, we performed an integrative analysis of whole-exome sequencing and transcriptome sequencing in a cohort of 1,001 DLBCL patients to comprehensively define the landscape of 150 genetic drivers of the disease. We characterized the functional impact of these genes using an unbiased CRISPR screen of DLBCL cell lines to define oncogenes that promote cell growth...
October 5, 2017: Cell
https://www.readbyqxmd.com/read/28985135/whole-body-diffusion-weighted-mr-imaging-of-iron-deposits-in-hodgkin-follicular-and-diffuse-large-b-cell-lymphoma
#11
Anne-Ségolène Cottereau, Sébastien Mulé, Chieh Lin, Karim Belhadj, Alexandre Vignaud, Christiane Copie-Bergman, Alice Boyez, Pierre Zerbib, Vania Tacher, Elodie Scherman, Corinne Haioun, Alain Luciani, Emmanuel Itti, Alain Rahmouni
Purpose To analyze the frequency and distribution of low-signal-intensity regions (LSIRs) in lymphoma lesions and to compare these to fluorodeoxyglucose (FDG) uptake and biologic markers of inflammation. Materials and Methods The authors analyzed 61 untreated patients with a bulky lymphoma (at least one tumor mass ≥7 cm in diameter). When a LSIR within tumor lesions was detected on diffusion-weighted images obtained with a b value of 50 sec/mm(2), a T2-weighted gradient-echo (GRE) sequence was performed and calcifications were searched for with computed tomography (CT)...
October 6, 2017: Radiology
https://www.readbyqxmd.com/read/28978846/molecular-pathogenesis-and-treatment-strategy-in-diffuse-large-b-cell-lymphoma
#12
Kazuyuki Shimada
Diffuse large B-cell lymphoma (DLBCL) represents the most common subtype of non-Hodgkin lymphoma, accounting for 30%-40% of all types of malignant lymphoma. Importantly, two distinct molecular subtypes, germinal center B-cell (GCB) type and activated B-cell (ABC) type, arising from B lymphocyte differentiation based on the gene expression profiling opened doors to uncover molecular pathogenesis in DLBCL. Since 2010, next-generation sequencing analyses have been revealing the landscape of genetic mutations in DLBCL...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28976967/a-viral-sm-class-rna-base-pairs-with-mrnas-and-recruits-micrornas-to-inhibit-apoptosis
#13
Carlos Gorbea, Tim Mosbruger, Demián Cazalla
Viruses express several classes of non-coding RNAs; the functions and mechanisms by which most of these act are unknown. Herpesvirus saimiri, a γ-herpesvirus that establishes latency in the T cells of New World primates and has the ability to cause aggressive leukaemias and lymphomas in non-natural hosts, expresses seven small nuclear uracil-rich non-coding RNAs (called HSURs) in latently infected cells. These HSURs associate with Sm proteins, and share biogenesis and structural features with cellular Sm-class small nuclear RNAs...
October 4, 2017: Nature
https://www.readbyqxmd.com/read/28973148/a-constitutive-bcl2-down-regulation-aggravates-the-phenotype-of-pkd1-mutant-induced-polycystic-kidney-disease
#14
Laurence Duplomb, Nathalie Droin, Olivier Bouchot, Christel Robinet Thauvin, Ange-Line Bruel, Julien Thevenon, Patrick Callier, Guillaume Meurice, Noémie Pata-Merci, Romaric Loffroy, David Vandroux, Romain Da Costa, Virginie Carmignac, Eric Solary, Laurence Faivre
The main identified function of BCL2 protein is to prevent cell death by apoptosis. Mice knock-out for Bcl2 demonstrate growth retardation, severe polycystic kidney disease (PKD), gray hair and lymphopenia, and die prematurely after birth. Here, we report a 40-year-old male referred to for abdominal and thoracic aortic dissection with associated aortic root aneurysm, PKD, lymphocytopenia with a history of T cell lymphoblastic lymphoma, white hair since the age of 20, and learning difficulties. PKD, which was also detected in the father and sister, was related to an inherited PKD1 mutation...
