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https://www.readbyqxmd.com/read/28646630/characteristics-of-systemic-inflammation-in-hepatitis-b-precipitated-aclf-differentiate-it-from-no-aclf
#1
Wei Wu, Huadong Yan, Hong Zhao, Wenjie Sun, Qiao Yang, Jifang Sheng, Yu Shi
BACKGROUND AND AIMS: Patients with severe exacerbation of chronic hepatitis B (SE-CHB) are at risk of developing acute-on-chronic liver failure (ACLF). Systemic inflammation (SI) is a major driver of ACLF. The aim of this study was to identify characteristics of SI in hepatitis B-precipitated-ACLF (HB-ACLF), which may be distinct from No-ACLF patients with SE-CHB. METHODS: Two cohorts of patients with SE-CHB were enrolled in two tertiary hospitals. The associations between circulating leukocyte counts/subsets and ACLF progression and prognoses were analysed in Cohort A...
June 24, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28646406/podocytes-and-the-quest-for-precision-medicines-for-kidney-diseases
#2
REVIEW
Peter Mundel
In this review, I describe a 30-year journey in the quest for precision medicines for patients with kidney diseases. In 1987, when I started my reseach career, most scientists studying glomerular disease biology were focused on mesangial cells. The crucial role of the podocyte in many kidney diseases characterized by proteinuria, including focal segmental glomerulosclerosis (FSGS) and diabetic nephropathy, had not yet been recognized. We were not aware of genetic causes or drivers of kidney diseases nor of molecular markers and cell culture systems for mechanistic studies of podocyte biology...
June 23, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28645942/mutational-heterogeneity-in-apc-and-kras-arises-at-the-crypt-level-and%C3%A2-leads-to-polyclonality-in-early-colorectal-tumorigenesis
#3
Mireia Gausachs, Ester Borras, Kyle Chang, Sara González, Daniel Azuara, Axel Delgado Amador, Adriana Lopez-Doriga, F Anthony San Lucas, Xavier Sanjuan, Maria jOSE Paules, Melissa Taggart, Gareth Davies, Erik A Ehli, Jerry Fowler, Victor Moreno, Marta Pineda, Y Nancy You, Patrick M Lynch, Conxi Lazaro, Nicholas E Navin, Paul Scheet, Ernest T Hawk, Gabriel Capella, Eduardo Vilar
Purpose:  The majority of genomic alterations causing intratumoral heterogeneity (ITH) in colorectal cancer (CRC) are thought to arise during early stages of carcinogenesis as a burst but only after truncal mutations in APC have expanded a single founder clone. We have investigated if the initial source of ITH is consequent to multiple independent lineages derived from different crypts harboring distinct truncal APC and driver KRAS mutations, thus challenging the prevailing monoclonal monocryptal model. <p>Experimental design: High-depth next-generation sequencing and SNP arrays were performed in whole lesion extracts of 37 FAP colorectal adenomas...
June 23, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28645305/high-expression-of-collagen-triple-helix-repeat-containing-1-cthrc1-facilitates-progression-of-oesophageal-squamous-cell-carcinoma-through-mapk-mek-erk-fra-1-activation
#4
Chunni Wang, Zitong Li, Fei Shao, Xueying Yang, Xiaoli Feng, Susheng Shi, Yibo Gao, Jie He
BACKGROUND: Oesophageal cancer is one of the most common malignancies worldwide,and oesophageal squamous cell carcinoma (ESCC) is the predominant histological type both globally and in China. Collagen triple helix repeat containing 1 (CTHRC1) has been found to be upregulated in ESCC. However, its role in tumourigenesis and progression of ESCC remains unclear. METHODS: Using our previous ESCC mRNA profiling data, we screened upregulated genes to identify those required for proliferation...
June 23, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#5
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643793/genomic-rearrangements-in-sporadic-lymphangioleiomyomatosis-an-evolving-genetic-story
#6
Stephen J Murphy, Simone B Terra, Faye R Harris, Aqsa Nasir, Jesse S Voss, James B Smadbeck, Sarah H Johnson, Vishnu Serla, Jay H Ryu, Eunhee S Yi, Benjamin R Kipp, George Vasmatzis, Eva M Carmona
Sporadic lymphangioleiomyomatosis is a progressive pulmonary cystic disease resulting from the infiltration of smooth muscle-like lymphangioleiomyomatosis cells into the lung. The migratory/metastasizing properties of the lymphangioleiomyomatosis cell together with the presence of somatic mutations, primarily in the tuberous sclerosis complex gene (TSC2), lead many to consider this a low-grade malignancy. As malignant tumors characteristically accumulate somatic structural variations, which have not been well studied in sporadic lymphangioleiomyomatosis, we utilized mate pair sequencing to define structural variations within laser capture microdissected enriched lymphangioleiomyomatosis cell populations from five sporadic lymphangioleiomyomatosis patients...
