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Rbm10

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https://www.readbyqxmd.com/read/28379442/an-rrm-znf-rna-recognition-module-targets-rbm10-to-exonic-sequences-to-promote-exon-exclusion
#1
Katherine M Collins, Yaroslav A Kainov, Evangelos Christodolou, Debashish Ray, Quaid Morris, Timothy Hughes, Ian A Taylor, Eugene V Makeyev, Andres Ramos
RBM10 is an RNA-binding protein that plays an essential role in development and is frequently mutated in the context of human disease. RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing. However, the molecular mechanisms underlying this seemingly relaxed sequence specificity are not understood and functional studies have focused on 3΄ intronic sites only. Here, we dissect the RNA code recognized by RBM10 and relate it to the splicing regulatory function of this protein...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28296677/rbm10-tfe3-renal-cell-carcinoma-a-potential-diagnostic-pitfall-due-to-cryptic-intrachromosomal-xp11-2-inversion-resulting-in-false-negative-tfe3-fish
#2
MULTICENTER STUDY
Pedram Argani, Lei Zhang, Victor E Reuter, Satish K Tickoo, Cristina R Antonescu
Xp11 translocation renal cell carcinoma (RCC) are defined by chromosome translocations involving the Xp11 breakpoint which results in one of a variety of TFE3 gene fusions. TFE3 break-apart florescence in situ hybridization (FISH) assays are generally preferred to TFE3 immunohistochemistry (IHC) as a means of confirming the diagnosis in archival material, as FISH is less sensitive to the variable fixation which can result in false positive or false negative IHC. Prompted by a case report in the cytogenetics literature, we identify 3 cases of Xp11 translocation RCC characterized by a subtle chromosomal inversion involving the short arm of the X chromosome, resulting in an RBM10-TFE3 gene fusion...
May 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28288037/xp11-translocation-renal-cell-carcinomas-rccs-with-rbm10-tfe3-gene-fusion-demonstrating-melanotic-features-and-overlapping-morphology-with-t-6-11-rcc-interest-and-diagnostic-pitfall-in-detecting-a-paracentric-inversion-of-tfe3
#3
MULTICENTER STUDY
Qiu-Yuan Xia, Xiao-Tong Wang, Xue-Mei Zhan, Xiao Tan, Hao Chen, Yi Liu, Shan-Shan Shi, Xuan Wang, Xue Wei, Sheng-Bing Ye, Rui Li, Heng-Hui Ma, Zhen-Feng Lu, Xiao-Jun Zhou, Qiu Rao
Xp11 translocation renal cell carcinomas (RCC) are characterized by several different translocations involving the TFE3 gene. Tumors with different specific gene fusions may have different clinicopathologic manifestations. Only 3 RBM10-TFE3 RCCs have been reported to date. Here, we added 4 cases of this rare type of tumors with clinicopathologic, immunohistochemical, molecular, and ultrastructural analyses. Most tumors had similar patterns with mixed architectures as follows: acinar, tubular and papillary patterns of epithelioid cells combined with sheets of small cells with "pseudorosette-like" architectures, mimicking the typical morphology of t(6;11) RCC...
May 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28091594/functional-analysis-reveals-that-rbm10-mutations-contribute-to-lung-adenocarcinoma-pathogenesis-by-deregulating-splicing
#4
Jiawei Zhao, Yue Sun, Yin Huang, Fan Song, Zengshu Huang, Yufang Bao, Ji Zuo, David Saffen, Zhen Shao, Wen Liu, Yongbo Wang
RBM10 is an RNA splicing regulator that is frequently mutated in lung adenocarcinoma (LUAD) and has recently been proposed to be a cancer gene. How RBM10 mutations observed in LUAD affect its normal functions, however, remains largely unknown. Here integrative analysis of RBM10 mutation and RNA expression data revealed that LUAD-associated RBM10 mutations exhibit a mutational spectrum similar to that of tumor suppressor genes. In addition, this analysis showed that RBM10 mutations identified in LUAD patients lacking canonical oncogenes are associated with significantly reduced RBM10 expression...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27763814/the-rna-binding-landscape-of-rbm10-and-its-role-in-alternative-splicing-regulation-in-models-of-mouse-early-development
#5
Julie Rodor, David R FitzPatrick, Eduardo Eyras, Javier F Cáceres
Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing...
