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https://www.readbyqxmd.com/read/28440912/performance-of-in-silico-tools-for-the-evaluation-of-p16ink4a-cdkn2a-variants-in-cagi
#1
Marco Carraro, Giovanni Minervini, Manuel Giollo, Yana Bromberg, Emidio Capriotti, Rita Casadio, Roland Dunbrack, Lisa Elefanti, Pietro Fariselli, Carlo Ferrari, Julian Gough, Panagiotis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Chiara Menin, Pier Luigi Martelli, Abhishek Niroula, Lipika R Pal, Susanna Repo, Maria Chiara Scaini, Mauno Vihinen, Qiong Wei, Qifang Xu, Yuedong Yang, Yizhou Yin, Jan Zaucha, Huiying Zhao, Yaoqi Zhou, Steven E Brenner, John Moult, Silvio C E Tosatto
Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of ten variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene...
April 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28439887/clinical-significance-of-recurrent-copy-number-aberrations-in-b-lineage-acute-lymphoblastic-leukaemia-without-recurrent-fusion-genes-across-age-cohorts
#2
Monica Messina, Sabina Chiaretti, Anna Lucia Fedullo, Alfonso Piciocchi, Maria Cristina Puzzolo, Alessia Lauretti, Valentina Gianfelici, Valerio Apicella, Paola Fazi, Geertruy Te Kronnie, Anna Maria Testi, Antonella Vitale, Anna Guarini, Robin Foà
Copy number aberrations (CNAs) represent cooperating events in B-lineage acute lymphoblastic leukaemia (B-ALL); however, their clinical relevance across different age cohorts is unclear. We analysed the recurrent CNAs in 157 age-stratified B-ALL negative cases for recurrent rearrangements (B-NEG ALL), and their association with patients' clinico-biological features. We found that: (i) CDKN2A/RB1-deleted and EBF1-deleted adults had a shorter disease-free survival than those with wild-type, (ii) among the unfavourable markers, CDKN2A/RB1 deletions and K/NRAS mutations retained their impact in multivariate analysis, encouraging the evaluation of CDKN2A/RB1 deletions and RAS mutations in the diagnostic/prognostic workflow to refine ALL risk assessment...
April 25, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28436958/local-clearance-of-senescent-cells-attenuates-the-development-of-post-traumatic-osteoarthritis-and-creates-a-pro-regenerative-environment
#3
Ok Hee Jeon, Chaekyu Kim, Remi-Martin Laberge, Marco Demaria, Sona Rathod, Alain P Vasserot, Jae Wook Chung, Do Hun Kim, Yan Poon, Nathaniel David, Darren J Baker, Jan M van Deursen, Judith Campisi, Jennifer H Elisseeff
Senescent cells (SnCs) accumulate in many vertebrate tissues with age and contribute to age-related pathologies, presumably through their secretion of factors contributing to the senescence-associated secretory phenotype (SASP). Removal of SnCs delays several pathologies and increases healthy lifespan. Aging and trauma are risk factors for the development of osteoarthritis (OA), a chronic disease characterized by degeneration of articular cartilage leading to pain and physical disability. Senescent chondrocytes are found in cartilage tissue isolated from patients undergoing joint replacement surgery, yet their role in disease pathogenesis is unknown...
April 24, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28435450/exome-sequencing-of-oral-squamous-cell-carcinoma-reveals-molecular-subgroups-and-novel-therapeutic-opportunities
#4
Shih-Chi Su, Chiao-Wen Lin, Yu-Fan Liu, Wen-Lang Fan, Mu-Kuan Chen, Chun-Ping Yu, Wei-En Yang, Chun-Wen Su, Chun-Yi Chuang, Wen-Hsiung Li, Wen-Hung Chung, Shun-Fa Yang
Oral squamous cell carcinoma (OSCC), an epithelial malignancy affecting a variety of subsites in the oral cavity, is prevalent in Asia. The survival rate of OSCC patients has not improved over the past decades due to its heterogeneous etiology, genetic aberrations, and treatment outcomes. Improvement in therapeutic strategies and tailored treatment options is an unmet need. To unveil the mutational spectrum, whole-exome sequencing of 120 OSCC from male individuals in Taiwan was conducted. Analyzing the contributions of the five mutational signatures extracted from the dataset of somatic variations identified four groups of tumors that were significantly associated with demographic and clinical features...
