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leukemia genomic

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https://www.readbyqxmd.com/read/28817678/family-based-exome-wide-association-study-of-childhood-acute-lymphoblastic-leukemia-among-hispanics-confirms-role-of-arid5b-in-susceptibility
#1
Natalie P Archer, Virginia Perez-Andreu, Ulrik Stoltze, Michael E Scheurer, Anna V Wilkinson, Ting-Nien Lin, Maoxiang Qian, Charnise Goodings, Michael D Swartz, Nalini Ranjit, Karen R Rabin, Erin C Peckham-Gregory, Sharon E Plon, Pedro A de Alarcon, Ryan C Zabriskie, Federico Antillon-Klussmann, Cesar R Najera, Jun J Yang, Philip J Lupo
We conducted an exome-wide association study of childhood acute lymphoblastic leukemia (ALL) among Hispanics to confirm and identify novel variants associated with disease risk in this population. We used a case-parent trio study design; unlike more commonly used case-control studies, this study design is ideal for avoiding issues with population stratification bias among this at-risk ethnic group. Using 710 individuals from 323 Guatemalan and US Hispanic families, two inherited SNPs in ARID5B reached genome-wide level significance: rs10821936, RR = 2...
2017: PloS One
https://www.readbyqxmd.com/read/28813500/telomere-biology-and-telomerase-mutations-in-cirrhotic-patients-with-hepatocellular-carcinoma
#2
Flávia S Donaires, Natália F Scatena, Raquel M Alves-Paiva, Joshua D Podlevsky, Dhenugen Logeswaran, Barbara A Santana, Andreza C Teixeira, Julian J-L Chen, Rodrigo T Calado, Ana L C Martinelli
Telomeres are repetitive DNA sequences at linear chromosome termini, protecting chromosomes against end-to-end fusion and damage, providing chromosomal stability. Telomeres shorten with mitotic cellular division, but are maintained in cells with high proliferative capacity by telomerase. Loss-of-function mutations in telomere-maintenance genes are genetic risk factors for cirrhosis development in humans and murine models. Telomerase deficiency provokes accelerated telomere shortening and dysfunction, facilitating genomic instability and oncogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28807723/identifying-consistent-disease-subnetworks-using-dnet
#3
Jiajie Peng, Junya Lu, Xuequn Shang, Jin Chen
It is critical to identify disease-specific subnetworks from the vastly available genome-wide gene expression data for elucidating how genes perform high-level biological functions together. Various algorithms have been developed for disease gene identification. However, the topological structure of the disease networks (or even the fraction of the networks) has been left largely unexplored. In this article, we present DNet, a method for the identification of significant disease subnetworks by integrating both the network structure and gene expression information...
August 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28806978/transcriptome-sequencing-in-pediatric-acute-lymphoblastic-leukemia-identifies-fusion-genes-associated-with-distinct-dna-methylation-profiles
#4
Yanara Marincevic-Zuniga, Johan Dahlberg, Sara Nilsson, Amanda Raine, Sara Nystedt, Carl Mårten Lindqvist, Eva C Berglund, Jonas Abrahamsson, Lucia Cavelier, Erik Forestier, Mats Heyman, Gudmar Lönnerholm, Jessica Nordlund, Ann-Christine Syvänen
BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes...
August 14, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28801450/genomic-analysis-of-hairy-cell-leukemia-identifies-novel-recurrent-genetic-alterations
#5
Benjamin H Durham, Bartlomiej Getta, Sascha Dietrich, Justin Taylor, Helen Won, James M Bogenberger, Sasinya Scott, Eunhee Kim, Young Rock Chung, Stephen S Chung, Jennifer Hüllein, Tatjana Walther, Lu Wang, Sydney X Lu, Christopher C Oakes, Raoul Tibes, Torsten Haferlach, Barry S Taylor, Martin S Tallman, Michael F Berger, Jae H Park, Thorsten Zenz, Omar Abdel-Wahab
Classical hairy cell leukemia (cHCL) is characterized by a near 100% frequency of the BRAFV600E mutation while ~30% of variant HCL (vHCL) have MAP2K1 mutations. However, recurrent genetic alterations cooperating with BRAFV600E or MAP2K1 mutations in HCL, as well as those in MAP2K1- wildtype vHCL, are not well defined. We therefore performed deep targeted mutational and copy number analysis of cHCL (n=53) and vHCL (n=8). The most common genetic alteration in cHCL outside of BRAFV600E was heterozygous loss of chromosome 7q, the minimally deleted region of which targeted wildtype BRAF, subdividing cHCL into those hemizygous versus heterozygous for the BRAFV600E mutation...
