메뉴 건너뛰기




Volumn 120, Issue 16, 2012, Pages 3288-3297

Transcriptome sequencing in Sézary syndrome identifies Sézary cell and mycosis fungoides-associated IncRNAs and novel transcripts

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LONG NON CODING RNA; PROTEIN KINASE B; RNA; TRANSCRIPTOME; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; LONG UNTRANSLATED RNA; MESSENGER RNA; TUMOR MARKER;

EID: 84868149174     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2012-04-423061     Document Type: Article
Times cited : (78)

References (49)
  • 1
    • 0042964834 scopus 로고    scopus 로고
    • Long-term outcome of 525 patients with mycosis fungoides and Sézary syndrome: Clinical prognostic factors and risk for disease progression
    • DOI 10.1001/archderm.139.7.857
    • Kim YH, Liu HL, Mraz-Gernhard S, Varghese A, Hoppe RT. Long-term outcome of 525 patients with mycosis fungoides and Sezary syndrome: clinical prognostic factors and risk for disease progression. Arch Dermatol. 2003;139(7):857-866. (Pubitemid 36898920)
    • (2003) Archives of Dermatology , vol.139 , Issue.7 , pp. 857-866
    • Kim, Y.H.1    Liu, H.L.2    Mraz-Gernhard, S.3    Varghese, A.4    Hoppe, R.T.5
  • 2
    • 79961202865 scopus 로고    scopus 로고
    • Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
    • Prensner JR, Iyer MK, Balbin OA, et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol. 2011;29(8):742-749.
    • (2011) Nat Biotechnol. , vol.29 , Issue.8 , pp. 742-749
    • Prensner, J.R.1    Iyer, M.K.2    Balbin, O.A.3
  • 3
    • 79953748673 scopus 로고    scopus 로고
    • A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
    • Wang KC, Yang YW, Liu B, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011;472(7341):120- 124.
    • (2011) Nature , vol.472 , Issue.7341 , pp. 120-124
    • Wang, K.C.1    Yang, Y.W.2    Liu, B.3
  • 4
    • 82155186923 scopus 로고    scopus 로고
    • The emergence of IncRNAs in cancer biology
    • Prensner JR, Chinnaiyan AM. The emergence of IncRNAs in cancer biology. Cancer Discov. 2011;1(5):391-407.
    • (2011) Cancer Discov. , vol.1 , Issue.5 , pp. 391-407
    • Prensner, J.R.1    Chinnaiyan, A.M.2
  • 6
    • 0029666161 scopus 로고    scopus 로고
    • Sezary syndrome T-cell clones display T-helper 2 cytokines and express the accessory factor-1 (interferon- receptor -chain)
    • Dummer R, Heald PW, Nestle FO, et al. Sézary syndrome T-cell clones display T-helper 2 cytokines and express the accessory factor-1 (interferon-gamma receptor beta-chain). Blood. 1996;88(4):1383-1389. (Pubitemid 26276814)
    • (1996) Blood , vol.88 , Issue.4 , pp. 1383-1389
    • Dummer, R.1    Heald, P.W.2    Nestle, F.O.3    Ludwig, E.4    Laine, E.5    Hemmi, S.6    Burg, G.7
  • 7
    • 0026721931 scopus 로고
    • Establishment of two continuous T-cell strains from a single plaque of a patient with mycosis fungoides
    • Kaltoft K, Bisballe S, Dyrberg T, et al. Establishment of two continuous T-cell strains from a single plaque of a patient with mycosis fungoides. In Vitro Cell Dev Biol. 1992;28A(3 Pt 1):161-167.
    • (1992) Vitro Cell Dev Biol. , vol.28 A , Issue.3 PART 1 , pp. 161-167
    • Kaltoft, K.1    Bisballe, S.2    Dyrberg, T.3
  • 8
  • 9
    • 77649314169 scopus 로고    scopus 로고
    • 3+-end sequencing for expression quantification (3SEQ) from archival tumor samples
    • Beck AH, Weng Z, Witten DM, et al. 3+-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One. 2010;5(1):e8768.
    • (2010) PLoS One. , vol.5 , Issue.1
    • Beck, A.H.1    Weng, Z.2    Witten, D.M.3
  • 11
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-1111.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 12
    • 80051941094 scopus 로고    scopus 로고
    • Identification of novel transcripts in annotated genomes using RNA-Seq
    • Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011;27(17):2325-2329.
    • (2011) Bioinformatics , vol.27 , Issue.17 , pp. 2325-2329
    • Roberts, A.1    Pimentel, H.2    Trapnell, C.3    Pachter, L.4
  • 13
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multiexonic structure of IincRNAs
    • Guttman M, Garber M, Levin JZ, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multiexonic structure of IincRNAs. Nat Biotechnol. 2010;28(5):503-510.
    • (2010) Nat Biotechnol. , vol.28 , Issue.5 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3
  • 14
    • 79960264362 scopus 로고    scopus 로고
    • Fulllength transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr MG, Haas BJ, Yassour M, et al. Fulllength transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644-652.
    • (2011) Nat Biotechnol. , vol.29 , Issue.7 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3
  • 17
    • 75549091651 scopus 로고    scopus 로고
    • ENCODE whole-genome data in the UCSC Genome Browser
    • Database issue
    • Rosenbloom KR, Dreszer TR, Pheasant M, et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010;38(Database issue):D620-D625.
    • (2010) Nucleic Acids Res. , vol.38
    • Rosenbloom, K.R.1    Dreszer, T.R.2    Pheasant, M.3
  • 18
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • DOI 10.1093/nar/gkl842
