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https://www.readbyqxmd.com/read/28344746/cpg-island-methylator-phenotype-in-adenocarcinomas-from-the-digestive-tract-methods-conclusions-and-controversies
#1
EDITORIAL
Francisco Sánchez-Vega, Valer Gotea, Yun-Ching Chen, Laura Elnitski
Over the last two decades, cancer-related alterations in DNA methylation that regulate transcription have been reported for a variety of tumors of the gastrointestinal tract. Due to its relevance for translational research, great emphasis has been placed on the analysis and molecular characterization of the CpG island methylator phenotype (CIMP), defined as widespread hypermethylation of CpG islands in clinically distinct subsets of cancer patients. Here, we present an overview of previous work in this field and also explore some open questions using cross-platform data for esophageal, gastric, and colorectal adenocarcinomas from The Cancer Genome Atlas...
March 15, 2017: World Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28341182/systematic-identification-of-key-genes-and-pathways-in-the-development-of-invasive-cervical-cancer
#2
Guoping Niu, Duping Wang, Yunfeng Pei, Li Sun
BACKGROUND: Cervical cancer progresses through different stages: a long stage of precancerous lesions, then high-grade squamous intraepithelial lesion (HSIL) stage in which precancerous lesions transform into invasive cervical carcinoma, and finally invasive squamous cell carcinomas (SCC) which is difficult to be treated and can be deadly. METHODS AND RESULTS: To identify critical genes for the development and progression of cervical cancer development, we analyzed an online database comprised of normal squamous cervical epithelia samples, HSIL samples and SCC of cervix...
March 21, 2017: Gene
https://www.readbyqxmd.com/read/28340115/cellular-senescence-in-mouse-hippocampus-after-irradiation-and-the-role-of-p53-and-p21
#3
Zoey Cheng, Yan Zhen Zheng, Yu-Qing Li, C Shun Wong
Diverse stress signals including irradiation may trigger cellular senescence. We asked whether irradiation induced senescence in mouse hippocampus, and whether p53 or p21 played a role in this response. Following whole-brain irradiation, polymerase chain reaction (PCR) arrays for senescence-associated genes showed increased expression of CDKN1A (p21) and CDKN2A (p19ARF) in mouse hippocampus at 9 weeks. Upregulation of p21 and p19ARF was confirmed using real-time PCR, which also demonstrated increased CDKN2A/p16INKa expression after irradiation...
March 14, 2017: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/28327999/comprehensive-genomic-profiling-of-salivary-mucoepidermoid-carcinomas-reveals-frequent-bap1-pik3ca-and-other-actionable-genomic-alterations
#4
K Wang, J D McDermott, A B Schrock, J A Elvin, L Gay, S D Karam, D Raben, H Somerset, S M Ali, J S Ross, D W Bowles
Background: We sought to identify genomic alterations (GAs) in salivary mucoepidermoid carcinomas. Patients and methods: DNA was extracted from 48 mucoepidermoid carcinomas. Comprehensive genomic profiling (CGP) including the calculation to tumor mutational burden (TMB) was performed on hybridization-captured adaptor ligation-based libraries of 315 cancer-related genes plus introns from 28 genes frequently rearranged for cancer and evaluated for all classes of GAs...
January 16, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28316892/from-big-data-to-diagnosis-and-prognosis-gene-expression-signatures-in-liver-hepatocellular-carcinoma
#5
Hong Yang, Xin Zhang, Xiao-Yong Cai, Dong-Yue Wen, Zhi-Hua Ye, Liang Liang, Lu Zhang, Han-Lin Wang, Gang Chen, Zhen-Bo Feng
BACKGROUND: Liver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in. METHODS: Big data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes...
2017: PeerJ
https://www.readbyqxmd.com/read/28300909/multiple-cutaneous-melanomas-associated-with-gastric-and-brain-metastases
#6
Lara Caroline Grander, Fernanda Cabral, Alice Paixão Lisboa, Gabrielle Vale, Carlos Baptista Barcaui, Juan Manuel Pineiro Maceira
The occurrence of multiple primary melanomas in a single individual is rare. Most commonly, malignant melanocytic lesions subsequent to the initial diagnosis of melanoma are secondary cutaneous metastases. We report a patient with gastrointestinal bleeding from gastric metastasis of cutaneous melanoma. During clinical evaluation and staging, we discovered a brain metastasis associated with 3 synchronous primary cutaneous melanomas. We suggest the research on the mutation in the cyclin-dependent kinase inhibitor 2A (CDKN2A) (INK4a) in such cases...
