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Exon skipping in humans

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https://www.readbyqxmd.com/read/29122468/an-intronic-variation-in-slc52a1-causes-exon-skipping-and-transient-riboflavin-responsive-multiple-acyl-coa-dehydrogenation-deficiency
#1
Signe Mosegaard, Gitte Hoffmann Bruun, Karen Freund Flyvbjerg, Yngve Thomas Bliksrud, Niels Gregersen, Maja Dembic, Ellen Annexstad, Trine Tangeraas, Rikke Katrine Jentoft Olsen, Brage S Andresen
Vitamin B2, riboflavin is essential for cellular function, as it participates in a diversity of redox reactions central to human metabolism, through its role as precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which are electron carriers. The electron transfer flavoprotein (ETF) and its dehydrogenase (ETFDH), uses FAD as cofactor. The ETF and ETFDH are forming the electron transport pathway for many mitochondrial flavoprotein dehydrogenases involved in fatty acid, amino acid and choline metabolism...
November 2, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29121990/identification-of-functional-single-nucleotide-polymorphisms-in-the-branchpoint-site
#2
Hung-Lun Chiang, Jer-Yuarn Wu, Yuan-Tsong Chen
BACKGROUND: The human genome contains millions of single nucleotide polymorphisms (SNPs); many of these SNPs are intronic and have unknown functional significance. SNPs occurring within intron branchpoint sites, especially at the adenine (A), would presumably affect splicing; however, this has not been systematically studied. We employed a splicing prediction tool to identify human intron branchpoint sites and screened dbSNP for identifying SNPs located in the predicted sites to generate a genome-wide branchpoint site SNP database...
November 9, 2017: Human Genomics
https://www.readbyqxmd.com/read/29059470/banf1-plod3-sf3b4-as-early-stage-cancer-decision-markers-and-drivers-of-hepatocellular-carcinoma
#3
Qingyu Shen, Jung Woo Eun, Kyungbun Lee, Hyung Seok Kim, Hee Doo Yang, Sang Yean Kim, Eun Kyung Lee, Taemook Kim, Keunsoo Kang, Seongchan Kim, Dal-Hee Min, Soon-Nam Oh, Young-Joon Lee, Hyuk Moon, Simon Weonsang Ro, Won Sang Park, Jung Young Lee, Suk Woo Nam
An accurate tool enabling early diagnosis of hepatocellular carcinoma (HCC) is clinically important, since early detection of HCC markedly improves survival. We aimed to investigate the molecular markers underlying early progression of HCC that can be detected in precancerous lesions. We designed a gene selection strategy to identify potential driver genes by integrative analysis of transcriptome and clinicopathologic data of human multi-stage HCC tissues including precancerous lesions, low- and high-grade dysplastic nodules...
October 23, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29025893/disease-specific-biases-in-alternative-splicing-and-tissue-specific-dysregulation-revealed-by-multitissue-profiling-of-lymphocyte-gene-expression-in-type-1-diabetes
#4
Jeremy R B Newman, Ana Conesa, Matthew Mika, Felicia N New, Suna Onengut-Gumuscu, Mark A Atkinson, Stephen S Rich, Lauren M McIntyre, Patrick Concannon
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D)...
November 2017: Genome Research
https://www.readbyqxmd.com/read/28984045/differentially-expressed-alternatively-spliced-genes-in-skeletal-muscle-from-cancer-patients-with-cachexia
#5
Ashok Narasimhan, Russell Greiner, Oliver F Bathe, Vickie Baracos, Sambasivarao Damaraju
BACKGROUND: Alternative splicing (AS) is a post-transcriptional gene regulatory mechanism that contributes to proteome diversity. Aberrant splicing mechanisms contribute to various cancers and muscle-related conditions such as Duchenne muscular dystrophy. However, dysregulation of AS in cancer cachexia (CC) remains unexplored. Our objectives were (i) to profile alternatively spliced genes (ASGs) on a genome-wide scale and (ii) to identify differentially expressed alternatively spliced genes (DASGs) associated with CC...
October 6, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28973015/a-small-molecule-drug-promoting-mirna-processing-induces-alternative-splicing-of-mdmx-transcript-and-rescues-p53-activity-in-human-cancer-cells-overexpressing-mdmx-protein
#6
Georgios Valianatos, Barbora Valcikova, Katerina Growkova, Amandine Verlande, Jitka Mlcochova, Lenka Radova, Monika Stetkova, Michaela Vyhnakova, Ondrej Slaby, Stjepan Uldrijan
MdmX overexpression contributes to the development of cancer by inhibiting tumor suppressor p53. A switch in the alternative splicing of MdmX transcript, leading to the inclusion of exon 6, has been identified as the primary mechanism responsible for increased MdmX protein levels in human cancers, including melanoma. However, there are no approved drugs, which could translate these new findings into clinical applications. We analyzed the anti-melanoma activity of enoxacin, a fluoroquinolone antibiotic inhibiting the growth of some human cancers in vitro and in vivo by promoting miRNA maturation...
