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https://www.readbyqxmd.com/read/29145046/genetic-and-clinical-characteristics-of-phyllodes-tumors-of-the-breast
#1
Ji-Yeon Kim, Jong Han Yu, Seok Jin Nam, Seok Won Kim, Se Kyung Lee, Woong-Yang Park, Dong-Young Noh, Do-Hyun Nam, Yeon Hee Park, Wonshik Han, Jeong Eon Lee
PURPOSE: Phyllodes tumors (PTs) of the breast are rare, accounting for less than 1% of all breast tumors. Among PTs, malignant PTs (MPTs) have malignant characteristics and distant metastases occur in about 20% to 30% of MPTs. However, there is no effective treatment for MPTs with distant metastasis, resulting in an abject prognosis. We performed targeted deep sequencing on PTs to identify the associations between genetic alterations and clinical prognosis. METHODS: We performed targeted deep sequencing to evaluate the genetic characteristics of PTs and analyzed the relationships between clinical and genetic characteristics...
November 12, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29132830/characterizing-recurrent-and-lethal-small-renal-masses-in-clear-cell-renal-cell-carcinoma-using-recurrent-somatic-mutations
#2
Brandon J Manley, Ed Reznik, Mazyar Ghanaat, Mahyar Kashan, Maria F Becerra, Jozefina Casuscelli, Daniel Tennenbaum, Almedina Redzematovic, Maria I Carlo, Yusuke Sato, Maria Arcila, Martin H Voss, Darren R Feldman, Robert J Motzer, Paul Russo, Jonathan Coleman, James J Hsieh, Ari A Hakimi
INTRODUCTION: Small renal masses (SRMs) with evidence of clear cell renal cell carcinoma (ccRCC) are understudied. Current algorithms for the management of SRMs include surgical resection, ablation, and active surveillance. We sought to identify genomic biomarkers that could potentially refine the management of ccRCC in SRMs, especially in patients being evaluated for active surveillance. METHODS: We identified patients who had SRMs (4cm or less) at time of surgery, had sequencing performed on their primary tumor and had a diagnosis of ccRCC...
November 10, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/29066084/comparative-genomic-profiling-of-matched-primary-and-metastatic-tumors-in-renal-cell-carcinoma
#3
Maria F Becerra, Ed Reznik, Almedina Redzematovic, Daniel M Tennenbaum, Mahyar Kashan, Mazyar Ghanaat, Jozefina Casuscelli, Brandon Manley, Philip Jonsson, Renzo G DiNatale, Kyle A Blum, Jeremy C Durack, Stephen B Solomon, Maria E Arcila, Caitlin Bourque, Nick Socci, Maria I Carlo, Chung-Han Lee, Martin H Voss, Darren R Feldman, Robert J Motzer, Jonathan A Coleman, Paul Russo, Emily H Cheng, A Ari Hakimi, James J Hsieh
BACKGROUND: Next-generation sequencing (NGS) studies of matched pairs of primary and metastatic tumors in renal cell carcinoma (RCC) have been limited to small cohorts. OBJECTIVE: To evaluate the discordance in somatic mutations between matched primary and metastatic RCC tumors. DESIGN, SETTING, AND PARTICIPANTS: Primary tumor (P), metastasis (M), and germline DNA from 60 patients with RCC was subjected to NGS with a targeted exon capture-based assay of 341 cancer-associated genes...
October 20, 2017: European Urology Focus
https://www.readbyqxmd.com/read/29018079/setd2-alterations-impair-dna-damage-recognition-and-lead-to-resistance-to-chemotherapy-in-leukemia
#4
Brenton G Mar, S Haihua Chu, Josephine D Kahn, Andrei V Krivstov, Richard Koche, Cecilia A Castellano, Jacob L Kotlier, Rebecca L Zon, Marie E McConkey, Jonathan Chabon, Ryan Chappell, Peter V Grauman, James J Hsieh, Scott A Armstrong, Benjamin L Ebert
Mutations in SETD2, encoding the histone 3 lysine 36 trimethyltransferase, are enriched in relapsed acute lymphoblastic leukemia and MLL rearranged acute leukemia. We investigated the impact of SETD2 mutations on chemotherapy sensitivity in isogenic leukemia cell lines and in murine leukemia generated from a conditional knockout of Setd2SETD2 mutations led to resistance to DNA-damaging agents, cytarabine, 6-thioguanine, doxorubicin, and etoposide, but not to a non-DNA damaging agent, L-asparaginase. H3K36me3 localizes components of the DNA damage response pathway and SETD2 mutation impaired the DNA damage response (DDR), blunting apoptosis induced by cytotoxic chemotherapy...
