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https://www.readbyqxmd.com/read/28109959/crispr-cas9-mediated-genome-editing-as-a-therapeutic-approach-for-leber-congenital-amaurosis-10
#1
Guo-Xiang Ruan, Elizabeth Barry, Dan Yu, Michael Lukason, Seng H Cheng, Abraham Scaria
As the most common subtype of Leber congenital amaurosis (LCA), LCA10 is a severe retinal dystrophy caused by mutations in the CEP290 gene. The most frequent mutation found in patients with LCA10 is a deep intronic mutation in CEP290 that generates a cryptic splice donor site. The large size of the CEP290 gene prevents its use in adeno-associated virus (AAV)-mediated gene augmentation therapy. Here, we show that targeted genomic deletion using the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system represents a promising therapeutic approach for the treatment of patients with LCA10 bearing the CEP290 splice mutation...
January 18, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28109652/epilepsy-in-patients-with-grin2a-alterations-genetics-neurodevelopment-epileptic-phenotype-and-response-to-anticonvulsive-drugs
#2
C von Stülpnagel, M Ensslen, R S Møller, D K Pal, S Masnada, P Veggiotti, E Piazza, M Dreesmann, T Hartlieb, T Herberhold, E Hughes, M Koch, C Kutzer, K Hoertnagel, J Nitanda, M Pohl, K Rostásy, T B Haack, K Stöhr, G Kluger, I Borggraefe
OBJECTIVE: To delineate the genetic, neurodevelopmental and epileptic spectrum associated with GRIN2A alterations with emphasis on epilepsy treatment. METHODS: Retrospective study of 19 patients (7 females; age: 1-38 years; mean 10.1 years) with epilepsy and GRIN2A alteration. Genetic variants were classified according to the guidelines and recommendations of the American College of Medical Genetics (ACMG). Clinical findings including epilepsy classification, treatment, EEG findings, early childhood development and neurodevelopmental outcome were collected with an electronic questionnaire...
January 14, 2017: European Journal of Paediatric Neurology: EJPN
https://www.readbyqxmd.com/read/28109431/proteogenomics-recycling-public-data-to-improve-genome-annotations
#3
A McAfee, L J Foster
Massively parallel sequencing is revealing species genomes faster than ever before, but the value of the raw sequence is limited unless the genes can be accurately annotated. This is typically achieved using gene prediction algorithms which, despite continual improvement, still require substantial verification and refinement. For example, in silico methods struggle with annotating splice isoforms accurately and empirical methods are needed to refine and verify the initial bioinformatic gene predictions. RNA-seq is an excellent way to confirm exon-exon boundaries and transcript termini, while mass spectrometry (MS) offers definitive proof that a gene is translated and a secondary means of confirming exon expression, protein termini, and posttranslational modifications...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28108816/decitabine-priming-prior-to-low-dose-chemotherapy-improves-patient-outcomes-in-myelodysplastic-syndromes-raeb-a-retrospective-analysis-vs-chemotherapy-alone
#4
Li Ye, Yanling Ren, Xinping Zhou, Chen Mei, Liya Ma, Xingnong Ye, Juying Wei, Weilai Xu, Haitao Meng, Wenbin Qian, Wenyuan Mai, Yinjun Lou, Gaixiang Xu, Jiejing Qian, Yejiang Lou, Yingwan Luo, Lili Xie, Peipei Lin, Chao Hu, Jie Jin, Hongyan Tong
PURPOSE: The aim of this study was to examine whether decitabine priming prior to low-dose chemotherapeutic regimens could improve outcomes in patients with myelodysplastic syndromes-refractory anemia with excess of blasts (MDS-RAEB). METHODS: The current retrospective analysis included all MDS-RAEB patients receiving idarubicin/cytarabine (IA) or aclacinomycin/cytarabine (AA), with or without decitabine priming during a period from February 2010 to May 2015. Treatment response and toxicity were compared between patients receiving decitabine priming and those who did not...