2017: Theranostics
https://www.readbyqxmd.com/read/28427506/recent-advances-in-genitourinary-tumors-a-review-focused-on-biology-and-systemic-treatment
#5
REVIEW
Aránzazu González Del Alba, José Ángel Arranz, Javier Puente, María José Méndez-Vidal, Enrique Gallardo, Enrique Grande, Begoña Pérez-Valderrama, Enrique González-Billalabeitia, Martín Lázaro-Quintela, Álvaro Pinto, Nuria Lainez, Josep M Piulats, Emilio Esteban, José Pablo Maroto Rey, Jorge A García, Cristina Suárez
Updated information published up to 2016 regarding major advances in renal cancer, bladder cancer, and prostate cancer is here presented. Based on an ever better understanding of the genetic and molecular alterations that govern the initial pathogenic mechanisms of tumor oncogenesis, an improvement in the characterization and treatment of urologic tumors has been achieved in the past year. According to the Cancer Genome Atlas (ATLAS) project, alterations in the MET pathway are characteristics of type 1 papillary renal cell carcinomas, and activation of NRF2-ARE pathway is associated with the biologically distinct type 2...
May 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28424409/clinical-genomic-profiling-to-identify-actionable-alterations-for-investigational-therapies-in-patients-with-diverse-sarcomas
#6
Roman Groisberg, David S Hong, Vijaykumar Holla, Filip Janku, Sarina Piha-Paul, Vinod Ravi, Robert Benjamin, Shreyas Kumar Patel, Neeta Somaiah, Anthony Conley, Siraj M Ali, Alexa B Schrock, Jeffrey S Ross, Philip J Stephens, Vincent A Miller, Shiraj Sen, Cynthia Herzog, Funda Meric-Bernstam, Vivek Subbiah
BACKGROUND: There are currently no United States Food and Drug Administration approved molecularly matched therapies for sarcomas except gastrointestinal stromal tumors. Complicating this is the extreme diversity, heterogeneity, and rarity of these neoplasms. Few therapeutic options exist for relapsed and refractory sarcomas. In clinical practice many oncologists refer patients for genomic profiling hoping for guidance on treatment options after standard therapy. However, a systematic analysis of actionable mutations has yet to be completed...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419547/perinatal-dna-methylation-at-cdkn2a-is-associated-with-offspring-bone-mass-findings-from-the-southampton-women-s-survey
#7
Elizabeth M Curtis, Robert Murray, Philip Titcombe, Eloïse Cook, Rebecca Clarke-Harris, Paula Costello, Emma Garratt, Joanna D Holbrook, Sheila Barton, Hazel Inskip, Keith M Godfrey, Christopher G Bell, Cyrus Cooper, Karen A Lillycrop, Nicholas C Harvey
Poor intrauterine and childhood growth has been linked with the risk of osteoporosis in later life, a relationship which may in part be mediated through altered epigenetic regulation of genes. We previously identified a region within the promoter of the long non-coding RNA ANRIL encoded by the CDKN2A locus, at which differential DNA methylation at birth showed correlations with offspring adiposity. Given the common lineage of adipocytes and osteoblasts, we investigated the relationship between perinatal CDKN2A methylation and bone mass at ages 4 and 6 years...
