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https://www.readbyqxmd.com/read/29775073/diffuse-gliomas-for-nonneuropathologists-the-new-integrated-molecular-diagnostics
#1
Sunhee C Lee
Diffuse gliomas comprise the bulk of "brain cancer" in adults. The recent update to the 4th edition of the World Health Organization's classification of tumors of the central nervous system reflects an unprecedented change in the landscape of the diagnosis and management of diffuse gliomas that will affect all those involved in the management and care of patients. Of the recently discovered gene alterations, mutations in the Krebs cycle enzymes isocitrate dehydrogenases (IDHs) 1 and 2 have fundamentally changed the way the gliomas are understood and classified...
May 18, 2018: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29755111/genomic-landscape-and-prognostic-analysis-of-mantle-cell-lymphoma
#2
Ping Yang, Weilong Zhang, Jing Wang, Yuanyuan Liu, Ran An, Hongmei Jing
To gain insight into the molecular pathogenesis of patients with mantle cell lymphoma (MCL), next-generation whole-exome sequencing of 16 MCL patients was performed. We identified recurrent mutations in genes that are well known to be functionally relevant in MCL, including ATM (37.5%), TP53 (31.3%), WHSC1 (31.3%), CCND1 (18.8%), NOTCH2 (6.3%), and CDKN2A (6.3%). We also identified somatic mutations in genes for which a functional role in MCL has not been previously suspected. These genes included CCDC15, APC, CDH1, S1PR1, ATRX, BRCA2, CASP8, and NOTCH3...
May 14, 2018: Cancer Gene Therapy
https://www.readbyqxmd.com/read/29748005/genomic-alterations-of-plasma-cell-free-dnas-in-small-cell-lung-cancer-and-their-clinical-relevance
#3
Meijun Du, Jonathan Thompson, Hannah Fisher, Peng Zhang, Chiang-Ching Huang, Liang Wang
OBJECTIVES: To identify genomic variations in cell-free DNA (cfDNA) and evaluate their clinical utility in small cell lung cancer (SCLC). MATERIALS AND METHODS: We performed whole genome sequencing using plasma cfDNAs derived from 24 SCLC patients for copy number variation (CNV) analysis, and targeted sequencing using 17 pairs of plasma cfDNA and their matched gDNA for mutation analysis. We defined somatic mutations by comparing cfDNA to its matched gDNA with 5% variant alleles as the cutoff for mutation calls...
June 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29730791/distinct-demographic-profile-and-molecular-markers-of-primary-cns-tumor-in-1873-adolescent-and-young-adult-patient-population
#4
Rohit Vadgaonkar, Sridhar Epari, Girish Chinnaswamy, Rahul Krishnatry, Raees Tonse, Tejpal Gupta, Rakesh Jalali
INTRODUCTION: We present detailed demographic profile, tumor types, and their molecular markers in adolescent and young adult (AYA) patients of age group between 15 and 39 years with primary central nervous system (PCNS) tumors, and compare with pediatric and adult patient populations. METHODOLOGY: Demographic- and disease-related information of 1873 PCNS tumor patients of age 15-39 years registered between 1 January 2011 and 31 December 2015 at our institution was analyzed with respect to their demographics and tumor subtypes...
May 5, 2018: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/29730439/a-metadynamic-approach-to-understand-the-recognition-mechanism-of-the-histone-h3-tail-with-the-atrx-add-domain
#5
Radha Charan Dash, Angela M Zaino, M Kyle Hadden
The binding affinity between the histone 3 (H3) tail and the ADD domain of ATRX (ATRXADD ) increases with the subsequent addition of methyl groups on lysine 9 on H3. To improve our understanding of how the difference in methylation state affects binding between H3 and the ATRXADD , we adopted a metadynamic approach to explore the recognition mechanism between the two proteins and identify the key intermolecular interactions that mediate this protein-peptide interaction (PPI). The non-methylated H3 peptide is recognized only by the PHD finger of ATRXADD while mono-, di-, and trimethylated H3 is recognized by both the PHD and GATA-like zinc finger of the domain...
May 3, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29728366/the-hush-complex-cooperates-with-trim28-to-repress-young-retrotransposons-and-new-genes
#6
Luisa Robbez-Masson, Christopher H C Tie, Lucia Conde, Hale Tunbak, Connor Husovsky, Iva A Tchasovnikarova, Richard T Timms, Javier Herrero, Paul J Lehner, Helen M Rowe
Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of a SVA retrotransposon reporter. By using naïve vs. primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development...