August 11, 2017: Blood
https://www.readbyqxmd.com/read/28798321/crispr-cas9-mediated-deletion-of-foxn1-in-nod-scid-il2rg-mice-results-in-severe-immunodeficiency
#6
Xinru Wei, Yunxin Lai, Baiheng Li, Le Qin, Youdi Xu, Simiao Lin, Suna Wang, Qiting Wu, Qiubin Liang, Guohua Huang, Qiuhua Deng, Pentao Liu, Donghai Wu, Liangxue Lai, Yao Yao, Peng Li
Immunodeficient mice engrafted with either normal or cancerous human cells are widely used in basic and translational research. In particular, NOD/SCID/IL2rg(-/-) mice can support the growth of various types of human cancer cells. However, the hairs of these mice interfere with the observation and imaging of engrafted tissues. Therefore, novel hairless strains exhibiting comparable immunodeficiency would be beneficial. Recently, the CRISPR/Cas9 system has been used for efficient multiplexed genome editing. In the present study, we generated a novel strain of nude NOD/SCID/IL2rg(-/-) (NSIN) mice by knocking out Foxn1 from NOD/SCID/IL2rg(-/-) (NSI) mice using the CRISPR/Cas9 system...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797519/treatment-of-acute-myeloid-leukemia-in-the-next-decade-towards-real-time-functional-testing-and-personalized-medicine
#7
REVIEW
Stephen Sze-Yuen Lam, Alex Bai-Liang He, Anskar Yu-Hung Leung
Information arising from next generation sequencing of leukemia genome has shed important light on the heterogeneous and combinatorial driver events in acute myeloid leukemia (AML). It has also provided insight into its intricate signaling pathways operative in the disease pathogenesis. These have also become biomarkers and targets for therapeutic intervention. Emerging evidence from in vitro drug screening has demonstrated its potential value in predicting clinical drug responses in specific AML subtypes. However, the best culture conditions and readouts have yet to be standardized and the drugs included in these screening exercises frequently revised in view of the rapid emergence of new therapeutic agents in the oncology field...
August 4, 2017: Blood Reviews
https://www.readbyqxmd.com/read/28795083/mechanical-instability-and-titanium-particles-induce-similar-transcriptomic-changes-in-a-rat-model-for-periprosthetic-osteolysis-and-aseptic-loosening
#8
Mehdi Amirhosseini, Göran Andersson, Per Aspenberg, Anna Fahlgren
Wear debris particles released from prosthetic bearing surfaces and mechanical instability of implants are two main causes of periprosthetic osteolysis. While particle-induced loosening has been studied extensively, mechanisms through which mechanical factors lead to implant loosening have been less investigated. This study compares the transcriptional profiles associated with osteolysis in a rat model for aseptic loosening, induced by either mechanical instability or titanium particles. Rats were exposed to mechanical instability or titanium particles...
December 2017: Bone Reports
https://www.readbyqxmd.com/read/28794467/tdp2-suppresses-chromosomal-translocations-induced-by-dna-topoisomerase-ii-during-gene-transcription
#9
Fernando Gómez-Herreros, Guido Zagnoli-Vieira, Ioanna Ntai, María Isabel Martínez-Macías, Rhona M Anderson, Andrés Herrero-Ruíz, Keith W Caldecott
DNA double-strand breaks (DSBs) induced by abortive topoisomerase II (TOP2) activity are a potential source of genome instability and chromosome translocation. TOP2-induced DNA double-strand breaks are rejoined in part by tyrosyl-DNA phosphodiesterase 2 (TDP2)-dependent non-homologous end-joining (NHEJ), but whether this process suppresses or promotes TOP2-induced translocations is unclear. Here, we show that TDP2 rejoins DSBs induced during transcription-dependent TOP2 activity in breast cancer cells and at the translocation 'hotspot', MLL...