April 17, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28418604/loss-of-ink4a-arf-gene-enhances-ultraviolet-radiation-induced-cutaneous-tumor-development
#8
Israr Ahmad, Purushotham Guroji, Amanda H DeBrot, Padma P Manapragada, Santosh K Katiyar, Craig A Elmets, Nabiha Yusuf
The CDKN2A locus encodes for tumor suppressor genes p16(INK)(4a) and p14(Arf) which are frequently inactivated in human skin tumors. The purpose of this study was to determine the relationship between loss of INK4a/Arf activity and inflammation in the development of ultraviolet (UV) radiation-induced skin tumors. Panels of INK4a/Arf(-/-) mice and wild type (WT) mice were treated with a single dose of UVB (200 mJ/cm(2) ). For long-term studies, these mice were irradiated with UVB (200 mJ/cm(2) ) three times weekly for 30 weeks...
April 18, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28413430/next-generation-sequencing-of-non-small-cell-lung-cancer-using-a-customized-targeted-sequencing-panel-emphasis-on-small-biopsy-and-cytology
#9
David M DiBardino, David W Rawson, Anjali Saqi, Jonas J Heymann, Carlos A Pagan, William A Bulman
BACKGROUND: Next-generation sequencing (NGS) with a multi-gene panel is now available for patients with lung adenocarcinoma, but the performance characteristics and clinical utility of this testing are not well-described. We present the results of an extended 467 gene panel in a series of advanced, highly selected nonsmall cell lung cancer (NSCLC) patients using a range of specimens, including predominantly small biopsy and cytology specimens. MATERIALS AND METHODS: A retrospective review of 22 NSCLC biopsies sent for NGS using an extended gene panel from January 2014 to July 2015...
2017: CytoJournal
https://www.readbyqxmd.com/read/28410231/genetic-alterations-in-seborrheic-keratoses
#10
Barbara Heidenreich, Evygenia Denisova, Sivaramakrishna Rachakonda, Onofre Sanmartin, Timo Dereani, Ismail Hosen, Eduardo Nagore, Rajiv Kumar
Seborrheic keratoses are common benign epidermal lesions that are associated with increased age and sun-exposure. Those lesions despite harboring multiple somatic alterations in contrast to malignant tumors appear to be genetically stable. In order to investigate and characterize the presence of recurrent mutations, we performed exome sequencing on DNA from one seborrheic keratosis lesion and corresponding blood cells from the same patients with follow up investigation of alterations identified by exome sequencing in 24 additional lesions from as many patients...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28403857/hypermethylation-of-cdkn2a-exon-2-in-tumor-tumor-adjacent-and-tumor-distant-tissues-from-breast-cancer-patients
#11
Melanie Spitzwieser, Elisabeth Entfellner, Bettina Werner, Walter Pulverer, Georg Pfeiler, Stefan Hacker, Margit Cichna-Markl
BACKGROUND: Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA methylation levels have, however, not only been found in tumors, but also in tumor-surrounding tissue appearing histologically normal. This phenomenon is called field cancerization. Knowledge of the existence of a cancer field and its spread are of clinical relevance...
April 12, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28395715/-subcellular-re-distribution-of-f-actin-in-mcf7-cells-upon-inducible-expression-of-cdkn2a-p16-ink4a
#12
Jianqing Liang, Manna Wang, Zhengrong Zhang, Long Yuan, You Zheng, Hongyan Huang, Qiang Sun, Jufang Wang, Xiaoning Wang
Objective To investigate the effect of CDKN2A/p16(INK4a), a cyclin-dependent kinase inhibitor, on cell morphology and cytoskeleton in MCF7 breast cancer cells by tetracycline operon (Tet-on) inducible gene expression system. Methods MCF7 cells, genetically null for p16(INK4a) expression, were sequentially infected with two viruses of Tet-on systems to make MCF7-pTet-on-p16(INK4a) cells, which were induced to express p16NK4a by doxycycline (Dox) treatment. Cell growth was evaluated by cell counting. To observe the effect of p16(INK4a) on cell adhesion and cytoskeleton, intercellular adhesion and intracellular F-actin were examined by fluorescent staining with anti-E-cadherin antibody and phalloidin, respectively...