September 2016: Anais Brasileiros de Dermatologia
https://www.readbyqxmd.com/read/28299358/a-novel-potentially-targetable-tmem106b-braf-fusion-in-pleomorphic-xanthoastrocytoma
#7
Susan J Hsiao, Matthias A Karajannis, Daniel Diolaiti, Mahesh M Mansukhani, Julia Glade Bender, Andrew L Kung, James H Garvin
Pleomorphic xanthoastrocytoma (PXA) is a World Health Organization (WHO) Grade II glioma occurring primarily in children and young adults. Most PXAs harbor the known activating mutation BRAF V600E. We report a case of locally recurrent PXA with anaplastic features in a 10-yr-old female. The PXA was negative by immunohistochemical (IHC) staining for BRAF V600E mutation. Whole-exome and transcriptome sequencing of the tumor confirmed the absence of BRAF V600E, but identified copy-number alterations (including loss of the tumor suppressor CDKN2A) and a novel TMEM106B-BRAF fusion...
March 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28295484/who-2016-classification-changes-and-advancements-in-the-diagnosis-of-miscellaneous-primary-cns-tumours
#8
Felix Sahm, David E Reuss, Caterina Giannini
This short review highlights significant changes and recent findings incorporated to varying extent in the WHO 2016 definition of a variety of tumours, including peripheral nerve sheath tumours, meningiomas, mesenchymal non-meningothelial tumours, melanocytic tumours, lymphomas and histiocytic tumours, germ cell tumours and non-neuroendocrine pituitary tumours. Most notable classification changes include: adding "hybrid nerve sheath tumours" to the spectrum of benign nerve sheath tumours; an updated definition of atypical meningioma (WHO grade II), including cases with brain invasion; recognizing dural solitary fibrous tumour (SFT) and haemangiopericytoma (HPC) as a single tumour entity characterized by NAB2 and STAT6 gene fusions for which the term solitary SFT/HPC was chosen; recognizing that pituitary granular cell tumour, spindle cell oncocytoma, and pituicytoma all share nuclear expression of TTF-1, possibly representing a spectrum of a single nosological entity derived from posterior pituitary glial cells...
March 12, 2017: Neuropathology and Applied Neurobiology
https://www.readbyqxmd.com/read/28283772/identification-genetic-testing-and-management-of-hereditary-melanoma
#9
Sancy A Leachman, Olivia M Lucero, Jone E Sampson, Pamela Cassidy, William Bruno, Paola Queirolo, Paola Ghiorzo
Several distinct melanoma syndromes have been defined, and genetic tests are available for the associated causative genes. Guidelines for melanoma genetic testing have been published as an informal "rule of twos and threes," but these guidelines apply to CDKN2A testing and are not intended for the more recently described non-CDKN2A melanoma syndromes. In order to develop an approach for the full spectrum of hereditary melanoma patients, we have separated melanoma syndromes into two types: "melanoma dominant" and "melanoma subordinate...
March 10, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28283584/clinical-benefit-in-response-to-palbociclib-treatment-in-refractory-uterine-leiomyosarcomas-with-a-common-cdkn2a-alteration
#10
Julia A Elvin, Laurie M Gay, Rita Ort, Joseph Shuluk, Jennifer Long, Lauren Shelley, Ronald Lee, Zachary R Chalmers, Garrett M Frampton, Siraj M Ali, Alexa B Schrock, Vincent A Miller, Philip J Stephens, Jeffrey S Ross, Richard Frank
BACKGROUND: Uterine leiomyosarcoma (uLMS) responds poorly to conventional chemotherapeutic agents, and personalized therapies have yet to be systematically explored. Comprehensive genomic profiling (CGP) can identify therapeutic targets and provide insight into the biology of this highly aggressive tumor. We report a case of uLMS treated with the CGP-matched therapy palbociclib, a CDK4/6 inhibitor, with sustained clinical benefit in this rare and deadly malignancy. MATERIALS AND METHODS: This study analyzed 279 clinically advanced/recurrent uLMS samples...
March 10, 2017: Oncologist
https://www.readbyqxmd.com/read/28280605/next-generation-sequencing-identifies-interactome-signatures-in-relapsed-and-refractory-metastatic-colorectal-cancer
#11
Benny Johnson, Laurence Cooke, Daruka Mahadevan
BACKGROUND: In the management of metastatic colorectal cancer (mCRC), KRAS, NRAS and BRAF mutational status individualizes therapeutic options and identify a cohort of patients (pts) with an aggressive clinical course. We hypothesized that relapsed and refractory mCRC pts develop unique mutational signatures that may guide therapy, predict for a response and highlight key signaling pathways important for clinical decision making. METHODS: Relapsed and refractory mCRC pts (N=32) were molecularly profiled utilizing commercially available next generation sequencing (NGS) platforms...