June 23, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28643781/recurrent-mutation-of-igf-signalling-genes-and-distinct-patterns-of-genomic-rearrangement-in-osteosarcoma
#7
Sam Behjati, Patrick S Tarpey, Kerstin Haase, Hongtao Ye, Matthew D Young, Ludmil B Alexandrov, Sarah J Farndon, Grace Collord, David C Wedge, Inigo Martincorena, Susanna L Cooke, Helen Davies, William Mifsud, Mathias Lidgren, Sancha Martin, Calli Latimer, Mark Maddison, Adam P Butler, Jon W Teague, Nischalan Pillay, Adam Shlien, Ultan McDermott, P Andrew Futreal, Daniel Baumhoer, Olga Zaikova, Bodil Bjerkehagen, Ola Myklebost, M Fernanda Amary, Roberto Tirabosco, Peter Van Loo, Michael R Stratton, Adrienne M Flanagan, Peter J Campbell
Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28642787/mutational-signatures-are-critical-for-proper-estimation-of-purifying-selection-pressures-in-cancer-somatic-mutation-data-when-using-the-dn-ds-metric
#8
Jimmy Van den Eynden, Erik Larsson
Large cancer genome sequencing initiatives have led to the identification of cancer driver genes based on signals of positive selection in somatic mutation data. Additionally, the identification of purifying (negative) selection has the potential to identify essential genes that may be of therapeutic interest. The most widely used way of quantifying selection pressures in protein-coding genes is the dN/dS metric, which compares non-synonymous to synonymous substitution rates. In this study, we examine whether and how this metric is influenced by the mutational processes that have been active during tumor evolution...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28642592/integrative-network-analysis-identifies-novel-drivers-of-pathogenesis-and-progression-in-newly-diagnosed-multiple-myeloma
#9
A Laganà, D Perumal, D Melnekoff, B Readhead, B A Kidd, V Leshchenko, P-Y Kuo, J Keats, M DeRome, J Yesil, D Auclair, S Lonial, A Chari, H J Cho, B Barlogie, S Jagannath, J T Dudley, S Parekh
Multiple Myeloma (MM) is an incurable malignancy of bone marrow plasma cells characterized by wide clinical and molecular heterogeneity. In this study we applied an integrative network biology approach to molecular and clinical data measured from 450 patients with newly diagnosed MM from the MMRF CoMMpass study. A novel network model of myeloma (MMNet) was constructed, revealing complex molecular disease patterns and novel associations between clinical traits and genomic markers. Genomic alterations and groups of co-expressed genes correlate with disease stage, tumor clonality, and early progression...
June 23, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#10
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642487/hypoxia-is-a-key-driver-of-alternative-splicing-in-human-breast-cancer-cells
#11
Jian Han, Jia Li, Jolene Caifeng Ho, Grace Sushin Chia, Hiroyuki Kato, Sudhakar Jha, Henry Yang, Lorenz Poellinger, Kian Leong Lee
Adaptation to hypoxia, a hallmark feature of many tumors, is an important driver of cancer cell survival, proliferation and the development of resistance to chemotherapy. Hypoxia-induced stabilization of hypoxia-inducible factors (HIFs) leads to transcriptional activation of a network of hypoxia target genes involved in angiogenesis, cell growth, glycolysis, DNA damage repair and apoptosis. Although the transcriptional targets of hypoxia have been characterized, the alternative splicing of transcripts that occurs during hypoxia and the roles they play in oncogenesis are much less understood...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642281/utility-of-genomic-analysis-in-circulating-tumor-dna-from-patients-with-carcinoma-of-unknown-primary
#12
Shumei Kato, Nithya Krishnamurthy, Kimberly C Banks, Pradip De, Kirstin Williams, Casey Williams, Brian Leyland-Jones, Scott M Lippman, Richard B Lanman, Razelle Kurzrock
Carcinoma of unknown primary (CUP) is a rare and difficult-to-treat malignancy, the management of which might be improved by the identification of actionable driver mutations. We interrogated interrogated 54-70 genes in 442 patients with CUP using targeted clinical-grade, next-generation sequencing (NGS) of circulating tumor DNA (ctDNA). Overall, 80% of patients exhibited ctDNA alterations; 66%, ≥ 1 characterized alteration(s) excluding variants of unknown significance. TP53-associated genes were most commonly altered (37...