April 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28389767/a-new-pot1-germline-mutation-expanding-the-spectrum-of-pot1-associated-cancers
#13
Tremika Le-Shan Wilson, Namita Hattangady, Antonio Marcondes Lerario, Carmen Williams, Erika Koeppe, Shane Quinonez, Jenae Osborne, Kelly B Cha, Tobias Else
Melanomas are associated with several hereditary conditions. We present a large family with several family members affected with primary melanomas and dysplastic nevi as well as thyroid cancer and other malignant tumors. Clinical work-up did not reveal a mutation in any of the genes usually considered with evaluation for predisposition to melanoma (BRCA1/2, CDKN2A, CDK4, PTEN, TP53). Whole exome sequencing of five affected family members showed a new variant in POT1. POT1 is associated with the telomere shelterin complex that regulates telomere protection and telomerase access...
April 7, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28388616/the-evolution-of-sex-linked-barring-alleles-in-chickens-involves-both-regulatory-and-coding-changes-in-cdkn2a
#14
Doreen Schwochow Thalmann, Henrik Ring, Elisabeth Sundström, Xiaofang Cao, Mårten Larsson, Susanne Kerje, Andrey Höglund, Jesper Fogelholm, Dominic Wright, Per Jemth, Finn Hallböök, Bertrand Bed'Hom, Ben Dorshorst, Michèle Tixier-Boichard, Leif Andersson
Sex-linked barring is a fascinating plumage pattern in chickens recently shown to be associated with two non-coding and two missense mutations affecting the ARF transcript at the CDKN2A tumor suppressor locus. It however remained a mystery whether all four mutations are indeed causative and how they contribute to the barring phenotype. Here, we show that Sex-linked barring is genetically heterogeneous, and that the mutations form three functionally different variant alleles. The B0 allele carries only the two non-coding changes and is associated with the most dilute barring pattern, whereas the B1 and B2 alleles carry both the two non-coding changes and one each of the two missense mutations causing the Sex-linked barring and Sex-linked dilution phenotypes, respectively...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28381541/personalized-management-of-pancreatic-ductal-adenocarcinoma-patients-through-computational-modeling
#15
Kimiyo N Yamamoto, Shinichi Yachida, Akira Nakamura, Atsushi Niida, Minoru Oshima, Subhajyoti De, Lauren M Rosati, Joseph M Herman, Christine A Iacobuzio-Donahue, Hiroshi Haeno
Phenotypic diversity in pancreatic ductal adenocarcinoma (PDAC) results in a variety of treatment responses. Rapid autopsy studies have revealed a subgroup of PDAC patients with a lower propensity to develop metastatic disease, challenging the common perception that all patients die of widely metastatic disease, but questions remain about root causes of this difference and the potential impact on treatment strategies. In this study, we addressed these questions through the development of a mathematical model of PDAC progression that incorporates the major alteration status of specific genes with predictive utility...
April 5, 2017: Cancer Research
https://www.readbyqxmd.com/read/28380439/dna-methylation-profiling-identifies-the-hoxa11-gene-as-an-early-diagnostic-and-prognostic-molecular-marker-in-human-lung-adenocarcinoma
#16
Qun Li, Chang Chen, Xiaohui Ren, Weihong Sun
DNA hypermethylation plays important roles in carcinogenesis by silencing key genes. The goal of our study was to identify pivotal genes using MethyLight and assessed their diagnostic and prognostic values in lung adenocarcinoma (AD). In the present study, we detected DNA methylation at sixteen loci promoter regions in twenty one pairs of primary human lung AD tissues and adjacent non-tumor lung (AdjNL) tissues using the real-time PCR (RT-PCR)-based method MethyLight. By comparing the sixteen analyzed loci in lung AD tissues and AdjNL and non-tumor (NL) tissues, we found that, among the six genes identified with hypermethylation, the HOXA11, CDKN2A-EX2 and EYA4 genes showed highly promising DNA hypermethylation diagnostic markers in the lung AD tissues...