February 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28276595/a-genetic-variant-in-cdkn2a-b-gene-is-associated-with-the-increased-risk-of-breast-cancer
#12
Soodabeh ShahidSales, Mehraneh Mehramiz, Faezeh Ghasemi, Amir Aledavood, Mehri Shamsi, Seyed Mahdi Hassanian, Majid Ghayour-Mobarhan, Amir Avan
BACKGROUND: Breast cancer is among the leading cause of cancer-related-deaths in women, supporting the need for the identification of novel prognostic and predictive biomarkers. Recent studies have identified common genetic variants in a region on chromosome 9p21 associated with an increased risk of developing different cancers. Here, we explored the association of a genetic variant in CDKN2A/B, rs10811661, for the first time in 564 subjects with/without breast cancer. METHOD: Genotyping was performed using TaqMan real time PCR method...
March 9, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28272465/reconstituting-development-of-pancreatic-intraepithelial-neoplasia-from-primary-human-pancreas-duct-cells
#13
Jonghyeob Lee, Emily R Snyder, Yinghua Liu, Xueying Gu, Jing Wang, Brittany M Flowers, Yoo Jung Kim, Sangbin Park, Gregory L Szot, Ralph H Hruban, Teri A Longacre, Seung K Kim
Development of systems that reconstitute hallmark features of human pancreatic intraepithelial neoplasia (PanINs), the precursor to pancreatic ductal adenocarcinoma, could generate new strategies for early diagnosis and intervention. However, human cell-based PanIN models with defined mutations are unavailable. Here, we report that genetic modification of primary human pancreatic cells leads to development of lesions resembling native human PanINs. Primary human pancreas duct cells harbouring oncogenic KRAS and induced mutations in CDKN2A, SMAD4 and TP53 expand in vitro as epithelial spheres...
March 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28265829/a-multicenter-study-of-a-fluorescence-in-situ-hybridization-probe-set-for-diagnosing-high-grade-dysplasia-and-adenocarcinoma-in-barrett-s-esophagus
#14
John M Poneros, Adam S Faye, Emily G Barr Fritcher, Ananda Sen, Sharmila Anandasabapathy, Robert S Bresalier, Norman Marcon, D Kim Turgeon, Henry Appelman, Daniel Normolle, Larry E Morrison, Dean E Brenner, Kevin C Halling
BACKGROUND AND AIMS: Preliminary single-institution data suggest that fluorescence in situ hybridization (FISH) may be useful for detecting high-grade dysplasia (HGD) and esophageal adenocarcinoma (EA) in patients with Barrett's esophagus (BE). This multicenter study aims to validate the measurement of polysomy (gain of at least two loci) by FISH as a way to discriminate degrees of dysplasia in BE specimens. METHODS: Tissue specimens were collected from four different hospitals and read by both the local pathology department ("Site diagnosis") and a single central pathologist ("Review diagnosis") at a separate institution...
March 6, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28265066/resistance-mechanisms-to-tp53-mdm2-inhibition-identified-by-in-vivo-piggybac-transposon-mutagenesis-screen-in-an-arf-mouse-model
#15
Emilie A Chapeau, Agnieszka Gembarska, Eric Y Durand, Emeline Mandon, Claire Estadieu, Vincent Romanet, Marion Wiesmann, Ralph Tiedt, Joseph Lehar, Antoine de Weck, Roland Rad, Louise Barys, Sebastien Jeay, Stephane Ferretti, Audrey Kauffmann, Esther Sutter, Armelle Grevot, Pierre Moulin, Masato Murakami, William R Sellers, Francesco Hofmann, Michael Rugaard Jensen
Inhibitors of double minute 2 protein (MDM2)-tumor protein 53 (TP53) interaction are predicted to be effective in tumors in which the TP53 gene is wild type, by preventing TP53 protein degradation. One such setting is represented by the frequent CDKN2A deletion in human cancer that, through inactivation of p14ARF, activates MDM2 protein, which in turn degrades TP53 tumor suppressor. Here we used piggyBac (PB) transposon insertional mutagenesis to anticipate resistance mechanisms occurring during treatment with the MDM2-TP53 inhibitor HDM201...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28263969/activated-mek-cooperates-with-cdkn2a-and-pten-loss-to-promote-the-development-and-maintenance-of-melanoma
#16
H Yang, D A Kircher, K H Kim, A H Grossmann, M W VanBrocklin, S L Holmen, J P Robinson
The development of targeted inhibitors, vemurafenib and dabrafenib, has led to improved clinical outcome for melanoma patients with BRAF(V600E) mutations. Although the initial response to these inhibitors can be dramatic, sometimes causing complete tumor regression, the majority of melanomas eventually become resistant. Mitogen-activated protein kinase kinase (MEK) mutations are found in primary melanomas and frequently reported in BRAF melanomas that develop resistance to targeted therapy; however, melanoma is a molecularly heterogeneous cancer, and which mutations are drivers and which are passengers remains to be determined...