January 2, 2017: RNA Biology
https://www.readbyqxmd.com/read/27545006/elucidating-genomic-characteristics-of-lung-cancer-progression-from-in-situ-to-invasive-adenocarcinoma
#6
Chanida Vinayanuwattikun, Florence Le Calvez-Kelm, Behnoush Abedi-Ardekani, David Zaridze, Anush Mukeria, Catherine Voegele, Maxime Vallée, Dewajani Purnomosari, Nathalie Forey, Geoffroy Durand, Graham Byrnes, James Mckay, Paul Brennan, Ghislaine Scelo
To examine the diversity of somatic alterations and clonal evolution according to aggressiveness of disease, nineteen tumor-blood pairs of 'formerly bronchiolo-alveolar carcinoma (BAC)' which had been reclassified into preinvasive lesion (adenocarcinoma in situ; AIS), focal invasive lesion (minimally invasive adenocarcinoma; MIA), and invasive lesion (lepidic predominant adenocarcinoma; LPA and non-lepidic predominant adenocarcinoma; non-LPA) according to IASLC/ATS/ERS 2011 classification were explored by whole exome sequencing...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27395407/three-novel-missense-mutations-in-the-filamin-b-gene-are-associated-with-isolated-congenital-talipes-equinovarus
#7
Haiou Yang, Zhaojing Zheng, Haiqing Cai, Huimin Li, Xingchen Ye, Xiaoqing Zhang, Zhigang Wang, Qihua Fu
Congenital talipes equinovarus (CTEV) is one of the most common musculoskeletal disorders. Genetic factors have been suggested to be an important contributor to its pathogenesis. Some genes, including PITX1, TBX4, and RBM10, have been associated with CTEV. We aimed to determine the disease-causing mutations in Chinese patients with isolated CTEV. Genomic DNA was extracted from peripheral blood samples of a three-generation pedigree and 53 sporadic patients with CTEV. Whole-exome sequencing and Sanger sequencing were used to identify and validate disease-causing mutations, respectively...
October 2016: Human Genetics
https://www.readbyqxmd.com/read/27149842/genomic-correlates-of-immune-cell-infiltrates-in-colorectal-carcinoma
#8
Marios Giannakis, Xinmeng Jasmine Mu, Sachet A Shukla, Zhi Rong Qian, Ofir Cohen, Reiko Nishihara, Samira Bahl, Yin Cao, Ali Amin-Mansour, Mai Yamauchi, Yasutaka Sukawa, Chip Stewart, Mara Rosenberg, Kosuke Mima, Kentaro Inamura, Katsuhiko Nosho, Jonathan A Nowak, Michael S Lawrence, Edward L Giovannucci, Andrew T Chan, Kimmie Ng, Jeffrey A Meyerhardt, Eliezer M Van Allen, Gad Getz, Stacey B Gabriel, Eric S Lander, Catherine J Wu, Charles S Fuchs, Shuji Ogino, Levi A Garraway
Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome sequencing of 619 incident colorectal cancers (CRCs) and integrated the results with tumor immunity, pathology, and survival data. We identified recurrently mutated genes in CRC, such as BCL9L, RBM10, CTCF, and KLF5, that were not previously appreciated in this disease. Furthermore, we investigated the genomic correlates of immune-cell infiltration and found that higher neoantigen load was positively associated with overall lymphocytic infiltration, tumor-infiltrating lymphocytes (TILs), memory T cells, and CRC-specific survival...
April 14, 2016: Cell Reports
https://www.readbyqxmd.com/read/26998913/identification-by-ffpe-rna-seq-of-a-new-recurrent-inversion-leading-to-rbm10-tfe3-fusion-in-renal-cell-carcinoma-with-subtle-tfe3-break-apart-fish-pattern
#9
Pierre-Alexandre Just, Franck Letourneur, Christelle Pouliquen, Florence Dome, Anne Audebourg, Philippe Biquet, Michel Vidaud, Benoit Terris, Mathilde Sibony, Eric Pasmant
Gene fusions involving TFE3 defines the "Xp11.2 translocations" subclass of renal cell carcinomas (RCCs) belonging to the MiT family translocation RCC. Four recurrent TFE3 fusion partners were identified to date: PRCC, ASPSCR1, SFPQ, and NONO. Break-apart TFE3 fluorescence in situ hybridization (FISH) on formalin-fixed and paraffin-embedded (FFPE) tissue sections is currently the gold standard for identification of TFE3 rearrangements. Herein, we report a case of RCC with a morphological appearance of Xp11...
