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https://www.readbyqxmd.com/read/28210881/comprehensive-genomic-profiling-of-malignant-phyllodes-tumors-of-the-breast
#1
Sahar Nozad, Christine E Sheehan, Laurie M Gay, Julia A Elvin, Jo-Anne Vergilio, James Suh, Shakti Ramkissoon, Alexa B Schrock, Kim M Hirshfield, Nadia Ali, Shridar Ganesan, Siraj M Ali, Vincent A Miller, Philip J Stephens, Jeffrey S Ross, Jon H Chung
PURPOSE: Malignant phyllodes tumors (MPT) are exceptionally rare, and the genomic drivers of these tumors are still being elucidated. We performed comprehensive genomic profiling (CGP) of MPT to identify genomic alterations that will inform approaches to targeted therapy for patients with MPT, including relapsed, refractory, and metastatic disease. METHODS: DNA was extracted from formalin-fixed, paraffin-embedded samples from 24 consecutive patient cases of MPT...
February 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28202837/association-of-common-polymorphisms-with-gestational-diabetes-mellitus-in-japanese-women-a-case-control-study
#2
Yoshifumi Kasuga, Kenichiro Hata, Atsushi Tajima, Daigo Ochiai, Yoshifumi Saisho, Tadashi Matsumoto, Naoko Arata, Kei Miyakoshi, Mamoru Tanaka
Gestational diabetes (GDM) and type 2 diabetes (T2DM) share part of pathomechanism and several T2DM susceptibility genes are demonstrated to be associated with GDM. No information on the genetics of GDM, however, was available in Japanese women. In this study, T2DM risk variants (45 single nucleotide polymorphisms [SNPs] from 36 genes) identified in previous studies were genotyped using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in a cohort of 171 Japanese women with GDM and 128 normal glucose tolerance (NGT) diagnosed by the new International Association of Diabetes in Pregnancy Study Group criteria...
February 16, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28202526/radiation-resistance-in-kras-mutated-lung-cancer-is-enabled-by-stem-like-properties-mediated-by-an-osteopontin-egfr-pathway
#3
Meng Wang, Jing Han, Lynnette Marcar, Josh Black, Qi Liu, Xiangyong Li, Kshithija Nagulapalli, Lecia V Sequist, Raymond H Mak, Cyril H Benes, Theodore S Hong, Kristin Gurtner, Mechthild Krause, Michael Baumann, Jing X Kang, Johnathan Whetstine, Henning Willers
Lung cancers with activating KRAS mutations are characterized by treatment resistance and poor prognosis. In particular, the basis for their resistance to radiation therapy is poorly understood. Here we describe a radiation resistance phenotype conferred by a stem-like subpopulation characterized by mitosis-like condensed chromatin (MLCC), high CD133 expression, invasive potential, and tumor-initiating properties. Mechanistic investigations defined a pathway involving osteopontin and the EGFR in promoting this phenotype...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28202519/correlates-of-prenatal-and-early-life-tobacco-smoke-exposure-and-frequency-of-common-gene-deletions-in-childhood-acute-lymphoblastic-leukemia
#4
Adam J de Smith, Maneet Kaur, Semira Gonseth, Alyson A Endicott, Steve Selvin, Luoping Zhang, Ritu Roy, Xiaorong Shao, Helen M Hansen, Alice Y Kang, Kyle M Walsh, Gary V Dahl, Roberta McKean-Cowdin, Catherine Metayer, Joseph L Wiemels
Tobacco smoke exposure has been associated with risk of childhood acute lymphoblastic leukemia (ALL). Understanding the relationship between tobacco exposures and specific mutations may yield etiologic insights. We carried out a case-only analysis to explore whether prenatal and early-life tobacco smoke exposure influences the formation of leukemogenic genomic deletions. Somatic copy-number of 8 genes frequently deleted in ALL (CDKN2A, ETV6, IKZF1, PAX5, RB1, BTG1, PAR1 region, and EBF1) was assessed in 559 pre-treatment tumor samples from the California Childhood Leukemia Study...