March 6, 2017: Oncogene
https://www.readbyqxmd.com/read/28262675/genomic-characterisation-of-e%C3%AE-myc-mouse-lymphomas-identifies-bcor-as-a-myc-co-operative-tumour-suppressor-gene
#17
Marcus Lefebure, Richard W Tothill, Elizabeth Kruse, Edwin D Hawkins, Jake Shortt, Geoffrey M Matthews, Gareth P Gregory, Benjamin P Martin, Madison J Kelly, Izabela Todorovski, Maria A Doyle, Richard Lupat, Jason Li, Jan Schroeder, Meaghan Wall, Stuart Craig, Gretchen Poortinga, Don Cameron, Megan Bywater, Lev Kats, Micah D Gearhart, Vivian J Bardwell, Ross A Dickins, Ross D Hannan, Anthony T Papenfuss, Ricky W Johnstone
The Eμ-Myc mouse is an extensively used model of MYC driven malignancy; however to date there has only been partial characterization of MYC co-operative mutations leading to spontaneous lymphomagenesis. Here we sequence spontaneously arising Eμ-Myc lymphomas to define transgene architecture, somatic mutations, and structural alterations. We identify frequent disruptive mutations in the PRC1-like component and BCL6-corepressor gene Bcor. Moreover, we find unexpected concomitant multigenic lesions involving Cdkn2a loss and other cancer genes including Nras, Kras and Bcor...
March 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28258440/comprehensive-characterization-of-genes-associated-with-the-tp53-signal-transduction-pathway-in-various-tumors
#18
Shumpei Ohnami, Keiichi Ohshima, Takeshi Nagashima, Kenichi Urakami, Yuji Shimoda, Junko Saito, Akane Naruoka, Keiichi Hatakeyama, Tohru Mochizuki, Masakuni Serizawa, Sumiko Ohnami, Masatoshi Kusuhara, Ken Yamaguchi
The TP53 signal transduction pathway is an attractive target for cancer treatments. In this study, we conducted a comprehensive molecular evaluation of 907 patients with cancer in Japan to identify genomic alterations in the TP53 pathway. TP53 mutations were frequently detected in many cancers, except melanoma, thymic tumors, gastrointestinal stromal tumors, and renal cancers. The frequencies of non-synonymous single nucleotide variants (SNVs) in the TP53 family members TP63 and TP73 were relatively low, although genes with increased frequencies of SNVs were as follows: PTEN (11...
March 3, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28257446/breastfeeding-effects-on-dna-methylation-in-the-offspring-a-systematic-literature-review
#19
Fernando Pires Hartwig, Christian Loret de Mola, Neil Martin Davies, Cesar Gomes Victora, Caroline L Relton
BACKGROUND: Breastfeeding benefits both infants and mothers. Recent research shows long-term health and human capital benefits among individuals who were breastfed. Epigenetic mechanisms have been suggested as potential mediators of the effects of early-life exposures on later health outcomes. We reviewed the literature on the potential effects of breastfeeding on DNA methylation. METHODS: Studies reporting original results and evaluating DNA methylation differences according to breastfeeding/breast milk groups (e...
2017: PloS One
https://www.readbyqxmd.com/read/28256616/dose-and-time-effect-responses-of-dna-methylation-and-histone-h3k9-acetylation-changes-induced-by-traffic-related-air-pollution
#20
Rui Ding, Yongtang Jin, Xinneng Liu, Huaizhuang Ye, Ziyi Zhu, Yuan Zhang, Ting Wang, Yinchun Xu
As an important risk factor of respiratory disorders, traffic-related air pollution (TRAP) has caused extensive concerns. Epigenetic change has been considered a link between TRAP and respiratory diseases. However, the exact effects of TRAP on epigenetic changes are still unclear. Here we investigated the dose- and time- effect responses of TRAP on DNA methylations and H3K9 acetylation (H3K9ac) in both blood and lung tissues of rats. The findings showed that every 1 μg/m(3) increase of TRAP components were associated with changes in %5 mC (95% CI) in LINE-1, iNOS, p16(CDKN2A), and APC ranging from -0...
March 3, 2017: Scientific Reports
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