2017: PloS One
https://www.readbyqxmd.com/read/28934498/widespread-intra-dependencies-in-the-removal-of-introns-from-human-transcripts
#7
Seong Won Kim, Allison J Taggart, Claire Heintzelman, Kamil J Cygan, Caitlin G Hull, Jing Wang, Barsha Shrestha, William G Fairbrother
Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28932105/changes-in-alternative-splicing-as-pharmacodynamic-markers-for-sudemycin-d6
#8
Morgan Thurman, Jacob van Doorn, Barbara Danzer, Thomas R Webb, Stefan Stamm
OBJECTIVE: The aim of the study was to define pharmacodynamic markers for sudemycin D6, an experimental cancer drug that changes alternative splicing in human blood. METHODS: Blood samples from 12 donors were incubated with sudemycin D6 for up to 24 hours, and at several time points total RNA from lymphocytes was prepared and the pre-messenger RNA (mRNA) splicing patterns were analyzed with reverse transcription-polymerase chain reaction. RESULTS: Similar to immortalized cells, blood lymphocytes change alternative splicing due to sudemycin D6 treatment...
2017: Biomarker Insights
https://www.readbyqxmd.com/read/28916811/an-enu-induced-splice-site-mutation-of-mouse-col1a1-causing-recessive-osteogenesis-imperfecta-and-revealing-a-novel-splicing-rescue
#9
Koichi Tabeta, Xin Du, Kei Arimatsu, Mai Yokoji, Naoki Takahashi, Norio Amizuka, Tomoka Hasegawa, Karine Crozat, Tomoki Maekawa, Sayuri Miyauchi, Yumi Matsuda, Takako Ida, Masaru Kaku, Kasper Hoebe, Kinji Ohno, Hiromasa Yoshie, Kazuhisa Yamazaki, Eva Marie Y Moresco, Bruce Beutler
GU-AG consensus sequences are used for intron recognition in the majority of cases of pre-mRNA splicing in eukaryotes. Mutations at splice junctions often cause exon skipping, short deletions, or insertions in the mature mRNA, underlying one common molecular mechanism of genetic diseases. Using N-ethyl-N-nitrosourea, a novel recessive mutation named seal was produced, associated with fragile bones and susceptibility to fractures (spine and limbs). A single nucleotide transversion (T → A) at the second position of intron 36 of the Col1a1 gene, encoding the type I collagen, α1 chain, was responsible for the phenotype...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28865998/quantitative-antisense-screening-and-optimization-for-exon-51-skipping-in-duchenne-muscular-dystrophy
#10
Yusuke Echigoya, Kenji Rowel Q Lim, Nhu Trieu, Bo Bao, Bailey Miskew Nichols, Maria Candida Vila, James S Novak, Yuko Hara, Joshua Lee, Aleksander Touznik, Kamel Mamchaoui, Yoshitsugu Aoki, Shin'ichi Takeda, Kanneboyina Nagaraju, Vincent Mouly, Rika Maruyama, William Duddy, Toshifumi Yokota
Duchenne muscular dystrophy (DMD), the most common lethal genetic disorder, is caused by mutations in the dystrophin (DMD) gene. Exon skipping is a therapeutic approach that uses antisense oligonucleotides (AOs) to modulate splicing and restore the reading frame, leading to truncated, yet functional protein expression. In 2016, the US Food and Drug Administration (FDA) conditionally approved the first phosphorodiamidate morpholino oligomer (morpholino)-based AO drug, eteplirsen, developed for DMD exon 51 skipping...
November 1, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28756020/identification-and-characterization-of-the-tyrosinase-gene-tyr-and-its-transcript-variants-tyr_1-and-tyr_2-in-the-crab-eating-macaque-macaca-fascicularis
#11
Young-Hyun Kim, Sang-Je Park, Se-Hee Choe, Ja-Rang Lee, Hyeon-Mu Cho, Sun-Uk Kim, Ji-Su Kim, Bo-Woong Sim, Bong-Seok Song, Youngjeon Lee, Yeung Bae Jin, Jung-Joo Hong, Kang-Jin Jeong, Philyong Kang, Seung-Ho Baek, Sang-Rae Lee, Jae-Won Huh, Kyu-Tae Chang
Tyrosinase is a copper-containing enzyme that regulates melanin biosynthesis and is encoded by the tyrosinase (TYR) gene. Previous studies demonstrated that mutations in TYR could lead to oculocutaneous albinism type 1 (OCA1) owing to the failure of melanin formation. Although a previous study found that albinism in the rhesus monkey was derived from a mutation in TYR, the identification and characterization of this gene in non-human primates has not been achieved thus far. Thus, using the rapid amplification of cDNA ends (RACE) and internal reverse transcription PCR (RT-PCR) we identified the full-length sequence of TYR in the crab-eating macaque, and two different transcript variants (TYR_1 and TYR_2)...
