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https://www.readbyqxmd.com/read/29762619/isolation-and-genome-sequencing-of-individual-circulating-tumor-cells-using-hydrogel-encapsulation-and-laser-capture-microdissection
#1
Emily S Park, Justin P Yan, Richard A Ang, Jeong Hyun Lee, Xiaoyan Deng, Simon P Duffy, Kevin Beja, Matti Annala, Peter C Black, Kim N Chi, Alexander W Wyatt, Hongshen Ma
Circulating tumor cells (CTCs) are malignant cells released into the bloodstream with the potential to form metastases in secondary sites. These cells, acquired non-invasively, represent a sample of highly relevant tumor tissue that is an alternative to difficult and low-yield tumor biopsies. In recent years, there has been growing interest in genomic profiling of CTCs to enable longitudinal monitoring of the tumor's adaptive response to therapy. However, due to their extreme rarity, genotyping CTCs has proved challenging...
May 15, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29755131/kmt2c-mediates-the-estrogen-dependence-of-breast-cancer-through-regulation-of-er%C3%AE-enhancer-function
#2
Kinisha Gala, Qing Li, Amit Sinha, Pedram Razavi, Madeline Dorso, Francisco Sanchez-Vega, Young Rock Chung, Ronald Hendrickson, James Hsieh, Michael Berger, Nikolaus Schultz, Alessandro Pastore, Omar Abdel-Wahab, Sarat Chandarlapaty
Estrogen receptor alpha (ERα) is a ligand-activated nuclear receptor that directs proliferation and differentiation in selected cancer cell types including mammary-derived carcinomas. These master-regulatory functions of ERα require trans-acting elements such as the pioneer factor FOXA1 to establish a genomic landscape conducive to ERα control. Here, we identify the H3K4 methyltransferase KMT2C as necessary for hormone-driven ERα activity and breast cancer proliferation. KMT2C knockdown suppresses estrogen-dependent gene expression and causes H3K4me1 and H3K27ac loss selectively at ERα enhancers...
May 14, 2018: Oncogene
https://www.readbyqxmd.com/read/29736783/spindle-epithelial-tumor-with-thymus-like-differentiation-settle-a-next-generation-sequencing-study
#3
Todd M Stevens, Diana Morlote, Jeff Swensen, Michelle Ellis, Shuko Harada, Sharon Spencer, Carlos N Prieto-Granada, Andrew L Folpe, Zoran Gatalica
Spindle epithelial tumor with thymus-like differentiation (SETTLE) is a malignant biphasic neoplasm of the thyroid or neck with propensity for late metastasis. Unlike synovial sarcoma, its main morphologic mimic, SETTLE lacks synovial sarcoma-associated translocations. A single case of SETTLE has shown a KRAS mutation but to date no comprehensive next generation sequencing studies of this rare neoplasm have been undertaken. Herein, we subjected 5 well defined cases of SETTLE to direct sequence analysis of 592 genes and fusion gene analysis of 52 genes frequently rearranged in human cancers...
May 7, 2018: Head and Neck Pathology
https://www.readbyqxmd.com/read/29734047/efficacy-and-safety-of-single-agent-pan-human-epidermal-growth-factor-receptor-her-inhibitor-dacomitinib-in-locally-advanced-unresectable-or-metastatic-skin-squamous-cell-cancer
#4
S Cavalieri, F Perrone, R Miceli, P A Ascierto, L D Locati, C Bergamini, R Granata, S Alfieri, C Resteghini, D Galbiati, A Busico, N Paielli, R Patuzzo, A Maurichi, G Gallino, R Ruggeri, L Mariani, M Palla, L Licitra, P Bossi
BACKGROUND: In recurrent or metastatic (R/M) skin squamous cell cancer (sSCC) not amenable to radiotherapy (RT) or surgery, chemotherapy (CT) has a palliative intent and limited clinical responses. The role of oral pan-HER inhibitor dacomitinib in this setting was investigated within a clinical trial. METHODS: Patients with diagnosis of R/M sSCC were treated. Dacomitinib was started at a dose of 30 mg daily (QD) for 15 d, followed by 45 mg QD. Primary end-point was response rate (RR)...
May 4, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29629950/a-survey-of-somatic-mutations-in-41-genes-in-a-cohort-of-t-cell-lymphomas-identifies-frequent-mutations-in-genes-involved-in-epigenetic-modification
#5
Sebastian Fernandez-Pol, Lisa Ma, Rohan P Joshi, Daniel A Arber
Here, we utilize a high throughput sequencing panel that covers several genes known to be recurrently mutated in certain T-cell lymphoma subtypes as well as genes frequently mutated in other hematolymphoid malignancies, including myeloid neoplasms. This panel was applied to formalin-fixed, paraffin-embedded tissue from 84 biopsies from 78 patients selected for this study. The biopsies included ones a with a diagnosis of T-cell lymphoma (n=79), including peripheral T-cell lymphoma not otherwise specified (PTCL-NOS; n=26) and angioimmunoblastic T-cell lymphoma (AITL; n=13), as well as 5 cases of atypical T-cell proliferations...