February 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28196015/genomic-characterization-of-low-and-high-grade-pancreatic-mucinous-cystic-neoplasms-reveals-recurrent-kras-alterations-in-high-risk-lesions
#5
James R Conner, Adrián Mariño-Enríquez, Mari Mino-Kenudson, Elizabeth Garcia, Martha B Pitman, Lynette M Sholl, Amitabh Srivastava, Leona A Doyle
OBJECTIVES: Pancreatic ductal adenocarcinoma arises from the following 3 distinct precursor lesions: pancreatic intraepithelial neoplasia, intraductal papillary mucinous neoplasm, and mucinous cystic neoplasm (MCN). Genetic abnormalities in the first 2 precursor lesions have been well characterized, but there are limited data on progression pathways in MCNs. This study aimed to characterize genomic differences between MCNs with low-grade (LG) and high-grade (HG) dysplasia or carcinoma...
February 14, 2017: Pancreas
https://www.readbyqxmd.com/read/28193567/genomic-analysis-of-adult-b-all-identifies-potential-markers-of-shorter-survival
#6
Shiven Patel, Clinton C Mason, Martha J Glenn, Christian N Paxton, Sara T South, Melissa H Cessna, Julie Asch, Erin F Cobain, Dale L Bixby, Lauren B Smith, Shalini Reshmi, Julie M Gastier-Foster, Joshua D Schiffman, Rodney R Miles
B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL, but data regarding genetic prognostic biomarkers are much more limited for adult patients. We identified 70 adult B-ALL patients from three institutions and performed genome-wide analysis via single nucleotide polymorphism (SNP) arrays on DNA isolated from their initial diagnostic sample and, when available, relapse bone marrow specimens to identify recurring copy number alterations (CNA)...
February 3, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28192277/cdkn2a-p16ink4-a-expression-is-associated-with-vascular-progeria-in-chronic-kidney-disease
#7
Peter Stenvinkel, Karin Luttropp, Dagmara McGuinness, Anna Witasp, Abdul Rashid Qureshi, Annika Wernerson, Louise Nordfors, Martin Schalling, Jonaz Ripsweden, Lars Wennberg, Magnus Söderberg, Peter Bárány, Hannes Olauson, Paul G Shiels
Patients with chronic kidney disease (CKD) display a progeric vascular phenotype linked to apoptosis, cellular senescence and osteogenic transformation. This has proven intractable to modelling appropriately in model organisms. We have therefore investigated this directly in man, using for the first time validated cellular biomarkers of ageing (CDKN2A/p16(INK4a), SA-β-Gal) in arterial biopsies from 61 CKD patients undergoing living donor renal transplantation. We demonstrate that in the uremic milieu, increased arterial expression of CDKN2A/p16(INK4a) associated with vascular progeria in CKD, independently of chronological age...
February 9, 2017: Aging
https://www.readbyqxmd.com/read/28188630/genetic-analyses-of-isolated-high-grade-pancreatic-intraepithelial-neoplasia-hg-panin-reveal-paucity-of-alterations-in-tp53-and-smad4
#8
Waki Hosoda, Peter Chianchiano, James F Griffin, Meredith E Pittman, Lodewijk A A Brosens, Michaël Noë, Jun Yu, Koji Shindo, Masaya Suenaga, Neda Rezaee, Raluca Yonescu, Yi Ning, Jorge Albores-Saavedra, Naohiko Yoshizawa, Kenichi Harada, Akihiko Yoshizawa, Keiji Hanada, Shuji Yonehara, Michio Shimizu, Takeshi Uehara, Jaswinder S Samra, Anthony J Gill, Christopher L Wolfgang, Michael G Goggins, Ralph H Hruban, Laura D Wood
High-grade pancreatic intraepithelial neoplasia (HG-PanIN) is the major precursor of pancreatic ductal adenocarcinoma (PDAC) and is an ideal target for early detection. To characterize pure HG-PanIN, we analysed 23 isolated HG-PanIN lesions occurring in the absence of PDAC. Whole-exome sequencing of five of these HG-PanIN lesions revealed a median of 33 somatic mutations per lesion, with a total of 318 mutated genes. Targeted next-generation sequencing of 17 HG-PanIN lesions identified KRAS mutations in 94% of the lesions...