September 30, 2017: Gene
https://www.readbyqxmd.com/read/28742140/short-16-mer-locked-nucleic-acid-splice-switching-oligonucleotides-restore-dystrophin-production-in-duchenne-muscular-dystrophy-myotubes
#12
Vanessa Borges Pires, Ricardo Simões, Kamel Mamchaoui, Célia Carvalho, Maria Carmo-Fonseca
Splice-switching antisense oligonucleotides (SSOs) offer great potential for RNA-targeting therapies, and two SSO drugs have been recently approved for treating Duchenne Muscular Dystrophy (DMD) and Spinal Muscular Atrophy (SMA). Despite promising results, new developments are still needed for more efficient chemistries and delivery systems. Locked nucleic acid (LNA) is a chemically modified nucleic acid that presents several attractive properties, such as high melting temperature when bound to RNA, potent biological activity, high stability and low toxicity in vivo...
2017: PloS One
https://www.readbyqxmd.com/read/28705773/recent-progress-in-circular-rnas-in-human-cancers
#13
Guanqun Huang, Shuaihu Li, Nuo Yang, Yongdong Zou, Duo Zheng, Tian Xiao
Circular RNAs (circRNAs) are a large class of endogenous RNAs, formed by exon skipping or back-splicing events as covalently closed loops, which are expressed abundantly in mammalian cells. Although their biological functions remain largely unknown, recent studies show that circRNAs have three main functions in mammalian cells. First, circRNAs can regulate transcription and RNA splicing. Second, circRNAs function as microRNA (miRNA) sponges. Third, they can be translated into protein driven by N(6)-methyladenosine modification...
September 28, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28684740/hur-dependent-editing-of-a-new-mineralocorticoid-receptor-splice-variant-reveals-an-osmoregulatory-loop-for-sodium-homeostasis
#14
Ingrid Lema, Larbi Amazit, Khadija Lamribet, Jérôme Fagart, Anne Blanchard, Marc Lombès, Nadia Cherradi, Say Viengchareun
Aldosterone and the Mineralocorticoid Receptor (MR) control hydroelectrolytic homeostasis and alterations of mineralocorticoid signaling pathway are involved in the pathogenesis of numerous human diseases, justifying the need to decipher molecular events controlling MR expression level. Here, we show in renal cells that the RNA-Binding Protein, Human antigen R (HuR), plays a central role in the editing of MR transcript as revealed by a RNA interference strategy. We identify a novel Δ6 MR splice variant, which lacks the entire exon 6, following a HuR-dependent exon skipping event...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679766/sym015-a-highly-efficacious-antibody-mixture-against-met-amplified-tumors
#15
Thomas Tuxen Poulsen, Michael Monrad Grandal, Niels Jørgen Østergaard Skartved, Rikke Hald, Lene Alifrangis, Klaus Koefoed, Trine Lindsted, Camilla Fröhlich, Sofie Ellebæk Pollmann, Karsten Wessel Eriksen, Anna Dahlman, Helle Jane Jacobsen, Thomas Bouquin, Mikkel Wandahl Pedersen, Ivan David Horak, Johan Lantto, Michael Kragh
Purpose: Activation of the receptor tyrosine kinase MET is associated with poor clinical outcome in certain cancers. To target MET more effectively, we developed an antagonistic antibody mixture, Sym015, consisting of two humanized mAbs directed against nonoverlapping epitopes of MET.Experimental Design/Results: We screened a large panel of well-annotated human cancer cell lines and identified a subset with highly elevated MET expression. In particular, cell lines of lung cancer and gastric cancer origin demonstrated high MET expression and activation, and Sym015 triggered degradation of MET and significantly inhibited growth of these cell lines...
July 5, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28663100/a-new-aav10-u7-mediated-gene-therapy-prolongs-survival-and-restores-function-in-an-als-mouse-model
#16
Maria Grazia Biferi, Mathilde Cohen-Tannoudji, Ambra Cappelletto, Benoit Giroux, Marianne Roda, Stéphanie Astord, Thibaut Marais, Corinne Bos, Thomas Voit, Arnaud Ferry, Martine Barkats
One of the most promising therapeutic approaches for familial amyotrophic lateral sclerosis linked to superoxide dismutase 1 (SOD1) is the suppression of toxic mutant SOD1 in the affected tissues. Here, we report an innovative molecular strategy for inducing substantial, widespread, and sustained reduction of mutant human SOD1 (hSOD1) levels throughout the body of SOD1(G93A) mice, leading to therapeutic effects in animals. Adeno-associated virus serotype rh10 vectors (AAV10) were used to mediate exon skipping of the hSOD1 pre-mRNA by expression of exon-2-targeted antisense sequences embedded in a modified U7 small-nuclear RNA (AAV10-U7-hSOD)...