April 7, 2018: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/29623014/genetic-alterations-and-pik3ca-gene-mutations-and-amplifications-analysis-in-cervical-cancer-by-racial-groups-in-the-united-states
#6
Odekunle Florence Femi
Introduction: A number of studies indicated racial differences in cervical cancer outcomes and several factors are associated with it such as stage, comorbidities, treatment pattern, and socioeconomic status. However, the associations of tumor genomic patterns such as phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) gene mutations and amplifications with cervical cancer racial disparities are largely unexplored. Objectives: Therefore, the present investigation aimed to identify genetic alterations (mutations and copy number variations) in cervical cancer and determine whether the PIK3CA gene mutations and amplifications in cervical cancer differ across racial/ethnic groups in the United States...
January 2018: International Journal of Health Sciences
https://www.readbyqxmd.com/read/29555671/a-screening-approach-to-identify-clinically-actionable-variants-causing-congenital-heart-disease-in-exome-data
#7
Justin O Szot, Hartmut Cuny, Gillian M Blue, David T Humphreys, Eddie Ip, Katrina Harrison, Gary F Sholler, Eleni Giannoulatou, Paul Leo, Emma L Duncan, Duncan B Sparrow, Joshua W K Ho, Robert M Graham, Nicholas Pachter, Gavin Chapman, David S Winlaw, Sally L Dunwoodie
BACKGROUND: Congenital heart disease (CHD)-structural abnormalities of the heart that arise during embryonic development-is the most common inborn malformation, affecting ≤1% of the population. However, currently, only a minority of cases can be explained by genetic abnormalities. The goal of this study was to identify disease-causal genetic variants in 30 families affected by CHD. METHODS: Whole-exome sequencing was performed with the DNA of multiple family members...
March 2018: Circulation. Genomic and precision medicine
https://www.readbyqxmd.com/read/29523860/allele-specific-expression-in-a-family-quartet-with-autism-reveals-mono-to-biallelic-switch-and-novel-transcriptional-processes-of-autism-susceptibility-genes
#8
Chun-Yen Lin, Kai-Wei Chang, Chia-Yi Lin, Jia-Ying Wu, Hilary Coon, Pei-Hsin Huang, Hong-Nerng Ho, Schahram Akbarian, Susan Shur-Fen Gau, Hsien-Sung Huang
Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder, and the exact causal mechanism is unknown. Dysregulated allele-specific expression (ASE) has been identified in persons with ASD; however, a comprehensive analysis of ASE has not been conducted in a family quartet with ASD. To fill this gap, we analyzed ASE using genomic DNA from parent and offspring and RNA from offspring's postmortem prefrontal cortex (PFC); one of the two offspring had been diagnosed with ASD. DNA- and RNA-sequencing revealed distinct ASE patterns from the PFC of both offspring...
March 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29483845/-mll2-kmt2d-and-mll3-kmt2c-expression-correlates-with-disease-progression-and-response-to-imatinib-mesylate-in-chronic-myeloid-leukemia
#9
Doralina do Amaral Rabello, Vivian D'Afonseca da Silva Ferreira, Maria Gabriela Berzoti-Coelho, Sandra Mara Burin, Cíntia Leticia Magro, Maira da Costa Cacemiro, Belinda Pinto Simões, Felipe Saldanha-Araujo, Fabíola Attié de Castro, Fabio Pittella-Silva
Background: Chronic myeloid leukemia (CML) is a clonal myeloproliferative neoplasm whose pathogenesis is linked to the Philadelphia chromosome presence that generates the BCR - ABL 1 fusion oncogene. Tyrosine kinase inhibitors (TKI) such as imatinib mesylate (IM) dramatically improved the treatment efficiency and survival of CML patients by targeting BCR-ABL tyrosine kinase. The disease shows three distinct clinical-laboratory stages: chronic phase, accelerated phase and blast crisis...
2018: Cancer Cell International
https://www.readbyqxmd.com/read/29367767/a-carcinogen-induced-mouse-model-recapitulates-the-molecular-alterations-of-human-muscle-invasive-bladder-cancer
#10
Damiano Fantini, Alexander P Glaser, Kalen J Rimar, Yiduo Wang, Matthew Schipma, Nobish Varghese, Alfred Rademaker, Amir Behdad, Aparna Yellapa, Yanni Yu, Christie Ching-Lin Sze, Lu Wang, Zibo Zhao, Susan E Crawford, Deqing Hu, Jonathan D Licht, Clayton K Collings, Elizabeth Bartom, Dan Theodorescu, Ali Shilatifard, Joshua J Meeks
The N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN) mouse model is an attractive model system of muscle-invasive bladder cancer (MIBC) as it recapitulates the histology of human tumors in a background with intact immune system. However, it was unknown whether this carcinogen-induced model also mimicked human MIBC at the molecular and mutational level. In our study, we analyzed gene expression and mutational landscape of the BBN model by next-generation sequencing followed by a bioinformatic comparison to human MIBC using data from The Cancer Genome Atlas and other repositories...