January 20, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28108448/arnapipe-a-balanced-efficient-and-distributed-pipeline-for-processing-rna-seq-data-in-high-performance-computing-environments
#5
Arnald Alonso, Brittany N Lasseigne, Kelly Williams, Josh Nielsen, Ryne C Ramaker, Andrew A Hardigan, Bobbi Johnston, Brian S Roberts, Sara J Cooper, Sara Marsal, Richard M Myers
The wide range of RNA-seq applications and their high computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing, and sequence variant calling...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108040/genetic-analysis-of-chchd2-and-chchd10-in-italian-patients-with-parkinson-s-disease
#6
Elisa Rubino, Livia Brusa, Ming Zhang, Silvia Boschi, Flora Govone, Alessandro Vacca, Annalisa Gai, Lorenzo Pinessi, Leonardo Lopiano, Ekaterina Rogaeva, Innocenzo Rainero
In recent years, CHCHD2 and CHCHD10 mutations were reported to be associated with a broad spectrum of neurodegenerative diseases, including Parkinson's disease (PD), although with conflicting results in different populations. The present study aimed to evaluate CHCHD2 and CHCHD10 coding variants in Italian patients with PD. All the coding regions and flanking intronic splice sites of CHCHD2 and CHCHD10 were sequenced. None of our 119 PD cases carried CHCHD2 mutations, whereas 1 sporadic PD patient showed the Pro34Ser substitution in CHCHD10...
January 5, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28107452/mice-lacking-hbp1-function-are-viable-and-fertile
#7
Cassy M Spiller, Dagmar Wilhelm, David A Jans, Josephine Bowles, Peter Koopman
Fetal germ cell development is tightly regulated by the somatic cell environment, and is characterised by cell cycle states that differ between XY and XX gonads. In the testis, gonocytes enter G1/G0 arrest from 12.5 days post coitum (dpc) in mice and maintain cell cycle arrest until after birth. Failure to correctly maintain G1/G0 arrest can result in loss of germ cells or, conversely, germ cell tumours. High mobility group box containing transcription factor 1 (HBP1) is a transcription factor that was previously identified in fetal male germ cells at the time of embryonic cell cycle arrest...
2017: PloS One
https://www.readbyqxmd.com/read/28106852/tumor-derived-tissue-factor-aberrantly-activates-complement-and-facilitates-lung-tumor-progression-via-recruitment-of-myeloid-derived-suppressor-cells
#8
Xiao Han, Haoran Zha, Fei Yang, Bo Guo, Bo Zhu
The initiator of extrinsic coagulation, tissue factor (TF), and its non-coagulant isoform alternatively spliced TF (asTF) are closely associated with tumor development. In the tumor microenvironment, the role of TF-induced coagulation in tumor progression remains to be fully elucidated. Using TF-knockdown lung tumor cells, we showed that TF is the dominant component of procoagulant activity but is dispensable in the cellular biology of tumor cells. In a xenograft model, using immunohistochemical analysis and flow cytometry analysis of the tumor microenvironment, we demonstrated that TF-induced fibrin deposition, which is correlated with complement activation and myeloid-derived suppressor cell (MDSC) recruitment, is positively associated with tumor progression...
January 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106838/molecular-characterization-of-voltage-gated-sodium-channels-and-their-relations-with-paralytic-shellfish-toxin-bioaccumulation-in-the-pacific-oyster-crassostrea-gigas
#9
Floriane Boullot, Justine Castrec, Adeline Bidault, Natanael Dantas, Laura Payton, Mickael Perrigault, Damien Tran, Zouher Amzil, Pierre Boudry, Philippe Soudant, Hélène Hégaret, Caroline Fabioux
Paralytic shellfish toxins (PST) bind to voltage-gated sodium channels (Nav) and block conduction of action potential in excitable cells. This study aimed to (i) characterize Nav sequences in Crassostrea gigas and (ii) investigate a putative relation between Nav and PST-bioaccumulation in oysters. The phylogenetic analysis highlighted two types of Nav in C. gigas: a Nav1 (CgNav1) and a Nav2 (CgNav2) with sequence properties of sodium-selective and sodium/calcium-selective channels, respectively. Three alternative splice transcripts of CgNav1 named A, B and C, were characterized...