September 6, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28642487/hypoxia-is-a-key-driver-of-alternative-splicing-in-human-breast-cancer-cells
#17
Jian Han, Jia Li, Jolene Caifeng Ho, Grace Sushin Chia, Hiroyuki Kato, Sudhakar Jha, Henry Yang, Lorenz Poellinger, Kian Leong Lee
Adaptation to hypoxia, a hallmark feature of many tumors, is an important driver of cancer cell survival, proliferation and the development of resistance to chemotherapy. Hypoxia-induced stabilization of hypoxia-inducible factors (HIFs) leads to transcriptional activation of a network of hypoxia target genes involved in angiogenesis, cell growth, glycolysis, DNA damage repair and apoptosis. Although the transcriptional targets of hypoxia have been characterized, the alternative splicing of transcripts that occurs during hypoxia and the roles they play in oncogenesis are much less understood...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28624223/evaluation-of-mybpc3-trans-splicing-and-gene-replacement-as-therapeutic-options-in-human-ipsc-derived-cardiomyocytes
#18
Maksymilian Prondzynski, Elisabeth Krämer, Sandra D Laufer, Aya Shibamiya, Ole Pless, Frederik Flenner, Oliver J Müller, Julia Münch, Charles Redwood, Arne Hansen, Monica Patten, Thomas Eschenhagen, Giulia Mearini, Lucie Carrier
Gene therapy is a promising option for severe forms of genetic diseases. We previously provided evidence for the feasibility of trans-splicing, exon skipping, and gene replacement in a mouse model of hypertrophic cardiomyopathy (HCM) carrying a mutation in MYBPC3, encoding cardiac myosin-binding protein C (cMyBP-C). Here we used human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from an HCM patient carrying a heterozygous c.1358-1359insC MYBPC3 mutation and from a healthy donor. HCM hiPSC-CMs exhibited ∼50% lower MYBPC3 mRNA and cMyBP-C protein levels than control, no truncated cMyBP-C, larger cell size, and altered gene expression, thus reproducing human HCM features...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28624186/gaa-deficiency-in-pompe-disease-is-alleviated-by-exon-inclusion-in-ipsc-derived-skeletal-muscle-cells
#19
Erik van der Wal, Atze J Bergsma, Tom J M van Gestel, Stijn L M In 't Groen, Holm Zaehres, Marcos J Araúzo-Bravo, Hans R Schöler, Ans T van der Ploeg, W W M Pim Pijnappel
Pompe disease is a metabolic myopathy caused by deficiency of the acid α-glucosidase (GAA) enzyme and results in progressive wasting of skeletal muscle cells. The c.-32-13T>G (IVS1) GAA variant promotes exon 2 skipping during pre-mRNA splicing and is the most common variant for the childhood/adult disease form. We previously identified antisense oligonucleotides (AONs) that promoted GAA exon 2 inclusion in patient-derived fibroblasts. It was unknown how these AONs would affect GAA splicing in skeletal muscle cells...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28607084/systems-guided-forward-genetic-screen-reveals-a-critical-role-of-the-replication-stress-response-protein-etaa1-in-t-cell-clonal-expansion
#20
Lisa A Miosge, Yovina Sontani, Aaron Chuah, Keisuke Horikawa, Tiffany A Russell, Yan Mei, Mayura V Wagle, Debbie R Howard, Anselm Enders, David C Tscharke, Christopher C Goodnow, Ian A Parish
T-cell immunity requires extremely rapid clonal proliferation of rare, antigen-specific T lymphocytes to form effector cells. Here we identify a critical role for ETAA1 in this process by surveying random germ line mutations in mice using exome sequencing and bioinformatic annotation to prioritize mutations in genes of unknown function with potential effects on the immune system, followed by breeding to homozygosity and testing for immune system phenotypes. Effector CD8(+) and CD4(+) T-cell formation following immunization, lymphocytic choriomeningitis virus (LCMV) infection, or herpes simplex virus 1 (HSV1) infection was profoundly decreased despite normal immune cell development in adult mice homozygous for two different Etaa1 mutations: an exon 2 skipping allele that deletes Gly78-Leu119, and a Cys166Stop truncating allele that eliminates most of the 877-aa protein...
June 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
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