May 4, 2018: Genome Research
https://www.readbyqxmd.com/read/29727696/h3-k27-m-mutant-diffuse-midline-gliomas-in-different-anatomical-locations
#7
Leiming Wang, Zhuo Li, Ming Zhang, Yueshan Piao, Li Chen, Huiying Liang, Yukui Wei, Zeliang Hu, Lihong Zhao, Lianghong Teng, Dehong Lu
The histone H3 K27 M mutation has been frequently reported in the majority of diffuse midline gliomas. However, the relationship between the H3 K27 M mutation and clinical outcomes of gliomas from different anatomical locations is still not fully understood. A total of 120 patients with diffuse midline gliomas were selected for this retrospective observational study. The status of H3 K27 M, ATRX, TP53 and IDH was evaluated using immunohistochemistry and Sanger sequencing. Of the 120 cases aged from 4 to 76years (median=27years), 61 (50...
May 1, 2018: Human Pathology
https://www.readbyqxmd.com/read/29725455/alternative-lengthening-of-telomeres-phenotype-and-loss-of-atrx-expression-in-sarcomas
#8
REVIEW
Xiaolei Ren, Chao Tu, Zhenchu Tang, Ruofei Ma, Zhihong Li
Sarcoma is a rare and heterogeneous type of cancer with an early mean onset age and a poor prognosis. However, its genetic basis remains unclear. A series of recent genomic studies in sarcomas have identified the occurrence of mutations in the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene. The ATRX protein belongs to the SWI/SNF family of chromatin remodeling proteins, which are frequently associated with α-thalassemia syndrome. Cancer cells depend on telomerase or the alternative lengthening of telomeres (ALT) pathway to overcome replicative programmed mortality...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29721688/radiogenomics-correlation-between-mr-imaging-features-and-major-genetic-profiles-in-glioblastoma
#9
Eun Kyoung Hong, Seung Hong Choi, Dong Jae Shin, Sang Won Jo, Roh-Eul Yoo, Koung Mi Kang, Tae Jin Yun, Ji-Hoon Kim, Chul-Ho Sohn, Sung-Hye Park, Jae-Kyung Won, Tae Min Kim, Chul-Kee Park, Il Han Kim, Soon Tae Lee
OBJECTIVES: To assess the association between MR imaging features and major genomic profiles in glioblastoma. METHODS: Qualitative and quantitative imaging features such as volumetrics and histogram analysis from normalised CBV (nCBV) and ADC (nADC) were evaluated based on both T2WI and CET1WI. The imaging parameters of different genetic profile groups were compared and regression analyses were used for identifying imaging-molecular associations. Progression-free survival (PFS) was analysed by a Kaplan-Meier test and Cox proportional hazards model...
May 2, 2018: European Radiology
https://www.readbyqxmd.com/read/29719265/mutant-idh1-promotes-glioma-formation-in-vivo
#10
Beatrice Philip, Diana X Yu, Mark R Silvis, Clifford H Shin, James P Robinson, Gemma L Robinson, Adam E Welker, Stephanie N Angel, Sheryl R Tripp, Joshua A Sonnen, Matthew W VanBrocklin, Richard J Gibbons, Ryan E Looper, Howard Colman, Sheri L Holmen
Isocitrate dehydrogenase 1 (IDH1) is the most commonly mutated gene in grade II-III glioma and secondary glioblastoma (GBM). A causal role for IDH1R132H in gliomagenesis has been proposed, but functional validation in vivo has not been demonstrated. In this study, we assessed the role of IDH1R132H in glioma development in the context of clinically relevant cooperating genetic alterations in vitro and in vivo. Immortal astrocytes expressing IDH1R132H exhibited elevated (R)-2-hydroxyglutarate levels, reduced NADPH, increased proliferation, and anchorage-independent growth...
May 1, 2018: Cell Reports
https://www.readbyqxmd.com/read/29706636/does-atrx-germline-variation-predispose-to-osteosarcoma-three-additional-cases-of-osteosarcoma-in-two-atr-x-syndrome-patients
#11
Julien Masliah-Planchon, Dominique Lévy, Delphine Héron, Fabienne Giuliano, Catherine Badens, Paul Fréneaux, Louise Galmiche, Jean-Marc Guinebretierre, Cécile Cellier, Joshua J Waterfall, Khadija Aït-Raïs, Gaëlle Pierron, Christophe Glorion, Isabelle Desguerre, Christine Soler, Anne Deville, Olivier Delattre, Jean Michon, Franck Bourdeaut
Osteosarcoma is the most common malignant bone tumor in adolescents and young adults. Most osteosarcomas are sporadic but the risk of osteosarcoma is also increased by germline variants in TP53, RB1 and RECQL4 genes. ATRX germline variations are responsible for the rare genetic disorder X-linked alpha-thalassemia mental retardation (ATR-X) syndrome characterized by severe developmental delay and alpha-thalassemia but no obvious increased risk of cancer. Here we report two children with ATR-X syndrome who developed osteosarcoma...