February 11, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28186602/-analysis-of-isodicentric-ph-chromosomes-in-chronic-myeloid-leukemia-blast-crisis
#9
Qian Li, Xiaoji Lin, Ying Lin, Rongxin Yao, Wu Huang, Handong Mei, Jian Gong, Hui Chen, Ningyan Teng
OBJECTIVE: To explore the genetic and clinical characteristics of isodicentric Ph chromosomes [idic(Ph)] in lymphoid blast crisis of chronic myeloid leukemia (CML-BLC). METHODS: Bone marrow aspirates of 2 patients with CML-BLC were analyzed by R banding after 24 hours of culturing. Genomic copy number variations (CNV) were analyzed by single nucleotide polymorphism array (SNP array) in case 1. The results were confirmed with fluorescence in situ hybridization (FISH)...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28184004/ets-proto-oncogene-1-transcriptionally-up-regulates-the-cholangiocyte-senescence-associated-protein-cyclin-dependent-kinase-inhibitor-2a
#10
Steven P O'Hara, Patrick L Splinter, Christy E Trussoni, Maria J Lorenzo Pisarello, Lorena Loarca, Noah S Splinter, Bryce F Schutte, Nicholas F LaRusso
Primary sclerosing cholangitis (PSC) is a chronic, fibro-inflammatory cholangiopathy (disease of the bile ducts) of unknown pathogenesis. We reported that cholangiocyte senescence features prominently in PSC and neuroblastoma RAS viral oncogene homolog (NRAS) is activated in PSC cholangiocytes. Additionally, persistent microbial insult (e.g., lipopolysaccharides [LPS]) induces Cyclin Dependent Kinase Inhibitor 2A (CDKN2A/p16INK4a) expression and senescence in cultured cholangiocytes in an NRAS-dependent manner...
February 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28181325/recurrent-copy-number-alterations-in-low-grade-and-anaplastic-pleomorphic-xanthoastrocytoma-with-and-without-braf-v600e-mutation
#11
Rachael A Vaubel, Alissa A Caron, Seiji Yamada, Paul A Decker, Jeanette E Eckel Passow, Fausto J Rodriguez, Amulya A Nageswara Rao, Daniel Lachance, Ian Parney, Robert Jenkins, Caterina Giannini
Pleomorphic xanthoastrocytoma (PXA) is a rare localized glioma characterized by frequent BRAF V600E mutation and CDKN2A/B deletion. We explored the association of copy-number variants (CNVs) with BRAF mutations, tumor grade, and patient survival in a cohort of 41 PXA patients using OncoScan chromosomal microarray. Primary resection specimens were available in 38 cases, including 24 PXA and 14 anaplastic PXA (A-PXA), 23 BRAF V600E mutant tumors (61%). CNVs were identified in all cases and most frequently involved chromosome 9 with homozygous CDKN2A/B deletion (n=33, 87%), a higher proportion than previously detected by comparative genomic hybridization (50-60%) (37)...
February 9, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28179162/loss-of-p16-ink4a-expression-and-homozygous-cdkn2a-deletion-are-associated-with-worse-outcome-and-younger-age-in-thymic-carcinomas
#12
Scott W Aesif, Marie Christine Aubry, Eunhee S Yi, Sara M Kloft-Nelson, Sarah M Jenkins, Grant M Spears, Patricia T Greipp, William R Sukov, Anja C Roden
PURPOSE: Thymic carcinomas are aggressive tumors. Biomarkers and alternative treatment modalities are needed. We studied the expression of p16 and cytogenetic abnormalities of CDKN2A and correlated findings with clinical features and outcome in a large cohort of thymic carcinomas. MATERIALS AND METHODS: Thymic carcinomas (1963-2013) were stained with p16. Fluorescence in situ hybridization was utilized to assess for the presence of CDKN2A gene (at 9p21). Statistical analysis was performed...