2016: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/26853560/tumor-suppressor-properties-of-the-splicing-regulatory-factor-rbm10
#10
Jordi Hernández, Elias Bechara, Doerte Schlesinger, Javier Delgado, Luis Serrano, Juan Valcárcel
RBM10 is an RNA binding protein and alternative splicing regulator frequently mutated in lung adenocarcinomas. Recent results indicate that RBM10 inhibits proliferation of lung cancer cells by promoting skipping of exon 9 of the gene NUMB, a frequent alternative splicing change in lung cancer generating a negative regulator of Notch signaling. Complementing these observations, we show that knock down of RBM10 in human cancer cells enhances growth of mouse tumor xenografts, confirming that RBM10 acts as a tumor suppressor, while knock down of an oncogenic mutant version of RBM10 reduces xenograft tumor growth...
2016: RNA Biology
https://www.readbyqxmd.com/read/26784654/co-and-post-transcriptional-regulation-of-rbm5-and-rbm10-in-mouse-cells-as-evidenced-by-tissue-specific-developmental-and-disease-associated-variation-of-splice-variant-and-protein-expression-levels
#11
Bartholomew Ozuemba, Twinkle J Masilamani, Julie J Loiselle, Benjamin Koenderink, Kaitlin A Vanderbeck, Jose Knee, Céline Larivière, Leslie C Sutherland
BACKGROUND: Expression and function of the two RNA binding proteins and regulators of alternative splicing, RBM5 and RBM10, have largely been studied in human tissue and cell lines. The objective of the study described herein was to examine their expression in mouse tissue, in order to lay the framework for comprehensive functional studies using mouse models. METHODS: All RNA variants of Rbm5 and Rbm10 were examined in a range of normal primary mouse tissues. RNA and protein were examined in differentiating C2C12 myoblasts and in denervated and dystonin-deficient mouse skeletal muscle...
April 10, 2016: Gene
https://www.readbyqxmd.com/read/26712279/nuclear-magnetic-resonance-structure-of-a-novel-globular-domain-in-rbm10-containing-ocre-the-octamer-repeat-sequence-motif
#12
Bryan T Martin, Pedro Serrano, Michael Geralt, Kurt Wüthrich
The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets...
January 5, 2016: Structure
https://www.readbyqxmd.com/read/26659391/post-transcriptional-regulation-of-rbm5-expression-in-undifferentiated-h9c2-myoblasts
#13
Julie J Loiselle, Sarah J Tessier, Leslie C Sutherland
We previously examined the expression of Rbm5 during myoblast differentiation and found significantly more protein in the early stages of skeletal myoblast differentiation than during the later stages. We decided to determine if this elevated level was necessary for differentiation. Our hypothesis was that if high levels of Rbm5 protein expression were necessary for the initiation of skeletal myoblast differentiation, then inhibition of expression would prevent differentiation. Our long-term objective is to inhibit Rbm5 expression and examine the effect on H9c2 differentiation...
March 2016: In Vitro Cellular & Developmental Biology. Animal
https://www.readbyqxmd.com/read/25889998/insight-into-the-role-of-alternative-splicing-within-the-rbm10v1-exon-10-tandem-donor-site
#14
Sarah J Tessier, Julie J Loiselle, Anne McBain, Celine Pullen, Benjamin W Koenderink, Justin G Roy, Leslie C Sutherland
BACKGROUND: RBM10 is an RNA binding protein involved in the regulation of transcription, alternative splicing and message stabilization. Mutations in RBM10, which maps to the X chromosome, are associated with TARP syndrome, lung and pancreatic cancers. Two predominant isoforms of RBM10 exist, RBM10v1 and RBM10v2. Both variants have alternate isoforms that differ by one valine residue, at amino acid 354 (RBM10v1) or 277 (RBM10v2). It was recently observed that a novel point mutation at amino acid 354 of RBM10v1, replacing valine with glutamic acid, correlated with preferential expression of an exon 11 inclusion variant of the proliferation regulatory protein NUMB, which is upregulated in lung cancer...
2015: BMC Research Notes
https://www.readbyqxmd.com/read/25855536/whole-exome-sequencing-of-pancreatic-cancer-defines-genetic-diversity-and-therapeutic-targets
#15
Agnieszka K Witkiewicz, Elizabeth A McMillan, Uthra Balaji, GuemHee Baek, Wan-Chi Lin, John Mansour, Mehri Mollaee, Kay-Uwe Wagner, Prasad Koduru, Adam Yopp, Michael A Choti, Charles J Yeo, Peter McCue, Michael A White, Erik S Knudsen
Pancreatic ductal adenocarcinoma (PDA) has a dismal prognosis and insights into both disease etiology and targeted intervention are needed. A total of 109 micro-dissected PDA cases were subjected to whole-exome sequencing. Microdissection enriches tumour cellularity and enhances mutation calling. Here we show that environmental stress and alterations in DNA repair genes associate with distinct mutation spectra. Copy number alterations target multiple tumour suppressive/oncogenic loci; however, amplification of MYC is uniquely associated with poor outcome and adenosquamous subtype...