April 30, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29693772/expression-of-granulosa-cell-micrornas-aven-and-atrx-are-associated-with-human-blastocyst-development
#12
A M O'Doherty, Y M O'Brien, J A Browne, M Wingfield, L C O'Shea
A greater understanding of the key molecules associated with embryo development during human assisted reproduction is imperative for the development of advanced diagnostics. Previous studies have shown that follicular microRNAs (miRNAs) are reliable markers of polycystic ovarian syndrome (PCOS). Leveraging the utility of miRNAs in PCOS, the aim of this study was to identify miRNAs in human granulosa cells that may be indicative of blastocyst development. Granulosa cells and oocytes were collected from the first follicle aspirated from patients undergoing oocyte retrieval for in-vitro fertilisation (IVF) or intra-cytoplasmic sperm injection (ICSI)...
April 25, 2018: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29670118/global-h3-3-dynamic-deposition-defines-its-bimodal-role-in-cell-fate-transition
#13
Hai-Tong Fang, Chadi A El Farran, Qiao Rui Xing, Li-Feng Zhang, Hu Li, Bing Lim, Yuin-Han Loh
H3.3 is a histone variant, which is deposited on genebodies and regulatory elements, by Hira, marking active transcription. Moreover, H3.3 is deposited on heterochromatin by Atrx/Daxx complex. The exact role of H3.3 in cell fate transition remains elusive. Here, we investigate the dynamic changes in the deposition of the histone variant H3.3 during cellular reprogramming. H3.3 maintains the identities of the parental cells during reprogramming as its removal at early time-point enhances the efficiency of the process...
April 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29669917/ribosomal-dna-copy-loss-and-repeat-instability-in-atrx-mutated-cancers
#14
Maheshi Udugama, Elaine Sanij, Hsiao P J Voon, Jinbae Son, Linda Hii, Jeremy D Henson, F Lyn Chan, Fiona T M Chang, Yumei Liu, Richard B Pearson, Paul Kalitsis, Jeffrey R Mann, Philippe Collas, Ross D Hannan, Lee H Wong
ATRX (alpha thalassemia/mental retardation X-linked) complexes with DAXX to deposit histone variant H3.3 into repetitive heterochromatin. Recent genome sequencing studies in cancers have revealed mutations in ATRX and their association with ALT (alternative lengthening of telomeres) activation. Here we report depletion of ATRX in mouse ES cells leads to selective loss in ribosomal RNA gene (rDNA) copy number. Supporting this, ATRX-mutated human ALT-positive tumors also show a substantially lower rDNA copy than ALT-negative tumors...
May 1, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29667086/contrast-enhancement-predicting-survival-in-integrated-molecular-subtypes-of-diffuse-glioma-an-observational-cohort-study
#15
Johann-Martin Hempel, Cornelia Brendle, Benjamin Bender, Georg Bier, Marco Skardelly, Irina Gepfner-Tuma, Franziska Eckert, Ulrike Ernemann, Jens Schittenhelm
INTRODUCTION: To assess the predictive value of magnetic resonance imaging (MRI) gadolinium enhancement as a prognostic factor in the 2016 World Health Organization Classification of Tumors of the Central Nervous System integrated glioma groups. METHODS: Four-hundred fifty patients with histopathologically confirmed glioma were retrospectively assessed between 07/1997 and 06/2014 using gadolinium enhancement, survival, and relevant prognostic molecular data [isocitrate dehydrogenase (IDH); alpha-thalassemia/mental retardation syndrome X-linked (ATRX); chromosome 1p/19q loss of heterozygosity; and O6-methylguanine DNA methyltransferase (MGMT)]...