August 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28794032/recombinant-origins-of-pathogenic-and-nonpathogenic-mouse-gammaretroviruses-of-polytropic-host-range
#10
Devinka Bamunusinghe, Qingping Liu, Ronald Plishka, Michael A Dolan, Matthew Skorski, Andrew J Oler, Venkat R K Yedavalli, Alicia Buckler-White, Janet W Hartley, Christine A Kozak
Ecotropic, xenotropic and polytropic mouse leukemia viruses (E-, X-, P-MLVs) exist in mice as infectious viruses and endogenous retroviruses (ERVs) inserted into mouse chromosomes. All 3 MLV subgroups are linked to leukemogenesis, which involves generation of recombinants with polytropic host range. Although P-MLVs are deemed to be the proximal agents of disease induction, few biologically characterized infectious P-MLVs have been sequenced for comparative analysis. We analyzed the complete genomes of 16 naturally occurring infectious P-MLVs, 12 of which were typed for pathogenic potential...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28793301/high-expression-of-ahsp-epb42-gypc-and-hemgn-predicts-favorable-prognosis-in-flt3-itd-negative-acute-myeloid-leukemia
#11
Gang-Zhi Zhu, Yong-Long Yang, Yan-Jiao Zhang, Wei Liu, Mu-Peng Li, Wen-Jing Zeng, Xie-Lan Zhao, Xiao-Ping Chen
BACKGROUND/AIMS: Acute myeloid leukemia (AML) is a heterogeneous clonal disease and patients with AML who harbor an FMS-like tyrosine kinase 3 (FLT3) mutation present several dilemmas for the clinician. This study aims to identify novel targets for explaining the dilemmas. METHODS: We analyzed four microarray gene expression profiles to investigate changes in whole genome expression associated with FLT3-ITD mutation. RESULTS: We identified 22 differentially expressed genes which are commonly expressed among all four profiles...
August 9, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28782884/chronic-lymphocytic-leukemia-2017-update-on-diagnosis-risk-stratification-and-treatment
#12
REVIEW
Michael Hallek
DISEASE OVERVIEW: Chronic lymphocytic leukemia (CLL) is the commonest leukemia in western countries. The disease typically occurs in elderly patients and has a highly variable clinical course. Leukemic transformation is initiated by specific genomic alterations that impair apoptosis of clonal B cells. DIAGNOSIS: The diagnosis is established by blood counts, blood smears, and immunophenotyping of circulating B lymphocytes, which identify a clonal B-cell population carrying the CD5 antigen and B-cell markers...
September 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28768854/presence-of-a-shared-5-leader-sequence-in-ancestral-human-and-mammalian-retroviruses-and-its-transduction-into-feline-leukemia-virus
#13
Junna Kawasaki, Maki Kawamura, Yoshiharu Ohsato, Jumpei Ito, Kazuo Nishigaki
Recombination events induce significant genetic changes, and this process can result in virus genetic diversity or in the generation of novel pathogenicity. We discovered a new recombinant feline leukemia virus (FeLV) gag gene harboring an unrelated insertion, termed the "X-region", which was derived from FcERV-gamma4, a feline endogenous gammaretrovirus. The identified FcERV-gamma4 proviruses have lost their coding capability, but some can express their viral RNA in feline tissues. Although the X-region-carrying recombinant FeLVs appeared to be replication-defective viruses, they were detected in 6...
August 2, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28768142/contributions-of-ikzf1-ddc-cdkn2a-cebpe-and-lmo1-gene-polymorphisms-to-acute-lymphoblastic-leukemia-in-a-yemeni-population
#14
Boshra Al-Absi, Muhammad F M Razif, Suzita M Noor, Riyadh Saif-Ali, Mohammed Aqlan, Sameer D Salem, Radwan H Ahmed, Sekaran Muniandy
BACKGROUND: Genome-wide and candidate gene association studies have previously revealed links between acute lymphoblastic leukemia (ALL) predisposition and genetic polymorphisms in these genes: IKZF1 (7p12.2; ID: 10320), DDC (7p12.2; ID: 1644), CDKN2A (9p21.3; ID: 1029), CEBPE (14q11.2; ID: 1053), and LMO1 (11p15; ID: 4004). In this study, we aimed to conduct an investigation into the possible association between polymorphisms in these genes and ALL within a sample of Yemeni children of Arab-Asian descent...
