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https://www.readbyqxmd.com/read/29451900/the-arid1a-p53-and-%C3%A3-catenin-statuses-are-strong-prognosticators-in-clear-cell-and-endometrioid-carcinoma-of-the-ovary-and-the-endometrium
#1
Marlene Heckl, Elisa Schmoeckel, Linda Hertlein, Miriam Rottmann, Udo Jeschke, Doris Mayr
AIM: The objective of this study was to evaluate the prognostic value of ARID1A, p53, p21, p16 and ß-Catenin in endometrioid and clear cell ovarian and endometrial carcinomas. MATERIALS AND METHODS: 97 tumors were available for analysis of ARID1A, p53, p21, p16 and ß-Catenin with the techniques of tissue microarray and immunohistochemistry. 32 were ovarian carcinomas and 65 were endometrial carcinomas. RESULTS: Endometrioid ovarian carcinomas showed negative staining for ARID1A (a) and p21 (b), aberrant expression of p53 (c) and p16 (d) and ß-Catenin positive nuclear expression (e) respectively in 19% (a), 100% (b), 28...
2018: PloS One
https://www.readbyqxmd.com/read/29449409/a-human-specific-switch-of-alternatively-spliced-afmid-isoforms-contributes-to-tp53-mutations-and-tumor-recurrence-in-hepatocellular-carcinoma
#2
Kuan-Ting Lin, Wai Kit Ma, Juergen Scharner, Yun-Ru Liu, Adrian R Krainer
Pre-mRNA splicing can contribute to the switch of cell identity that occurs in carcinogenesis. Here, we analyze a large collection of RNA-seq data sets and report that splicing changes in hepatocyte-specific enzymes, such as AFMID and KHK , are associated with HCC patients' survival and relapse. The switch of AFMID isoforms is an early event in HCC development and is associated with driver mutations in TP53 and ARID1A The switch of AFMID isoforms is human-specific and not detectable in other species, including primates...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29438172/gastric-carcinomas-with-lymphoid-stroma-an-evaluation-of-the-histopathologic-and-molecular-features
#3
Erika Hissong, Girish Ramrattan, Pan Zhang, Xi Kathy Zhou, Gloria Young, David S Klimstra, Jinru Shia, Helen Fernandes, Rhonda K Yantiss
Gastric carcinoma with lymphoid stroma is an uncommon variant enriched for mutually exclusive Epstein-Barr virus (EBV) positivity and mismatch repair (MMR) deficiency. We performed this study to evaluate molecular alterations in this morphologically homogeneous subtype and compare them with 295 conventional gastric cancers analyzed in The Cancer Genome Atlas study. We identified 31 study cases and subjected them to in situ hybridization for EBV-encoded RNAs and assessment for MMR status. Immunostains for PD-L1, β-catenin, and HER2 were performed; extracted DNA was sequenced with a Comprehensive Cancer Panel...
February 12, 2018: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29435122/apobec-mediated-mutagenesis-in-urothelial-carcinoma-is-associated-with-improved-survival-mutations-in-dna-damage-response-genes-and-immune-response
#4
Alexander P Glaser, Damiano Fantini, Yiduo Wang, Yanni Yu, Kalen J Rimar, Joseph R Podojil, Stephen D Miller, Joshua J Meeks
APOBEC enzymes are responsible for a mutation signature (TCW>T/G) implicated in a wide variety of tumors. We explore the APOBEC mutational signature in bladder cancer and the relationship with specific mutations, molecular subtype, gene expression, and survival using sequencing data from The Cancer Genome Atlas (n = 395), Beijing Genomics Institute (n = 99), and Cancer Cell Line Encyclopedia. Tumors were split into "APOBEC-high" and "APOBEC-low" based on APOBEC enrichment. Patients with APOBEC-high tumors have better overall survival compared to those with APOBEC-low tumors (38...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29426961/tissue-microarray-is-suitable-for-scientific-biomarkers-studies-in-endometrial-cancer
#5
Nicole C M Visser, Anneke A M van der Wurff, Johanna M A Pijnenborg, Leon F A G Massuger, Johan Bulten, Iris D Nagtegaal
The aim of this study was to define the concordance between tissue microarrays (TMAs) of different sizes and whole slide for 15 different antibodies in endometrial cancer and study the use of TMAs in preoperative endometrial samples. Cores of preoperative and hysterectomy specimens of 14 endometrial cancer and three atypical hyperplasia cases were collected in TMA blocks. Two 0.6-mm and two 2.0-mm cores were used from each sample. Different antibodies were tested in TMAs and compared with results of whole slides of hysterectomy...