January 19, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28106752/the-promoting-effect-of-the-extracellular-matrix-peptide-tniiia2-derived-from-tenascin-c-in-colon-cancer-cell-infiltration
#10
Hideo Suzuki, Manabu Sasada, Sadahiro Kamiya, Yuka Ito, Hikaru Watanabe, Yuko Okada, Kazuma Ishibashi, Takuya Iyoda, Akinori Yanaka, Fumio Fukai
The extracellular matrix (ECM) molecule tenascin C (TNC) is known to be highly expressed under various pathological conditions such as inflammation and cancer. It has been reported that the expression of TNC is correlated with the malignant potential of cancer. In our laboratory, it was found that the peptide derived from the alternative splicing domain A2 in TNC, termed TNIIIA2, has been shown to influence a variety of cellular processes, such as survival, proliferation, migration, and differentiation. In this study, we investigated the effect of TNC/TNIIIA2 on the invasion and metastasis of colon cancer cells, Colon26-M3...
January 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106506/ectodysplasin-a-in-biological-fluids-and-diagnosis-of-ectodermal-dysplasia
#11
J Podzus, C Kowalczyk-Quintas, S Schuepbach-Mallepell, L Willen, G Staehlin, M Vigolo, A Tardivel, D Headon, N Kirby, M L Mikkola, H Schneider, P Schneider
The tumor necrosis factor (TNF) family ligand ectodysplasin A (EDA) is produced as 2 full-length splice variants, EDA1 and EDA2, that bind to EDA receptor (EDAR) and X-linked EDA receptor (XEDAR/EDA2R), respectively. Inactivating mutations in Eda or Edar cause hypohidrotic ectodermal dysplasia (HED), a condition characterized by malformations of the teeth, hair and glands, with milder deficiencies affecting only the teeth. EDA acts early during the development of ectodermal appendages-as early as the embryonic placode stage-and plays a role in adult appendage function...
February 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28106138/srrm4-dependent-neuron-specific-alternative-splicing-of-protrudin-transcripts-regulates-neurite-outgrowth
#12
Takafumi Ohnishi, Michiko Shirane, Keiichi I Nakayama
Alternative splicing gives rise to diversity of the proteome, and it is especially prevalent in the mammalian nervous system. Indeed, many factors that control the splicing process govern nervous system development. Among such factors, SRRM4 is an important regulator of aspects of neural differentiation including neurite outgrowth. The mechanism by which SRRM4 regulates neurite outgrowth has remained poorly understood, however. We now show that SRRM4 regulates the splicing of protrudin gene (Zfyve27) transcripts in neuronal cells...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105922/differential-expression-of-alternatively-spliced-transcripts-related-to-energy-metabolism-in-colorectal-cancer
#13
Anastasiya Vladimirovna Snezhkina, George Sergeevich Krasnov, Andrew Rostislavovich Zaretsky, Alex Zhavoronkov, Kirill Mikhailovich Nyushko, Alexey Alexandrovich Moskalev, Irina Yurievna Karpova, Anastasiya Isaevna Afremova, Anastasiya Valerievna Lipatova, Dmitriy Vladimitovich Kochetkov, Maria Sergeena Fedorova, Nadezhda Nikolaevna Volchenko, Asiya Fayazovna Sadritdinova, Nataliya Vladimirovna Melnikova, Dmitry Vladimirovich Sidorov, Anatoly Yurievich Popov, Dmitry Valerievich Kalinin, Andrey Dmitrievich Kaprin, Boris Yakovlevich Alekseev, Alexey Alexandrovich Dmitriev, Anna Viktorovna Kudryavtseva
BACKGROUND: Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. CRC molecular pathogenesis is heterogeneous and may be followed by mutations in oncogenes and tumor suppressor genes, chromosomal and microsatellite instability, alternative splicing alterations, hypermethylation of CpG islands, oxidative stress, impairment of different signaling pathways and energy metabolism. In the present work, we have studied the alterations of alternative splicing patterns of genes related to energy metabolism in CRC...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105912/dgw-an-exploratory-data-analysis-tool-for-clustering-and-visualisation-of-epigenomic-marks
#14
Saulius Lukauskas, Roberto Visintainer, Guido Sanguinetti, Gabriele B Schweikert
BACKGROUND: Functional genomic and epigenomic research relies fundamentally on sequencing based methods like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high dimensional data sets with visually complex structures, such as multi-modal peaks extended over large genomic regions. Current tools for visualisation and data exploration represent and leverage these complex features only to a limited extent. RESULTS: We present DGW, an open source software package for simultaneous alignment and clustering of multiple epigenomic marks...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105192/akt-dependent-activation-of-erk-by-cyclin-d1b-contributes-to-cell-invasiveness-and-tumorigenicity
#15
Chul Jang Kim, Yukihiro Tambe, Ken-Ichi Mukaisho, Hiroyuki Sugihara, Akihiro Kawauchi, Hirokazu Inoue
A total of two major isoforms, cyclin D1a and cyclin D1b, are generated from the human cyclin D1 gene by alternative splicing. Cyclin D1b is scarcely expressed in normal tissues; however, it is expressed at a high frequency in certain types of cancerous tissue. The present authors previously constructed cyclin D1b transgenic (Tg) mice and identified rectal tumors, including adenocarcinoma and sessile serrated adenoma, in 62.5% of female Tg mice. In addition, the present authors indicated that cyclin D1b expression enhances phosphorylation of extracellular signal-regulated kinase (Erk) in these rectal tumors, and in mouse embryonic fibroblast (MEF) cells and human 293T cells...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28104749/alberto-kornblihtt-coupling-alternative-splicing-with-transcription
#16
Melina Casadio
Kornblihtt studies how gene expression is controlled in mammals and plants.