January 25, 2018: Oncogene
https://www.readbyqxmd.com/read/29341862/identification-of-three-genetic-variants-as-novel-susceptibility-loci-for-body-mass-index-in-a-japanese-population
#11
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Recent genome-wide association studies have identified various obesity or metabolic syndrome (MetS) susceptibility loci. However, most studies were conducted in a cross-sectional manner. To address this gap, we performed a longitudinal exome-wide association study to identify susceptibility loci for obesity and MetS in a Japanese population. We traced clinical data of 6,022 Japanese subjects who had annual health check-ups for several years (mean follow-up period, 5 yr) and genotyped ~244,000 genetic variants...
March 1, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29276005/histone-lysine-methylases-and-demethylases-in-the-landscape-of-human-developmental-disorders
#12
Víctor Faundes, William G Newman, Laura Bernardini, Natalie Canham, Jill Clayton-Smith, Bruno Dallapiccola, Sally J Davies, Michelle K Demos, Amy Goldman, Harinder Gill, Rachel Horton, Bronwyn Kerr, Dhavendra Kumar, Anna Lehman, Shane McKee, Jenny Morton, Michael J Parker, Julia Rankin, Lisa Robertson, I Karen Temple, Siddharth Banka
Histone lysine methyltransferases (KMTs) and demethylases (KDMs) underpin gene regulation. Here we demonstrate that variants causing haploinsufficiency of KMTs and KDMs are frequently encountered in individuals with developmental disorders. Using a combination of human variation databases and existing animal models, we determine 22 KMTs and KDMs as additional candidates for dominantly inherited developmental disorders. We show that KMTs and KDMs that are associated with, or are candidates for, dominant developmental disorders tend to have a higher level of transcription, longer canonical transcripts, more interactors, and a higher number and more types of post-translational modifications than other KMT and KDMs...
January 4, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29113313/whole-exome-analysis-in-osteosarcoma-to-identify-a-personalized-therapy
#13
Caterina Chiappetta, Massimiliano Mancini, Francesca Lessi, Paolo Aretini, Veronica De Gregorio, Chiara Puggioni, Raffaella Carletti, Vincenzo Petrozza, Prospero Civita, Sara Franceschi, Antonio G Naccarato, Carlo Della Rocca, Chiara M Mazzanti, Claudio Di Cristofano
Osteosarcoma is the most common pediatric primary non-hematopoietic bone tumor. Survival of these young patients is related to the response to chemotherapy and development of metastases. Despite many advances in cancer research, chemotherapy regimens for osteosarcoma are still based on non-selective cytotoxic drugs. It is essential to investigate new specific molecular therapies for osteosarcoma to increase the survival rate of these patients. We performed exomic sequence analyses of 8 diagnostic biopsies of patients with conventional high grade osteosarcoma to advance our understanding of their genetic underpinnings and to correlate the genetic alteration with the clinical and pathological features of each patient to identify a personalized therapy...
October 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/29109099/targeted-gene-sequencing-of-gallbladder-carcinoma-identifies-high-impact-somatic-and-rare-germline-mutations
#14
Saurabh Yadav, Navonil DE Sarkar, Niraj Kumari, Narendra Krishnani, Ashok Kumar, Balraj Mittal
BACKGROUND: Gallbladder carcinoma (GBC) is a subtype of biliary tract malignancy with poor prognosis and high fatality rate. The present study was designed to uncover somatic and rare germline mutations in GBC to reveal the disease biology and understand the clinical importance of mutation profile in terms of prognostics and actionability. MATERIALS AND METHODS: We performed ultra-deep sequencing across 409 cancer-related genes in 11 GBC patients of North-Indian descent...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29069077/functional-convergence-of-histone-methyltransferases-ehmt1-and-kmt2c-involved-in-intellectual-disability-and-autism-spectrum-disorder
#15
Tom S Koemans, Tjitske Kleefstra, Melissa C Chubak, Max H Stone, Margot R F Reijnders, Sonja de Munnik, Marjolein H Willemsen, Michaela Fenckova, Connie T R M Stumpel, Levinus A Bok, Margarita Sifuentes Saenz, Kyna A Byerly, Linda B Baughn, Alexander P A Stegmann, Rolph Pfundt, Huiqing Zhou, Hans van Bokhoven, Annette Schenck, Jamie M Kramer
Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C...