February 9, 2018: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29422640/mutational-landscape-of-goblet-cell-carcinoids-and-adenocarcinoma-ex-goblet-cell-carcinoids-of-the-appendix-is-distinct-from-typical-carcinoids-and-colorectal-adenocarcinomas
#6
Melanie Johncilla, Matthew Stachler, Joseph Misdraji, Mikhail Lisovsky, Masato Yozu, Neal Lindeman, Gregory Y Lauwers, Robert D Odze, Amitabh Srivastava
There is limited data on the spectrum of molecular alterations in goblet cell carcinoids and adenocarcinoma ex goblet cell carcinoids of the appendix. We used next generation sequencing to determine mutations of potential pathogenetic and therapeutic significance in this rare group of tumors. Adequate DNA was successfully extracted in 34/46 cases and the final group included 18 goblet cell carcinoids and 16 adenocarcinoma ex goblet cell carcinoids. Illumina TruSeq™ was used for sequencing exons of a custom 282 gene panel using an Illumina HiSeq 2000...
February 8, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29408647/whole-exome-mutational-and-transcriptional-landscapes-of-combined-hepatocellular-cholangiocarcinoma-and-intrahepatic-cholangiocarcinoma-reveal-molecular-diversity
#7
Zhen-Hao Liu, Bao-Feng Lian, Qiong-Zhu Dong, Han Sun, Jin-Wang Wei, Yuan-Yuan Sheng, Wei Li, Yixue Li, Lu Xie, Lei Liu, Lun-Xiu Qin
BACKGROUND: Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). CHC is a distinct, albeit rare, subtype of PLC and is comprised of cells with histopathological features of both HCC and ICC. Several studies have focused on the mutation and expression landscapes of HCC and ICC...
January 31, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29401002/phosphatidylinositol-3-kinase-%C3%AE-selective-inhibition-with-alpelisib-byl719-in-pik3ca-altered-solid-tumors-results-from-the-first-in-human-study
#8
Dejan Juric, Jordi Rodon, Josep Tabernero, Filip Janku, Howard A Burris, Jan H M Schellens, Mark R Middleton, Jordan Berlin, Martin Schuler, Marta Gil-Martin, Hope S Rugo, Ruth Seggewiss-Bernhardt, Alan Huang, Douglas Bootle, David Demanse, Lars Blumenstein, Christina Coughlin, Cornelia Quadt, José Baselga
Purpose We report the first-in-human phase Ia study to our knowledge ( ClinicalTrials.gov identifier: NCT01219699) identifying the maximum tolerated dose and assessing safety and preliminary efficacy of single-agent alpelisib (BYL719), an oral phosphatidylinositol 3-kinase α (PI3Kα)-selective inhibitor. Patients and Methods In the dose-escalation phase, patients with PIK3CA-altered advanced solid tumors received once-daily or twice-daily oral alpelisib on a continuous schedule. In the dose-expansion phase, patients with PIK3CA-altered solid tumors and PIK3CA-wild-type, estrogen receptor-positive/human epidermal growth factor receptor 2-negative breast cancer received alpelisib 400 mg once daily...