April 9, 2015: Nature Communications
https://www.readbyqxmd.com/read/25777194/insight-into-the-role-of-alternative-splicing-within-the-rbm10v1-exon-10-tandem-donor-site
#16
Sarah J Tessier, Julie J Loiselle, Anne McBain, Celine Pullen, Benjamin W Koenderink, Justin G Roy, Leslie C Sutherland
BACKGROUND: RBM10 is an RNA binding protein involved in the regulation of transcription, alternative splicing and message stabilization. Mutations in RBM10, which maps to the X chromosome, are associated with TARP syndrome, lung and pancreatic cancers. Two predominant isoforms of RBM10 exist, RBM10v1 and RBM10v2. Both variants have alternate isoforms that differ by one valine residue, at amino acid 354 (RBM10v1) or 277 (RBM10v2). It was recently observed that a novel point mutation at amino acid 354 of RBM10v1, replacing valine with glutamic acid, correlated with preferential expression of an exon 11 inclusion variant of the proliferation regulatory protein NUMB, which is upregulated in lung cancer...
December 2015: BMC Research Notes
https://www.readbyqxmd.com/read/25586139/the-nuclear-splicing-factor-rna-binding-motif-5-promotes-caspase-activation-in-human-neuronal-cells-and-increases-after-traumatic-brain-injury-in-mice
#17
Travis C Jackson, Lina Du, Keri Janesko-Feldman, Vincent A Vagni, Cameron Dezfulian, Samuel M Poloyac, Edwin K Jackson, Robert S B Clark, Patrick M Kochanek
Splicing factors (SFs) coordinate nuclear intron/exon splicing of RNA. Splicing factor disturbances can cause cell death. RNA binding motif 5 (RBM5) and 10 (RBM10) promote apoptosis in cancer cells by activating detrimental alternative splicing of key death/survival genes. The role(s) of RBM5/10 in neurons has not been established. Here, we report that RBM5 knockdown in human neuronal cells decreases caspase activation by staurosporine. In contrast, RBM10 knockdown augments caspase activation. To determine whether brain injury alters RBM signaling, we measured RBM5/10 protein in mouse cortical/hippocampus homogenates after controlled cortical impact (CCI) traumatic brain injury (TBI) plus hemorrhagic shock (CCI+HS)...
April 2015: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/25437182/proteomic-profile-and-in-silico-analysis-in-metastatic-melanoma-with-and-without-braf-mutation
#18
Vito Michele Garrisi, Sabino Strippoli, Simona De Summa, Rosamaria Pinto, Antonella Perrone, Gabriella Guida, Amalia Azzariti, Michele Guida, Stefania Tommasi, Tommasi Stefania
INTRODUCTION: Selective inhibitors of BRAF, vemurafenib and dabrafenib are the standard of care for metastatic melanoma patients with BRAF V600, while chemotherapy continued to be widely used in BRAF wild type patients. MATERIALS AND METHODS: In order to discover novel candidate biomarkers predictive to treatment, serum of 39 metastatic melanoma vemurafenib (n = 19) or chemotherapy (n = 20) treated patients at baseline, at disease control and at progression, were analyzed using SELDI-TOF technology...
2014: PloS One
https://www.readbyqxmd.com/read/25389269/binding-site-discovery-from-nucleic-acid-sequences-by-discriminative-learning-of-hidden-markov-models
#19
Jonas Maaskola, Nikolaus Rajewsky
We present a discriminative learning method for pattern discovery of binding sites in nucleic acid sequences based on hidden Markov models. Sets of positive and negative example sequences are mined for sequence motifs whose occurrence frequency varies between the sets. The method offers several objective functions, but we concentrate on mutual information of condition and motif occurrence. We perform a systematic comparison of our method and numerous published motif-finding tools. Our method achieves the highest motif discovery performance, while being faster than most published methods...
December 1, 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/25079552/comprehensive-molecular-profiling-of-lung-adenocarcinoma
#20
(no author information available yet)
Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification...
July 31, 2014: Nature
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