October 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29061174/de-novo-chromosome-7q36-1q36-2-triplication-in-a-child-with-developmental-delay-growth-failure-distinctive-facial-features-and-multiple-congenital-anomalies-a-case-report
#16
Muna A Al Dhaibani, Diane Allingham-Hawkins, Ayman W El-Hattab
BACKGROUND: Studying human genome using chromosomal microarrays has significantly improved the accuracy and yield of diagnosing genomic disorders. Chromosome 7q36 deletions and duplications are rare genomic disorders that have been reported in a limited number of children with developmental delay, growth retardation, and congenital malformation. Altered dosage of SHH and HLXB9, both located in 7q36.3, is believed to play roles in the phenotypes associated with these rearrangements. In this report we describe a child with 7q36...
October 23, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28967912/histone-h3k4-monomethylation-catalyzed-by-trr-and-mammalian-compass-like-proteins-at-enhancers-is-dispensable-for-development-and-viability
#17
Ryan Rickels, Hans-Martin Herz, Christie C Sze, Kaixiang Cao, Marc A Morgan, Clayton K Collings, Maria Gause, Yoh-Hei Takahashi, Lu Wang, Emily J Rendleman, Stacy A Marshall, Annika Krueger, Elizabeth T Bartom, Andrea Piunti, Edwin R Smith, Nebiyu A Abshiru, Neil L Kelleher, Dale Dorsett, Ali Shilatifard
Histone H3 lysine 4 monomethylation (H3K4me1) is an evolutionarily conserved feature of enhancer chromatin catalyzed by the COMPASS-like methyltransferase family, which includes Trr in Drosophila melanogaster and MLL3 (encoded by KMT2C) and MLL4 (encoded by KMT2D) in mammals. Here we demonstrate that Drosophila embryos expressing catalytically deficient Trr eclose and develop to productive adulthood. Parallel experiments with a trr allele that augments enzyme product specificity show that conversion of H3K4me1 at enhancers to H3K4me2 and H3K4me3 is also compatible with life and results in minimal changes in gene expression...
November 2017: Nature Genetics
https://www.readbyqxmd.com/read/28940816/clinical-impact-of-kmt2c-and-spry4-expression-levels-in-intensively-treated-younger-adult-acute-myeloid-leukemia-patients
#18
Sabine Kayser, Maximilian Feszler, Julia Krzykalla, Matthias Schick, Michael Kramer, Axel Benner, Felicitas Thol, Uwe Platzbecker, Carsten Müller-Tidow, Anthony D Ho, Gerhard Ehninger, Michael Heuser, Richard F Schlenk, Christian Thiede, Christoph Röllig, Alwin Krämer
OBJECTIVE: To evaluate the prognostic impact of gene expression levels (ELs) of two tumor suppressor genes, sprouty 4 (SPRY4, located on 5q) and lysine methyltransferase 2C (KMT2C, located on 7q) in correlation with clinical characteristics and genetic abnormalities assessed at initial diagnosis in acute myeloid leukemia (AML). METHOD: Gene expression levels were measured on cDNA by RT-qPCR from diagnostic bone marrow samples of 275 intensively treated adult AML patients (median age, 48 years)...
September 22, 2017: European Journal of Haematology
https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#19
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
January 11, 2018: Oncogene
https://www.readbyqxmd.com/read/28801450/genomic-analysis-of-hairy-cell-leukemia-identifies-novel-recurrent-genetic-alterations
#20
Benjamin H Durham, Bartlomiej Getta, Sascha Dietrich, Justin Taylor, Helen Won, James M Bogenberger, Sasinya Scott, Eunhee Kim, Young Rock Chung, Stephen S Chung, Jennifer Hüllein, Tatjana Walther, Lu Wang, Sydney X Lu, Christopher C Oakes, Raoul Tibes, Torsten Haferlach, Barry S Taylor, Martin S Tallman, Michael F Berger, Jae H Park, Thorsten Zenz, Omar Abdel-Wahab
Classical hairy cell leukemia (cHCL) is characterized by a near 100% frequency of the BRAF V600E mutation, whereas ∼30% of variant HCLs (vHCLs) have MAP2K1 mutations. However, recurrent genetic alterations cooperating with BRAF V600E or MAP2K1 mutations in HCL, as well as those in MAP2K1 wild-type vHCL, are not well defined. We therefore performed deep targeted mutational and copy number analysis of cHCL (n = 53) and vHCL (n = 8). The most common genetic alteration in cHCL apart from BRAF V600E was heterozygous loss of chromosome 7q, the minimally deleted region of which targeted wild-type BRAF , subdividing cHCL into those hemizygous versus heterozygous for the BRAF V600E mutation...
October 5, 2017: Blood
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