February 5, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29399196/microarray-pathway-analysis-indicated-that-mitogen-activated-protein-kinase-extracellular-signal-regulated-kinase-and-insulin-growth-factor-1-signaling-pathways-were-inhibited-by-small-interfering-rna-against-at-rich-interactive-domain-1a-in-endometrial-cancer
#9
Ye Yang, Wei Bao, Zhengyu Sang, Yongbing Yang, Meng Lu, Xiaowei Xi
Mutations in the gene encoding AT-rich interactive domain 1A (ARID1A) are frequently observed in endometrial cancer (EC) but the molecular mechanisms linking the genetic changes remain to be fully understood. The present study aimed to elucidate the influence of ARID1A mutations on signaling pathways. Missense, synonymous and nonsense heterozygous ARID1A mutations in the EC HEC-1-A cell line were verified by Sanger sequencing. Mutated ARID1A small interfering RNA was transfected into HEC-1-A cells. Biochemical microarray analysis revealed 13 upregulated pathways, 17 downregulated pathways, 14 significantly affected disease states and functions, 662 upstream and 512 downstream genes in mutated ARID1A-depleted HEC-1-A cells, among which the mitogen-activated protein kinase/extracellular signal-regulated kinase and insulin-like growth factor-1 (IGF1) signaling pathways were the 2 most downregulated pathways...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29392887/high-level-expression-of-arid1a-predicts-a-favourable-outcome-in-triple-negative-breast-cancer-patients-receiving-paclitaxel-based-chemotherapy
#10
Yuan-Feng Lin, Ing-Jy Tseng, Chih-Jung Kuo, Hui-Yu Lin, I-Jen Chiu, Hui-Wen Chiu
Paclitaxel-based chemotherapy is a common strategy to treat patients with triple-negative breast cancer (TNBC). As paclitaxel resistance is still a clinical issue in treating TNBCs, identifying molecular markers for predicting pathologic responses to paclitaxel treatment is thus urgently needed. Here, we report that an AT-rich interaction domain 1A (ARID1A) transcript is up-regulated in paclitaxel-sensitive TNBC cells but down-regulated in paclitaxel-resistant cells upon paclitaxel treatment. Moreover, ARID1A expression was negatively correlated with the IC50 concentration of paclitaxel in the tested TNBC cell lines...
February 1, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29389935/novel-pedigree-analysis-implicates-dna-repair-and-chromatin-remodeling-in-multiple-myeloma-risk
#11
Rosalie G Waller, Todd M Darlington, Xiaomu Wei, Michael J Madsen, Alun Thomas, Karen Curtin, Hilary Coon, Venkatesh Rajamanickam, Justin Musinsky, David Jayabalan, Djordje Atanackovic, S Vincent Rajkumar, Shaji Kumar, Susan Slager, Mridu Middha, Perrine Galia, Delphine Demangel, Mohamed Salama, Vijai Joseph, James McKay, Kenneth Offit, Robert J Klein, Steven M Lipkin, Charles Dumontet, Celine M Vachon, Nicola J Camp
The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs...
February 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29389895/ovarian-cancers-genetic-abnormalities-tumor-heterogeneity-and-progression-clonal-evolution-and-cancer-stem-cells
#12
REVIEW
Ugo Testa, Eleonora Petrucci, Luca Pasquini, Germana Castelli, Elvira Pelosi
Four main histological subtypes of ovarian cancer exist: serous (the most frequent), endometrioid, mucinous and clear cell; in each subtype, low and high grade. The large majority of ovarian cancers are diagnosed as high-grade serous ovarian cancers (HGS-OvCas). TP53 is the most frequently mutated gene in HGS-OvCas; about 50% of these tumors displayed defective homologous recombination due to germline and somatic BRCA mutations, epigenetic inactivation of BRCA and abnormalities of DNA repair genes; somatic copy number alterations are frequent in these tumors and some of them are associated with prognosis; defective NOTCH, RAS/MEK, PI3K and FOXM1 pathway signaling is frequent...