October 10, 2017: Blood
https://www.readbyqxmd.com/read/28977912/functional-role-of-setd2-bap1-parp-3-and-pbrm1-candidate-genes-on-the-regulation-of-htert-gene-expression
#5
Hannah Linne, Hemad Yasaei, Alison Marriott, Amanda Harvey, Kefah Mokbel, Robert Newbold, Terry Roberts
Narrowing the search for the critical hTERT repressor sequence(s) has identified three regions on chromosome 3p (3p12-p21.1, 3p21.2 and 3p21.3-p22). However, the precise location and identity of the sequence(s) responsible for hTERT transcriptional repression remains elusive. In order to identify critical hTERT repressor sequences located within human chromosome 3p12-p22, we investigated hTERT transcriptional activity within 21NT microcell hybrid clones containing chromosome 3 fragments. Mapping of chromosome 3 structure in a single hTERT-repressed 21NT-#3fragment hybrid clone, revealed a 490kb region of deletion localised to 3p21...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28968686/the-genomic-and-epigenomic-landscape-in-thymic-carcinoma
#6
Motonobu Saito, Yutaka Fujiwara, Tetsuhiko Asao, Takayuki Honda, Yoko Shimada, Yae Kanai, Koji Tsuta, Koji Kono, Shunichi Watanabe, Yuichiro Ohe, Takashi Kohno
Thymic carcinoma (TC) is a rare cancer whose genomic features have been examined in only a limited number of patients of European descent. Here, we characterized both genomic and epigenomic aberrations by whole exome sequencing, RNA sequencing, methylation array and copy number analyses in TCs from Asian patients and compared them with those in TCs from USA/European patients. Samples analyzed were 10 pairs of snap-frozen surgical specimens of cancerous and non-cancerous thymic tissue. All 10 cases were Japanese patients treated at the National Cancer Center Hospital, Japan, between 1994 and 2010...
October 26, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28925385/fine-tuning-type-i-ifn-signaling-a-new-chapter-in-the-ifn-saga
#7
Hideyuki Yanai, Tadatsugu Taniguchi
Type I interferon (IFN) signaling is critical for intracellular antimicrobial programmes, affecting both innate and adaptive immune responses. The paper recently published in Cell demonstrates a new regulatory mechanism of the type I IFN signaling pathway by histone-lysine N-methyltransferase SETD2.
September 19, 2017: Cell Research
https://www.readbyqxmd.com/read/28910456/identification-of-alk-rearrangements-in-malignant-peritoneal-mesothelioma
#8
Yin P Hung, Fei Dong, Jaclyn C Watkins, Valentina Nardi, Raphael Bueno, Paola Dal Cin, John J Godleski, Christopher P Crum, Lucian R Chirieac
Importance: Malignant peritoneal mesothelioma is a rare, aggressive tumor arising from the peritoneal lining, induced by asbestos, therapeutic radiation, or germline mutations. Nevertheless, the molecular features remain largely unknown. Objective: To investigate anaplastic lymphoma kinase (ALK) rearrangements in a large series of peritoneal mesothelioma and characterize the mutational landscape of these tumors. Design, Setting, and Participants: We studied 88 consecutive patients (39 men, 49 women; median age 61, range 17-84 years) with peritoneal mesotheliomas diagnosed at a single institution between 2005 and 2015...
September 14, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28903048/set2-methyltransferase-facilitates-dna-replication-and-promotes-genotoxic-stress-responses-through-mbf-dependent-transcription
#9
Chen-Chun Pai, Anastasiya Kishkevich, Rachel S Deegan, Andrea Keszthelyi, Lisa Folkes, Stephen E Kearsey, Nagore De León, Ignacio Soriano, Robertus Antonius Maria de Bruin, Antony M Carr, Timothy C Humphrey
Chromatin modification through histone H3 lysine 36 methylation by the SETD2 tumor suppressor plays a key role in maintaining genome stability. Here, we describe a role for Set2-dependent H3K36 methylation in facilitating DNA replication and the transcriptional responses to both replication stress and DNA damage through promoting MluI cell-cycle box (MCB) binding factor (MBF)-complex-dependent transcription in fission yeast. Set2 loss leads to reduced MBF-dependent ribonucleotide reductase (RNR) expression, reduced deoxyribonucleoside triphosphate (dNTP) synthesis, altered replication origin firing, and a checkpoint-dependent S-phase delay...