August 2, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28767428/suppression-of-mir-708-inhibits-the-wnt-%C3%AE-catenin-signaling-pathway-by-activating-dkk3-in-adult-b-all
#15
Yingjie Zhang, Huibo Li, Rongyi Cao, Lili Sun, Yan Wang, Shengjin Fan, Yanqiu Zhao, Desheng Kong, Lin Cui, Leilei Lin, Ke Wang, Yinghua Li, Jin Zhou
Inactivation of Dickkopf-3 (DKK3) is closely associated with a poor prognosis in various solid tumor and hematologic malignancies. Promoter hypermethylation is one potential cause of DKK3 inactivation. However, whether other mechanisms lead to DKK3 inactivation and the subsequent effects of these inactivations on cell proliferation and the Wnt signaling pathway in adult B acute lymphoblastic leukemia (B-ALL) remain unclear. In the present study, we found that low DKK3 expression levels were associated with high miR-708 expression and promoter hypermethylation in adult B-ALL...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28767419/b-lymphoblastic-leukemia-lymphoma-new-insights-into-genetics-molecular-aberrations-subclassification-and-targeted-therapy
#16
Xiaohui Zhang, Prerna Rastogi, Bijal Shah, Ling Zhang
B lymphoblastic leukemia/lymphoma (B-ALL) is a clonal hematopoietic stem cell neoplasm derived from B-cell progenitors, which mostly occurs in children and adolescents and is regarded as one of top leading causes of death related to malignancies in this population. Despite the majority of patients with B-ALL have fairly good response to conventional chemotherapeutic interventions followed by hematopoietic stem cell transplant for the last decades, a subpopulation of patients show chemo-resistance and a high relapse rate...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28765516/next-generation-sequencing-in-chronic-lymphocytic-leukemia-recent-findings-and-new-horizons
#17
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/28760306/high-risk-multiple-myeloma-definition-and-management
#18
REVIEW
Nisha S Joseph, Silvia Gentili, Jonathan L Kaufman, Sagar Lonial, Ajay K Nooka
The prognosis of patients with multiple myeloma has significantly improved after the introduction of novel concepts of immunomodulation and proteasome inhibition in myeloma therapies. In conjunction with the use of high-dose therapy and autologous stem cell transplantation, these newer antimyeloma agents facilitated the augmentation of deeper responses and as a result, enhanced survival outcomes. Despite mounting clinical evidence that novel therapies may mitigate the poor prognostic impact of some predictors historically considered "harbingers of doom" in myeloma such as t(4;14), the benefit of these advances is less evident in patients who present with genetically defined high-risk features such as presence of chromosomal abnormalities del17p, t(14;16), or t(14;20), or among patients presenting with plasma cell leukemia...
July 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/28758283/copy-number-profiling-of-adult-relapsed-b-cell-precursor-acute-lymphoblastic-leukemia-reveals-potential-leukemia-progression-mechanisms
#19
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/28758276/brief-report-human-acute-myeloid-leukemia-reprograming-to-pluripotency-is-a-rare-event-and-selects-for-patient-hematopoietic-cells-devoid-of-leukemic-mutations
#20
Jong-Hee Lee, Kyle R Salci, Jennifer C Reid, Luca Orlando, Borko Tanasijevic, Zoya Shapovalova, Mickie Bhatia
Induced pluripotent stem cell reprogramming has provided critical insights into disease processes by modeling the genetics and related clinical pathophysiology. Human cancer represents highly diverse genetics, as well as inter- and intra-patient heterogeneity, where cellular model systems capable of capturing this disease complexity would be invaluable. Acute myeloid leukemia (AML) represents one of most heterogeneous cancers and has been divided into genetic subtypes correlated with unique risk stratification over the decades...
July 31, 2017: Stem Cells
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