February 1, 2018: Medicines (Basel, Switzerland)
https://www.readbyqxmd.com/read/29386312/tumor-mutational-burden-guides-therapy-in-a-treatment-refractory-pole-mutant-uterine-carcinosarcoma
#13
Munveer S Bhangoo, Peter Boasberg, Pareen Mehta, Julia A Elvin, Siraj M Ali, Winnie Wu, Samuel J Klempner
Gynecologic carcinosarcomas, previously known as malignant mixed Müllerian tumors, are uncommon malignancies that demonstrate an aggressive biology and lack a standard therapeutic approach. Molecular analyses have revealed recurrent alterations in chromatin remodeling genes, but clinical support for therapeutic significance is lacking. We prospectively identified a patient with refractory uterine carcinosarcoma whose tumor was subject to molecular profiling at diagnosis and again at radiographic progression...
January 31, 2018: Oncologist
https://www.readbyqxmd.com/read/29374058/glioma-tumor-suppressor-candidate-region-gene-1-gltscr1-and-its-paralog-gltscr1-like-form-swi-snf-chromatin-remodeling-subcomplexes
#14
Aktan Alpsoy, Emily C Dykhuizen
The mammalian SWI/SNF chromatin remodeling complex is a heterogeneous collection of related protein complexes required for gene regulation and genome integrity. It contains a central ATPase (BRM or BRG1) and various combinations of 10-14 accessory subunits (BAFs for BRM/BRG1 Associated Factors). Two distinct complexes differing in size, BAF and the slightly larger Polybromo-BAF (PBAF), share many of the same core subunits but are differentiated primarily by having either AT-rich interaction domain 1A/B (ARID1A/B in BAF) or ARID2 (in PBAF)...
January 26, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29360550/genomic-characterization-of-biliary-tract-cancers-identifies-driver-genes-and-predisposing-mutations
#15
Christopher P Wardell, Masashi Fujita, Toru Yamada, Michele Simbolo, Matteo Fassan, Rosa Karlic, Paz Polak, Jaegil Kim, Yutaka Hatanaka, Kazuhiro Maejima, Rita T Lawlor, Yoshitsugu Nakanishi, Tomoko Mitsuhashi, Akihiro Fujimoto, Mayuko Furuta, Andrea Ruzzenente, Simone Conci, Ayako Oosawa, Aya Sasaki-Oku, Kaoru Nakano, Hiroko Tanaka, Yujiro Yamamoto, Kubo Michiaki, Yoshiiku Kawakami, Hiroshi Aikata, Masaki Ueno, Shinya Hayami, Kunihito Gotoh, Shun-Ichi Ariizumi, Masakazu Yamamoto, Hiroki Yamaue, Kazuaki Chayama, Satoru Miyano, Gad Getz, Aldo Scarpa, Satoshi Hirano, Toru Nakamura, Hidewaki Nakagawa
BACKGROUND & AIMS: Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous with poor response to treatments. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed large scale genome sequencing analyses on BTCs to investigate their somatic and germline driver events and characterize their genomic landscape. METHODS: We analyzed 412 BTC samples from Japanese and Italian populations, with 107 whole exome sequencing (WES), 39 whole genome sequencing (WGS), and targeted sequencing of a further 266 samples...
January 19, 2018: Journal of Hepatology
https://www.readbyqxmd.com/read/29354491/opportunities-of-next-generation-sequencing-in-non-muscle-invasive-bladder-cancer-outcome-prediction
#16
REVIEW
Karl H Pang, Francesco Esperto, Aidan P Noon
Bladder cancer (BC) is a common disease in both sexes and majority of cases present as non-muscle invasive BC (NMIBC). The percentage of NMIBC progressing to muscle invasive BC (MIBC) varies between 25% and 75% and currently there are no reliable biomarkers that may predict the outcome of high-risk (HR) NMIBC. Whilst The Cancer Genome Atlas (TCGA) project has identified genetic alteration in MIBC using next-generation sequencing (NGS), genetic data in HR-NMIBC outcome prediction using this new technology are limited...