June 22, 2017: Cancer Research
https://www.readbyqxmd.com/read/28642015/convergent-and-unidirectional-evolution-of-extremely-long-aedeagi-in-the-largest-feather-mite-genus-proctophyllodes-acari-proctophyllodidae-evidence-from-comparative-molecular-and-morphological-phylogenetics
#13
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Proctophyllodid feather mites (400+ species) are permanent (full-time) symbionts commonly occurring on passerine birds. Phenotypic evolution of these mites appears to be greatly influenced by characters related to reproduction (>87.5% of a total of 32 taxonomically important discrete characters) and male genitalic characters (21.9%). Because sexual selection could the major evolutionary driver in this system, we test the theoretical expectation that genitalic or sexually dimorphic characters should evolve more rapidly and divergently then other characters...
June 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28641404/ph-rather-than-nitrification-and-urease-inhibitors-determines-the-community-of-ammonia-oxidizers-in-a-vegetable-soil
#14
Ruijiao Xi, Xi-En Long, Sha Huang, Huaiying Yao
Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of ammonia oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28641396/geneticization-in-mim-omim%C3%A2-exploring-historic-and-epistemic-drivers-of-contemporary-understandings-of-genetic-disease
#15
Rachel A Ankeny
Prior to the genomic sequencing era, the bible for those working in clinical genetics was McKusick's Mendelian Inheritance in Man (MIM), which appeared in multiple editions between the 1960s and the late 1990s. This catalogue was organized according to general patterns of inheritance and focused on phenotypes. Beginning in the mid-1980s, it was replaced by Online Mendelian Inheritance in Man (OMIM®), a continuously updated catalogue documenting molecular relationships between genetic variation and phenotypic expression...
June 21, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28640846/endothelial-angiogenesis-is-directed-by-runx1t1-regulated-vegfa-bmp4-and-tgf-%C3%AE-2-expression
#16
Ko-Hsun Liao, Shing-Jyh Chang, Hsin-Chuan Chang, Chen-Li Chien, Tse-Shun Huang, Te-Chia Feng, Wen-Wei Lin, Chuan-Chi Shih, Muh-Hwa Yang, Shung-Haur Yang, Chi-Hung Lin, Wei-Lun Hwang, Oscar K Lee
Tissue angiogenesis is intimately regulated during embryogenesis and postnatal development. Defected angiogenesis contributes to aberrant development and is the main complication associated with ischemia-related diseases. We previously identified the increased expression of RUNX1T1 in umbilical cord blood-derived endothelial colony-forming cells (ECFCs) by gene expression microarray. However, the biological relevance of RUNX1T1 in endothelial lineage is not defined clearly. Here, we demonstrate RUNX1T1 regulates the survival, motility and tube forming capability of ECFCs and EA...
2017: PloS One
https://www.readbyqxmd.com/read/28637865/an-evolutionarily-distinct-family-of-polysaccharide-lyases-removes-rhamnose-capping-of-complex-arabinogalactan-proteins
#17
José Munoz-Munoz, Alan Cartmell, Nicolas Terrapon, Arnaud Baslé, Bernard Henrissat, Harry J Gilbert
The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selective selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were upregulated by arabinogalactan arabinogalactan proteins or AGPs...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637623/ddx41-related-myeloid-neoplasia
#18
REVIEW
Jaroslaw P Maciejewski, Richard A Padgett, Anna L Brown, Carsten Müller-Tidow
While early presentation of familial leukemia syndromes is typical, long disease anticipation may mask cases of familial traits in seemingly spontaneous disease. Germline mutations in DDX41 gene have been discovered in several leukemia families, as well as in mostly adult patients with seemingly spontaneous disease but having strong family histories of myeloid neoplasia. As with other familial genes, DDX41 mutation carriers can develop neoplasia through acquisition of another somatic mutation, thereby affecting both DDX41 alleles...
April 2017: Seminars in Hematology
https://www.readbyqxmd.com/read/28637487/the-nf1-somatic-mutational-landscape-in-sporadic-human-cancers
#19
REVIEW
Charlotte Philpott, Hannah Tovell, Ian M Frayling, David N Cooper, Meena Upadhyaya
BACKGROUND: Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia...
June 21, 2017: Human Genomics
https://www.readbyqxmd.com/read/28637323/evolution-of-transcription-activator-like-effectors-in-xanthomonas-oryzae
#20
Annett Erkes, Maik Reschke, Jens Boch, Jan Grau
Transcription activator-like effectors (TALEs) are secreted by plant-pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid tandem repeats, where amino acid 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs...
June 14, 2017: Genome Biology and Evolution
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