September 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/28852847/distinct-molecular-profile-of-diffuse-cerebellar-gliomas
#10
Masashi Nomura, Akitake Mukasa, Genta Nagae, Shogo Yamamoto, Kenji Tatsuno, Hiroki Ueda, Shiro Fukuda, Takayoshi Umeda, Tomonari Suzuki, Ryohei Otani, Keiichi Kobayashi, Takashi Maruyama, Shota Tanaka, Shunsaku Takayanagi, Takahide Nejo, Satoshi Takahashi, Koichi Ichimura, Taishi Nakamura, Yoshihiro Muragaki, Yoshitaka Narita, Motoo Nagane, Keisuke Ueki, Ryo Nishikawa, Junji Shibahara, Hiroyuki Aburatani, Nobuhito Saito
Recent studies have demonstrated that tumor-driving alterations are often different among gliomas that originated from different brain regions and have underscored the importance of analyzing molecular characteristics of gliomas stratified by brain region. Therefore, to elucidate molecular characteristics of diffuse cerebellar gliomas (DCGs), 27 adult, mostly glioblastoma cases were analyzed. Comprehensive analysis using whole-exome sequencing, RNA sequencing, and Infinium methylation array (n = 17) demonstrated their distinct molecular profile compared to gliomas in other brain regions...
December 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28825595/histone-methyltransferase-setd2-modulates-alternative-splicing-to-inhibit-intestinal-tumorigenesis
#11
Huairui Yuan, Ni Li, Da Fu, Jiale Ren, Jingyi Hui, Junjie Peng, Yongfeng Liu, Tong Qiu, Min Jiang, Qiang Pan, Ying Han, Xiaoming Wang, Qintong Li, Jun Qin
The histone H3K36 methyltransferase SETD2 is frequently mutated or deleted in a variety of human tumors. Nevertheless, the role of SETD2 loss in oncogenesis remains largely undefined. Here, we found that SETD2 counteracts Wnt signaling and its inactivation promotes intestinal tumorigenesis in mouse models of colorectal cancer (CRC). SETD2 was not required for intestinal homeostasis under steady state; however, upon irradiation, genetic inactivation of Setd2 in mouse intestinal epithelium facilitated the self-renewal of intestinal stem/progenitor cells as well as tissue regeneration...
September 1, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28812986/epigenome-aberrations-emerging-driving-factors-of-the-clear-cell-renal-cell-carcinoma
#12
REVIEW
Ali Mehdi, Yasser Riazalhosseini
Clear cell renal cell carcinoma (ccRCC), the most common form of Kidney cancer, is characterized by frequent mutations of the von Hippel-Lindau (VHL) tumor suppressor gene in ~85% of sporadic cases. Loss of pVHL function affects multiple cellular processes, among which the activation of hypoxia inducible factor (HIF) pathway is the best-known function. Constitutive activation of HIF signaling in turn activates hundreds of genes involved in numerous oncogenic pathways, which contribute to the development or progression of ccRCC...
August 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28780132/commentary-on-comprehensive-molecular-characterization-of-papillary-renal-cell-carcinoma-cancer-genome-atlas-research-network-n-engl-j-med-2016-jan-14-374-2-135-45
#13
Byron H Lee
BACKGROUND: Papillary renal-cell carcinoma, which accounts for 15%-20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation, and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. METHODS: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis...
August 2, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28768201/human-tfiih-kinase-cdk7-regulates-transcription-associated-chromatin-modifications
#14
Christopher C Ebmeier, Benjamin Erickson, Benjamin L Allen, Mary A Allen, Hyunmin Kim, Nova Fong, Jeremy R Jacobsen, Kaiwei Liang, Ali Shilatifard, Robin D Dowell, William M Old, David L Bentley, Dylan J Taatjes
CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3' ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5' ends and H3K36me3 was displaced toward gene 3' ends in CDK7as cells...
August 1, 2017: Cell Reports
https://www.readbyqxmd.com/read/28754676/nsd1-inactivation-and-setd2-mutation-drive-a-convergence-toward-loss-of-function-of-h3k36-writers-in-clear-cell-renal-cell-carcinomas
#15
Xiaoping Su, Jianping Zhang, Roger Mouawad, Eva Compérat, Morgan Rouprêt, Frederick Allanic, Jérôme Parra, Marc-Olivier Bitker, Erika J Thompson, Banumathy Gowrishankar, Jane Houldsworth, John N Weinstein, Jorg Tost, Bradley M Broom, David Khayat, Jean-Philippe Spano, Nizar M Tannir, Gabriel G Malouf
Extensive dysregulation of chromatin-modifying genes in clear cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the cross-talk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear cell CpG island methylator phenotype (C-CIMP) subgroup associated with promoter methylation of VEGF genes (FLT4, FLT1, and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development...