December 2017: Translational Andrology and Urology
https://www.readbyqxmd.com/read/29351919/high-yield-of-pathogenic-germline-mutations-causative-or-likely-causative-of-the-cancer-phenotype-in-selected-children-with-cancer
#17
Illja Diets, Esmé Waanders, Marjolijn J L Ligtenberg, Diede van Bladel, Eveline J Kamping, Peter M Hoogerbrugge, Saskia Hopman, Maran J W Olderode-Berends, Erica H Gerkes, David Koolen, Carlo Marcelis, Gijs We Santen, Martine van Belzen, Dylan Mordaunt, Lesley McGregor, Elizabeth Thompson, Antonis Kattamis, Agata Pastorczak, Wojciech Mlynarski, Denisa Ilencikova, Anneke Vulto-van Silfhout, Thatjana Gardeitchik, E S J M de Bont, Jan Loeffen, Anja Wagner, Arjen R Mensenkamp, Roland P Kuiper, Nicoline Hoogerbrugge, Marjolijn Jongmans
PURPOSE: In many children with cancer and characteristics suggestive of a genetic predisposition syndrome, the genetic cause is still unknown. We studied the yield of pathogenic mutations by applying whole exome sequencing on a selected cohort of children with cancer. EXPERIMENTAL DESIGN: To identify mutations in known and novel cancer predisposing genes, we performed trio-based whole exome sequencing on germline DNA of 40 selected children and their parents. These children were diagnosed with cancer and had at least one of the following features: (1) intellectual disability and/or congenital anomalies, (2) multiple malignancies, (3) family history of cancer or (4) an adult type of cancer...
January 19, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29338553/comprehensive-clinicopathologic-and-updated-immunohistochemical-characterization-of-primary-ovarian-mucinous-carcinoma
#18
Dina Bassiouny, Nadia Ismiil, Valerie Dubé, Guangming Han, Matthew Cesari, Fang-I Lu, Elzbieta Slodkowska, Carlos Parra-Herran, Hak Fai Chiu, Magda Naeim, Nim Li, Mahmoud Khalifa, Sharon Nofech-Mozes
The distinction of primary mucinous ovarian carcinoma (PMOC) from other primaries or secondaries is essential for selecting therapeutic options and prognostication. We aimed to characterize the immunohistochemical profile of 36 PMOCs using an extended immunohistochemical panel, with clinicopathologic features and outcome. PAX8 was negative in 30 (83.3%), and SATB2 was negative in 32/35. HNF1B, AMACR, and napsin-A were detected in 33 (91.7%), 35 (97.2%), and 0 (0%), respectively. MMR proteins and ARID1A were retained in 100%; PTEN was lost in 4 (11...
January 1, 2018: International Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29317648/nf-%C3%AE%C2%BAb-mir-223-3p-arid1a-axis-is-involved-in-helicobacter-pylori-caga-induced-gastric-carcinogenesis-and-progression
#19
Fenghua Yang, Yugang Xu, Chao Liu, Cunying Ma, Shuiyan Zou, Xia Xu, Jihui Jia, Zhifang Liu
Infection with Helicobacter pylori (H. pylori) and the resulting gastric inflammation is regarded as the strongest risk factor for gastric carcinogenesis and progression. NF-κB plays an important role in linking H. pylori-mediated inflammation to cancer. However, the underlying mechanisms are poorly understood. In this study, we find that H. pylori infection induces miR-223-3p expression in H. pylori CagA-dependent manner. NF-κB stimulates miR-223-3p expression via directly binding to the promoter of miR-223-3p and is required for H...
January 9, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29316428/arid1a-has-context-dependent-oncogenic-and-tumor-suppressor-functions-in-liver-cancer
#20
Xuxu Sun, Sam C Wang, Yonglong Wei, Xin Luo, Yuemeng Jia, Lin Li, Purva Gopal, Min Zhu, Ibrahim Nassour, Jen-Chieh Chuang, Thomas Maples, Cemre Celen, Liem H Nguyen, Linwei Wu, Shunjun Fu, Weiping Li, Lijian Hui, Feng Tian, Yuan Ji, Shuyuan Zhang, Mahsa Sorouri, Tae Hyun Hwang, Lynda Letzig, Laura James, Zixi Wang, Adam C Yopp, Amit G Singal, Hao Zhu
No abstract text is available yet for this article.
January 8, 2018: Cancer Cell
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