April 17, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29660202/molecular-biomarkers-for-uterine-leiomyosarcoma-and-endometrial-stromal-sarcoma
#16
REVIEW
Hideaki Tsuyoshi, Yoshio Yoshida
Uterine leiomyosarcoma (u{\hyphen}LMS) and endometrial stromal sarcoma (ESS) are among the most frequent soft tissue sarcomas, which, in adults, lead to fatal lung metastases and have an extremely poor prognosis. Due to their rarity and heterogeneity, there are no suitable biomarkers for diagnosis and prognosis, though some biomarker candidates have appeared. Recently, The Cancer Genome Atlas (TCGA) projects dealing with u{\hyphen}LMS confirmed mutations and deletions in RB1, TP53, and PTEN. In addition, whole{\hyphen}exome sequencing of u{\hyphen}LMS has confirmed and demonstrated frequent alterations in TP53, RB1, α-thalassemia/mental retardation syndrome X-linked (ATRX), and mediator complex subunit 12 (MED12)...
April 16, 2018: Cancer Science
https://www.readbyqxmd.com/read/29619482/a-comprehensive-review-of-the-prevalence-of-beta-globin-gene-variations-and-the-co-inheritance-of-related-gene-variants-in-saudi-arabians-with-beta-thalassemia
#17
Mousa A Alaithan, Sayed AbdulAzeez, J Francis Borgio
Beta-thalassemia is a genetic disorder that is caused by variations in the beta-hemoglobin (HBB) gene. Saudi Arabia is among the countries most affected bybeta-thalassemia, and this is particularly problematic in the Eastern regions. This review article is an attempt to compile all the reported mutations to facilitate further national-level studies to prepare a Saudi repository of HBB gene variations. In Saudi Arabians, IVSI-5 (G greater than C) and Cd 39 (C greater than T) are the most prevalent HBB gene variations out of 42 variations...
April 2018: Saudi Medical Journal
https://www.readbyqxmd.com/read/29617666/systematic-analysis-of-splice-site-creating-mutations-in-cancer
#18
Reyka G Jayasinghe, Song Cao, Qingsong Gao, Michael C Wendl, Nam Sy Vo, Sheila M Reynolds, Yanyan Zhao, Héctor Climente-González, Shengjie Chai, Fang Wang, Rajees Varghese, Mo Huang, Wen-Wei Liang, Matthew A Wyczalkowski, Sohini Sengupta, Zhi Li, Samuel H Payne, David Fenyö, Jeffrey H Miner, Matthew J Walter, Benjamin Vincent, Eduardo Eyras, Ken Chen, Ilya Shmulevich, Feng Chen, Li Ding
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29615461/molecular-diagnosis-of-diffuse-gliomas-through-sequencing-of-cell-free-circulating-tumour-dna-from-cerebrospinal-fluid
#19
Francisco Martínez-Ricarte, Regina Mayor, Elena Martínez-Sáez, Carlota Rubio-Pérez, Estela Pineda, Esteban Cordero, Marta Cicuéndez, Maria A Poca, Nuria Lopez-Bigas, Santiago Ramón Y Cajal, María Vieito, Joan Carles, Josep Tabernero, Ana Vivancos, Soledad Gallego, Francesc Graus, Juan Sahuquillo, Joan Seoane
PURPOSE: Diffuse gliomas are the most common primary tumour of the brain and include different subtypes with diverse prognosis. The genomic characterization of diffuse gliomas facilitates their molecular diagnosis. The anatomical localization of diffuse gliomas complicates access to tumour specimens for diagnosis, in some cases incurring high-risk surgical procedures and stereotactic biopsies. Recently, cell-free circulating tumour DNA (ctDNA) has been identified in the cerebrospinal fluid (CSF) of patients with brain malignancies...
April 3, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29615337/immunohistochemical-and-molecular-genetic-study-on-epithelioid-glioblastoma-series-of-seven-cases-with-review-of-literature
#20
Gaurav Khanna, Pankaj Pathak, Vaishali Suri, Mehar Chand Sharma, Sujata Chaturvedi, Arvind Ahuja, M Bhardwaj, Ajay Garg, Chitra Sarkar, Rajeev Sharma
Epithelioid glioblastoma (e-gbm) is a recently described variant of glioblastoma (GBM) which is associated with short survival and now added as a provisional entity to WHO 2016 classification of CNStumors. About half of these tumors show characteristic BRAF-V600E mutation. However, unlike conventional GBMs, e-gbm lack specific diagnostic and prognostic markers. Hence, we aimed to molecularly characterize these tumors. An extensive review of literature was performed.In a multi-institutional effort, all the cases of glioblastoma of year 2017 were reviewed...
March 22, 2018: Pathology, Research and Practice
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