January 19, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28104536/exome-wide-association-study-identifies-low-frequency-coding-variants-in-2p23-2-and-7p11-2-associated-with-survival-of-non-small-cell-lung-cancer-patients
#17
Meng Zhu, Liguo Geng, Wei Shen, Yuzhuo Wang, Jia Liu, Yang Cheng, Cheng Wang, Juncheng Dai, Guangfu Jin, Zhibin Hu, Hongxia Ma, Hongbing Shen
INTRODUCTION: A growing body of evidence has suggested that low-frequency or rare variants might have strong effects on the development and prognosis of cancer. Here, we aim to assess the role of low-frequency and rare coding variants in the survival of non-small cell lung cancer (NSCLC) in Chinese populations. METHODS: We performed an exome-wide scan of 247,870 variants in 1,008 NSCLC patients and replicated the promising variants by using imputed genotype data of The Cancer Genome Atlas (TCGA) with a cox regression model...
January 16, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28104311/comprehensive-profiling-of-the-androgen-receptor-in-liquid-biopsies-from-castration-resistant-prostate-cancer-reveals-novel-intra-ar-structural-variation-and-splice-variant-expression-patterns
#18
Bram De Laere, Pieter-Jan van Dam, Tom Whitington, Markus Mayrhofer, Emanuela Henao Diaz, Gert Van den Eynden, Jean Vandebroek, Jurgen Del-Favero, Steven Van Laere, Luc Dirix, Henrik Grönberg, Johan Lindberg
BACKGROUND: Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. OBJECTIVE: To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. DESIGN, SETTING, AND PARTICIPANTS: Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy...
January 16, 2017: European Urology
https://www.readbyqxmd.com/read/28103786/crh-receptor-signalling-potential-roles-in-pathophysiology
#19
Styliani Ourailidou, Dimitris Grammatopoulos
To maintain homeostatic equilibrium, living organisms have evolved complex adaptation systems that control an array of behavioural, autonomic, neuroendocrine and immune responses. One of the important switches The master switch of this system is the hypothalamic hormone corticotropin-releasing hormone (CRH), which together with a family of related peptides (urocortins, UCNs) orchestrate stress-coping responses that reinstate homeostasis. Persistent disturbances in the homeostatic equilibrium either due to inadequate or persistently uncontrolled responses have been associated with pathogenic mechanisms of disease...
January 10, 2017: Current Molecular Pharmacology
https://www.readbyqxmd.com/read/28103691/sudemycin-k-a-synthetic-antitumor-splicing-inhibitor-variant-with-improved-activity-and-versatile-chemistry
#20
Kamil Makowski, Luisa Vigevani, Fernando Albericio, Juan Valcárcel, Mercedes Álvarez
Important links exist between the process of pre-mRNA splicing and cancer, as illustrated by the frequent mutation of splicing factors in tumors and the emergence of various families of antitumor drugs that target components of the splicing machinery, notably SF3B1, a protein subunit of spliceosomal U2 small nuclear ribonucleoprotein particle (snRNP). Sudemycins are synthetic compounds that harbor a pharmacophore common to various classes of splicing inhibitors. Here, we describe the synthesis and functional characterization of novel sudemycin analogues that functionally probe key chemical groups within this pharmacophore...
January 20, 2017: ACS Chemical Biology
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