February 4, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28146043/characterization-of-melanoma-susceptibility-genes-in-high-risk-patients-from-central-italy
#13
Cristina Pellegrini, Maria Giovanna Maturo, Claudia Martorelli, Mariano Suppa, Ambra Antonini, Dimitra Kostaki, Lucilla Verna, Maria Teresa Landi, Ketty Peris, Maria Concetta Fargnoli
Genetic susceptibility to cutaneous melanoma has been investigated in Italian high-risk melanoma patients from different geographical regions. CDKN2A, CDK4, and MC1R genes have been screened in most studies, MITF and POT1 were screened in only one study, and none analyzed the TERT promoter. We carried out a mutational analysis of CDKN2A, CDK4 exon 2, POT1 p.S270N, MITF exon 10, MC1R, and the TERT promoter in 106 high-risk patients with familial melanoma (FM) and sporadic multiple primary melanoma (spMPM) from Central Italy and evaluated mutations according to the clinicopathological characteristics of patients and lesions...
January 31, 2017: Melanoma Research
https://www.readbyqxmd.com/read/28145465/molecular-morphological-and-survival-analysis-of-177-resected-pancreatic-ductal-adenocarcinomas-pdacs-identification-of-prognostic-subtypes
#14
Anna Melissa Schlitter, Angela Segler, Katja Steiger, Christoph W Michalski, Carsten Jäger, Björn Konukiewitz, Nicole Pfarr, Volker Endris, Markus Bettstetter, Bo Kong, Ivonne Regel, Jörg Kleeff, Günter Klöppel, Irene Esposito
Pancreatic ductal adenocarcinoma (PDAC) has generally a poor prognosis, but recent data suggest that there are molecular subtypes differing in clinical outcome. This study examines the association between histopathologic heterogeneity, genetic profile, and survival. Tumor histology from 177 resected PDAC patients with follow-up data was subclassified according to predominant growth pattern, and four key genes were analyzed. PDACs were classified as conventional (51%), combined with a predominant component (41%), variants and special carcinomas (8%)...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28139539/association-of-type-2-diabetes-mellitus-genes-in-polycystic-ovary-syndrome-aetiology-among-women-from-southern-india
#15
Battini Mohan Reddy, Uma Jyothi Kommoju, Shilpi Dasgupta, Pranavchand Rayabarapu
BACKGROUND & OBJECTIVES: Polycystic ovary syndrome (PCOS) is the most common reproductive endocrine disorder of premenopausal women. Given the phenotypic overlap between PCOS and type 2 diabetes mellitus (T2DM), this study was carried out to investigate whether genes implicated in T2DM were also involved in the susceptibility to PCOS among women from southern India. METHODS: A total of 248 women with PCOS and 210 healthy women as controls were genotyped for a panel of 15 single nucleotide polymorphisms (SNPs) from the nine T2DM genes, such as TCF7L2, IGF2BP2, SLC30A8, HHEX, CDKAL1, CDKN2A, IRS1, CAPN10 and PPARG, on Sequenom MassARRAY platform...
September 2016: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/28138026/preclinical-evaluation-of-sequential-combination-of-oncolytic-adenovirus-delta-24-rgd-and-phosphatidylserine-targeting-antibody-in-pancreatic-ductal-adenocarcinoma
#16
Bingbing Dai, David Roife, Ya'an Kang, Joy Gumin, Mayrim V Rios Perez, Xinqun Li, Michael Pratt, Rolf A Brekken, Juan Fueyo-Margareto, Frederick F Lang, Jason B Fleming
Delta-24-RGD (DNX-2401) is a conditional replication-competent oncolytic virus engineered to preferentially replicate in and lyse tumor cells with abnormality of p16/RB/E2F pathway. In a phase 1 clinical trial, Delta-24-RGD has shown favorable safety profile and promising clinical efficacy in brain tumor, which prompted us to evaluate its anticancer activity in pancreatic ductal adenocarcinoma (PDAC), which also has high frequency of homozygous deletion and promoter methylation of CDKN2A encoding the p16 protein...