September 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28753426/methyltransferase-setd2-mediated-methylation-of-stat1-is-critical-for-interferon-antiviral-activity
#16
Kun Chen, Juan Liu, Shuxun Liu, Meng Xia, Xiaomin Zhang, Dan Han, Yingming Jiang, Chunmei Wang, Xuetao Cao
Interferon-α (IFNα) signaling is essential for antiviral response via induction of IFN-stimulated genes (ISGs). Through a non-biased high-throughput RNAi screening of 711 known epigenetic modifiers in cellular models of IFNα-mediated inhibition of HBV replication, we identified methyltransferase SETD2 as a critical amplifier of IFNα-mediated antiviral immunity. Conditional knockout mice with hepatocyte-specific deletion of Setd2 exhibit enhanced HBV infection. Mechanistically, SETD2 directly mediates STAT1 methylation on lysine 525 via its methyltransferase activity, which reinforces IFN-activated STAT1 phosphorylation and antiviral cellular response...
July 27, 2017: Cell
https://www.readbyqxmd.com/read/28731045/renal-cell-tumors-with-clear-cell-histology-and-intact-vhl-and-chromosome-3p-a-histological-review-of-tumors-from-the-cancer-genome-atlas-database
#17
Laura Favazza, Dhananjay A Chitale, Ravi Barod, Craig G Rogers, Shanker Kalyana-Sundaram, Nallasivam Palanisamy, Nilesh S Gupta, Sean R Williamson
Clear cell renal cell carcinoma is by far the most common form of kidney cancer; however, a number of histologically similar tumors are now recognized and considered distinct entities. The Cancer Genome Atlas published data set was queried (http://cbioportal.org) for clear cell renal cell carcinoma tumors lacking VHL gene mutation and chromosome 3p loss, for which whole-slide images were reviewed. Of the 418 tumors in the published Cancer Genome Atlas clear cell renal cell carcinoma database, 387 had VHL mutation, copy number loss for chromosome 3p, or both (93%)...
November 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28723630/functional-role-of-setd2-bap1-parp-3-and-pbrm1-candidate-genes-on-the-regulation-of-htert-gene-expression
#18
Hannah Linne, Hemad Yasaei, Alison Marriott, Amanda Harvey, Kefah Mokbel, Robert Newbold, Terry Roberts
Narrowing the search for the critical hTERT repressor sequence(s) has identified three regions on chromosome 3p (3p12-p21.1, 3p21.2 and 3p21.3-p22). However, the precise location and identity of the sequence(s) responsible for hTERT transcriptional repression remains elusive. In order to identify critical hTERT repressor sequences located within human chromosome 3p12-p22, we investigated hTERT transcriptional activity within 21NT microcell hybrid clones containing chromosome 3 fragments. Mapping of chromosome 3 structure in a single hTERT-repressed 21NT-#3fragment hybrid clone, revealed a 490kb region of deletion localised to 3p21...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28673974/mrg15-mediated-tethering-of-palb2-to-unperturbed-chromatin-protects-active-genes-from-genotoxic-stress
#19
Jean-Yves Bleuyard, Marjorie Fournier, Ryuichiro Nakato, Anthony M Couturier, Yuki Katou, Christine Ralf, Svenja S Hester, Daniel Dominguez, Daniela Rhodes, Timothy C Humphrey, Katsuhiko Shirahige, Fumiko Esashi
The partner and localiser of BRCA2 (PALB2) plays important roles in the maintenance of genome integrity and protection against cancer. Although PALB2 is commonly described as a repair factor recruited to sites of DNA breaks, recent studies provide evidence that PALB2 also associates with unperturbed chromatin. Here, we investigated the previously poorly described role of chromatin-associated PALB2 in undamaged cells. We found that PALB2 associates with active genes through its major binding partner, MRG15, which recognizes histone H3 trimethylated at lysine 36 (H3K36me3) by the SETD2 methyltransferase...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28663576/setd2-and-histone-h3-lysine-36-methylation-deficiency-in-advanced-systemic-mastocytosis
#20
G Martinelli, M Mancini, C De Benedittis, M Rondoni, C Papayannidis, M Manfrini, M Meggendorfer, R Calogero, V Guadagnuolo, M C Fontana, L Bavaro, A Padella, E Zago, L Pagano, R Zanotti, L Scaffidi, G Specchia, F Albano, S Merante, C Elena, P Savini, D Gangemi, P Tosi, F Ciceri, G Poletti, L Riccioni, F Morigi, M Delledonne, T Haferlach, M Cavo, P Valent, S Soverini
The molecular basis of advanced systemic mastocytosis (SM) is not fully understood and despite novel therapies the prognosis remains dismal. Exome sequencing of an index-patient with mast cell leukemia (MCL) uncovered biallelic loss-of-function mutations in the SETD2 histone methyltransferase gene. Copy-neutral loss-of-heterozygosity at 3p21.3 (where SETD2 maps) was subsequently found in SM patients and prompted us to undertake an in-depth analysis of SETD2 copy number, mutation status, transcript expression and methylation levels, as well as functional studies in the HMC-1 cell line and in a validation cohort of 57 additional cases with SM, including MCL, aggressive SM and indolent SM...
June 16, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
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