September 11, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28970558/detection-of-known-and-novel-alk-fusion-transcripts-in-lung-cancer-patients-using-next-generation-sequencing-approaches
#15
Julie A Vendrell, Sylvie Taviaux, Benoît Béganton, Sylvain Godreuil, Patricia Audran, David Grand, Estelle Clermont, Isabelle Serre, Vanessa Szablewski, Peter Coopman, Julien Mazières, Valérie Costes, Jean-Louis Pujol, Pierre Brousset, Isabelle Rouquette, Jérôme Solassol
Rearrangements of the anaplastic lymphoma kinase (ALK) gene in non-small cell lung cancer (NSCLC) represent a novel molecular target in a small subset of tumors. Although ALK rearrangements are usually assessed by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), molecular approaches have recently emerged as relevant alternatives in routine laboratories. Here, we evaluated the use of two different amplicon-based next-generation sequencing (NGS) methods (AmpliSeq and Archer(®)FusionPlex(®)) to detect ALK rearrangements, and compared these with IHC and FISH...
October 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28964938/impact-of-dna-methylation-programming-on-normal-and-pre-leukemic-hematopoiesis
#16
REVIEW
Jens Langstein, Michael D Milsom, Daniel B Lipka
Epigenome regulation is a critical mechanism that governs cell identity, lineage specification and developmental cell fates. With the advent of low-input and single-cell technologies as well as sophisticated cell labeling techniques, our understanding of transcriptional and epigenetic regulation of hematopoiesis is currently undergoing dramatic changes. Increasingly, evidence suggests that the epigenome conformation acts as a critical decision-making mechanism that instructs self-renewal, differentiation and developmental fates of hematopoietic progenitor cells...
September 27, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28933999/minimal-residual-disease-assessment-in-lymphoma-methods-and-applications
#17
Alex F Herrera, Philippe Armand
Standard methods for disease response assessment in patients with lymphoma, including positron emission tomography and computed tomography scans, are imperfect. In other hematologic malignancies, particularly leukemias, the ability to detect minimal residual disease (MRD) is increasingly influencing treatment paradigms. However, in many subtypes of lymphoma, the application of MRD assessment techniques, like flow cytometry or polymerase chain reaction-based methods, has been challenging because of the absence of readily detected circulating disease or canonic chromosomal translocations...
September 21, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28924718/comprehensive-annotation-and-evolutionary-insights-into-the-canine-canis-lupus-familiaris-antigen-receptor-loci
#18
Jolyon Martin, Hannes Ponstingl, Marie-Paule Lefranc, Joy Archer, David Sargan, Allan Bradley
Dogs are an excellent model for human disease. For example, the treatment of canine lymphoma has been predictive of the human response to that treatment. However, an incomplete picture of canine (Canis lupus familiaris) immunoglobulin (IG) and T cell receptor (TR)-or antigen receptor (AR)-gene loci has restricted their utility. This work advances the annotation of the canine AR loci and looks into breed-specific features of the loci. Bioinformatic analysis of unbiased RNA sequence data was used to complete the annotation of the canine AR genes...
September 19, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28916317/presence-of-human-herpesvirus-8-hhv-8-dna-sequences-in-patients-with-lymphoproliferative-diseases-and-chronic-blood-disorders
#19
Hossein Keyvani, Mohammad Hadi Karbalaie Niya, Maryam Esghaei, Farah Bokharaei-Salim, Seyed Hamid Reza Monavari
OBJECTIVE: Human herpesvirus 8 (HHV-8) is the causative agent of Kaposi's sarcoma (KS), but it has also been associated with different hematologic malignancies, including plasmablastic lymphoma, Multicentric Castleman's disease (MCD), primary effusion lymphoma (PEL) and various atypical lymphoproliferative disorders. Patients with underlying lymphoproliferative diseases and chronic blood disorders who become infected with this virus are at risk for human malignancies. This small study reported the frequency of human herpesvirus 8 in 81 Iranian patients with lymphoproliferative disorders for estimation of possible factors affecting malignancy...
October 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28915671/integration-of-alv-into-ctdspl-and-ctdspl2-genes-in-b-cell-lymphomas-promotes-cell-immortalization-migration-and-survival
#20
Shelby Winans, Alyssa Flynn, Sanandan Malhotra, Vidya Balagopal, Karen L Beemon
Avian leukosis virus induces tumors in chickens by integrating into the genome and altering expression of nearby genes. Thus, ALV can be used as an insertional mutagenesis tool to identify novel genes involved in tumorigenesis. Deep sequencing analysis of viral integration sites has identified CTDSPL and CTDSPL2 as common integration sites in ALV-induced B-cell lymphomas, suggesting a potential role in driving oncogenesis. We show that in tumors with integrations in these genes, the viral promoter is driving the expression of a truncated fusion transcript...
August 22, 2017: Oncotarget
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