March 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28380361/efficient-generation-of-glucose-responsive-beta-cells-from-isolated-gp2-human-pancreatic-progenitors
#17
Jacqueline Ameri, Rehannah Borup, Christy Prawiro, Cyrille Ramond, Karen A Schachter, Raphael Scharfmann, Henrik Semb
Stem cell-based therapy for type 1 diabetes would benefit from implementation of a cell purification step at the pancreatic endoderm stage. This would increase the safety of the final cell product, allow the establishment of an intermediate-stage stem cell bank, and provide a means for upscaling β cell manufacturing. Comparative gene expression analysis revealed glycoprotein 2 (GP2) as a specific cell surface marker for isolating pancreatic endoderm cells (PECs) from differentiated hESCs and human fetal pancreas...
April 4, 2017: Cell Reports
https://www.readbyqxmd.com/read/28377727/transcriptomic-analysis-of-the-claudin-interactome-in-malignant-pleural-mesothelioma-evaluation-of-the-effect-of-disease-phenotype-asbestos-exposure-and-cdkn2a-deletion-status
#18
Erasmia Rouka, Georgios D Vavougios, Evgeniy I Solenov, Konstantinos I Gourgoulianis, Chrissi Hatzoglou, Sotirios G Zarogiannis
Malignant pleural mesothelioma (MPM) is a highly aggressive tumor primarily associated with asbestos exposure. Early detection of MPM is restricted by the long latency period until clinical presentation, the ineffectiveness of imaging techniques in early stage detection and the lack of non-invasive biomarkers with high sensitivity and specificity. In this study we used transcriptome data mining in order to determine which CLAUDIN (CLDN) genes are differentially expressed in MPM as compared to controls. Using the same approach we identified the interactome of the differentially expressed CLDN genes and assessed their expression profile...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28377483/vulvar-squamous-cell-carcinoma-vscc-as-two-diseases-hpv-status-identifies-distinct-mutational-profiles-including-oncogenic-fibroblast-growth-factor-receptor-3
#19
Johanne I Weberpals, Bryan Lo, Marc M Duciaume, Johanna N Spaans, Aisling A Clancy, Jim Dimitroulakos, Glenwood D Goss, Harman S Sekhon
PURPOSE: Patients with advanced or recurrent invasive vulvar squamous cell carcinoma (VSCC) have limited treatment options and a grave prognosis. Understanding the genomic landscape may facilitate the identification of new therapies and improve clinical outcomes. EXPERIMENTAL DESIGN: A retrospective chart review and molecular analysis of patients with VSCC from 2000-2016 was performed at the Ottawa Hospital Research Institute. The presence of oncogenic HPV was determined by nested PCR and amplified DNA was sequenced using the Ion AmpliSeq Cancer Hotspot v2 Panel...
April 4, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28373361/pancreatic-cancer-a-riddle-wrapped-in-a-mystery-inside-an-enigma
#20
EDITORIAL
Erkut Borazanci, Chi V Dang, Robert W Robey, Susan E Bates, John A Chabot, Daniel D Von Hoff
Pancreatic ductal adenocarcinoma (PDAC) is one of the most difficult-to-treat cancers. With an increasing incidence and inability to make major progress, it represents the very definition of unmet medical need. Progress has been made in understanding the basic biology-systematic genomic sequencing has led to the recognition that PDAC is not typically a heavily mutated tumor, although there are exceptions. The most consistently mutated genes are KRAS, CDKN2A, TP53, and SMAD4/DPC4 Study of familial PDAC has led to the recognition that a variety of defects in DNA repair genes can be associated with the emergence of pancreatic cancer...
April 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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