January 30, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28135145/cancer-susceptibility-gene-mutations-in-individuals-with-colorectal-cancer
#17
Matthew B Yurgelun, Matthew H Kulke, Charles S Fuchs, Brian A Allen, Hajime Uno, Jason L Hornick, Chinedu I Ukaegbu, Lauren K Brais, Philip G McNamara, Robert J Mayer, Deborah Schrag, Jeffrey A Meyerhardt, Kimmie Ng, John Kidd, Nanda Singh, Anne-Renee Hartman, Richard J Wenstrup, Sapna Syngal
Purpose Hereditary factors play an important role in colorectal cancer (CRC) risk, yet the prevalence of germline cancer susceptibility gene mutations in patients with CRC unselected for high-risk features (eg, early age at diagnosis, personal/family history of cancer or polyps, tumor microsatellite instability [MSI], mismatch repair [MMR] deficiency) is unknown. Patients and Methods We recruited 1,058 participants who received CRC care in a clinic-based setting without preselection for age at diagnosis, personal/family history, or MSI/MMR results...
January 30, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28130839/abnormal-p53-and-p16-staining-patterns-distinguish-uterine-leiomyosarcoma-from-inflammatory-myofibroblastic-tumour
#18
Inga-Marie Schaefer, Jason L Hornick, Lynette Marie Sholl, Bradley J Quade, Marisa R Nucci, Carlos Parra-Herran
AIMS: Uterine myxoid leiomyosarcoma may show relatively bland histologic appearances despite its aggressive behaviour. Distinguishing uterine leiomyosarcoma from the more indolent inflammatory myofibroblastic tumour (IMT), which is amenable to targeted therapies, can be challenging. A significant subset of leiomyosarcomas harbour TP53 and/or CDKN2A genomic alterations. Here, we examined the diagnostic value of p53 and p16 immunohistochemistry in the distinction of uterine conventional and myxoid leiomyosarcoma from IMT, in correlation with targeted sequencing of TP53 and CDKN2A...
January 28, 2017: Histopathology
https://www.readbyqxmd.com/read/28126143/-copy-number-alterations-in-adult-patients-with-mature-b-acute-lymphoblastic-leukemia-treated-with-specific-immunochemotherapy
#19
Jordi Ribera, Lurdes Zamora, Olga García, Jesús-María Hernández-Rivas, Eulàlia Genescà, Josep-Maria Ribera
BACKGROUND AND OBJECTIVE: Unlike Burkitt lymphoma, molecular abnormalities other than C-MYC rearrangements have scarcely been studied in patients with mature B acute lymphoblastic leukemia (B-ALL). The aim of this study was to analyze the frequency and prognostic significance of copy number alterations (CNA) in genes involved in lymphoid differentiation, cell cycle and tumor suppression in adult patients with B-ALL. PATIENTS AND METHODS: We have analyzed by multiplex ligation-dependent probe amplification the genetic material from bone marrow at diagnosis from 25 adult B-ALL patients treated with rituximab and specific chemotherapy...
December 2, 2016: Medicina Clínica
https://www.readbyqxmd.com/read/28124441/confirmation-of-mutation-landscape-of-nf1-associated-malignant-peripheral-nerve-sheath-tumors
#20
Pierre Sohier, Armelle Luscan, Angharad Lloyd, Kevin Ashelford, Ingrid Laurendeau, Audrey Briand-Suleau, Dominique Vidaud, Nicolas Ortonne, Eric Pasmant, Meena Upadhyaya
The commonest tumors associated with neurofibromatosis type 1 (NF1) are benign peripheral nerve sheath tumors, called neurofibromas. Malignant transformation of neurofibromas into aggressive MPNSTs may occur with a poor patient prognosis. A co-operative role of SUZ12 or EED inactivation, along with NF1, TP53, and CDKN2A loss-of-function, has been proposed to drive progression to MPNSTs. An exome sequencing analysis of eight MPNSTs, one plexiform neurofibroma, and seven cutaneous neurofibromas was undertaken...
January 25, 2017: Genes, Chromosomes & Cancer
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