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated nonredundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35(Database issue):D61-D65. (Pubitemid 46056171)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 20
    • 79953177468 scopus 로고    scopus 로고
    • Aligning short sequencing reads with Bowtie
    • Chapter 11:Unit 11.7
    • Langmead B. Aligning short sequencing reads with Bowtie. Curr Protoc Bioinformatics. 2010; Chapter 11:Unit 11.7.
    • (2010) Curr Protoc Bioinformatics
    • Langmead, B.1
  • 21
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25(18):1915-1927.
    • (2011) Genes Dev. , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3
  • 22
    • 79551634894 scopus 로고    scopus 로고
    • PHAST and RPHAST: Phylogenetic analysis with space/time models
    • Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinformatics. 2011;12(1):41-51.
    • (2011) Brief Bioinformatics. , vol.12 , Issue.1 , pp. 41-51
    • Hubisz, M.J.1    Pollard, K.S.2    Siepel, A.3
  • 23
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski M, Schein J, Birol I, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639-1645.
    • (2009) Genome Res. , vol.19 , Issue.9 , pp. 1639-1645
    • Krzywinski, M.1    Schein, J.2    Birol, I.3
  • 24
    • 79959446962 scopus 로고    scopus 로고
    • PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions
    • Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011;27(13):i275-i282.
    • (2011) Bioinformatics , vol.27 , Issue.13
    • Lin, M.F.1    Jungreis, I.2    Kellis, M.3
  • 25
    • 79958135926 scopus 로고    scopus 로고
    • Molecular signatures database (MSigDB) 3.0
    • Liberzon A, Subramanian A, Pinchback R, et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27(12):1739-1740.
    • (2011) Bioinformatics , vol.27 , Issue.12 , pp. 1739-1740
    • Liberzon, A.1    Subramanian, A.2    Pinchback, R.3
  • 26
    • 84859770226 scopus 로고    scopus 로고
    • Rapid identification of non-human sequences in high-throughput sequencing datasets
    • Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA. Rapid identification of non-human sequences in high-throughput sequencing datasets. Bioinformatics. 2012;28(8):1174-1175.
    • (2012) Bioinformatics , vol.28 , Issue.8 , pp. 1174-1175
    • Bhaduri, A.1    Qu, K.2    Lee, C.S.3    Ungewickell, A.4    Khavari, P.A.5
  • 27
    • 79957829805 scopus 로고    scopus 로고
    • De-Fuse: An algorithm for gene fusion discovery in tumor RNA-Seq data
    • McPherson A, Hormozdiari F, Zayed A, et al. De-Fuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011;7(5):e1001138.
    • (2011) PLoS Comput Biol. , vol.7 , Issue.5
    • McPherson, A.1    Hormozdiari, F.2    Zayed, A.3
  • 28
    • 80054003528 scopus 로고    scopus 로고
    • Chimera-Scan: A tool for identifying chimeric transcription in sequencing data
    • Iyer MK, Chinnaiyan AM, Maher CA. Chimera-Scan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011;27(20):2903- 2904.
    • (2011) Bioinformatics , vol.27 , Issue.20 , pp. 2903-2904
    • Iyer, M.K.1    Chinnaiyan, A.M.2    Maher, C.A.3
  • 29
  • 30
    • 80053571383 scopus 로고    scopus 로고
    • Evolving insights in the pathogenesis and therapy of cutaneous T-cell lymphoma (mycosis fungoides and Sezary syndrome)
    • Wong HK, Mishra A, Hake T, Porcu P. Evolving insights in the pathogenesis and therapy of cutaneous T-cell lymphoma (mycosis fungoides and Sezary syndrome). Br J Haematol. 2011;155(2):150-166.
    • (2011) Br J Haematol. , vol.155 , Issue.2 , pp. 150-166
    • Wong, H.K.1    Mishra, A.2    Hake, T.3    Porcu, P.4
  • 31
    • 4143079424 scopus 로고    scopus 로고
    • Aberrant expression of the tyrosine kinase receptor EphA4 and the transcription factor twist in Sézary syndrome identified by gene expression analysis
    • DOI 10.1158/0008-5472.CAN-04-1253
    • van Doorn R, Dijkman R, Vermeer MH, et al. Aberrant expression of the tyrosine kinase receptor EphA4 and the transcription factor twist in Sézary syndrome identified by gene expression analysis. Cancer Res. 2004;64(16):5578-5586. (Pubitemid 39095552)
    • (2004) Cancer Research , vol.64 , Issue.16 , pp. 5578-5586
    • Van Doorn, R.1    Dijkman, R.2    Vermeer, M.H.3    Out-Luiting, J.J.4    Van Der Raaij-Helmer, E.M.H.5    Willemze, R.6    Tensen, C.P.7
  • 34
    • 33644755512 scopus 로고    scopus 로고
    • Down-regulating constitutive activation of the NF-B canonical pathway overcomes the resistance of cutaneous T-cell lymphoma to apoptosis
    • DOI 10.1182/blood-2005-06-2536
    • Sors A, Jean-Louis F, Pellet C, et al. Down-regulating constitutive activation of the NF-kappaB canonical pathway overcomes the resistance of cutaneous T-cell lymphoma to apoptosis. Blood. 2006;107(6):2354-2363. (Pubitemid 43345555)
    • (2006) Blood , vol.107 , Issue.6 , pp. 2354-2363
    • Sors, A.1    Jean-Louis, F.2    Pellet, C.3    Laroche, L.4    Dubertret, L.5    Courtois, G.6    Bachelez, H.7    Michel, L.8
  • 36
    • 77954526989 scopus 로고    scopus 로고
    • Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma
    • Palanisamy N, Ateeq B, Kalyana-Sundaram S, et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med. 2010;16(7):793-798.
    • (2010) Nat Med. , vol.16 , Issue.7 , pp. 793-798
    • Palanisamy, N.1    Ateeq, B.2    Kalyana-Sundaram, S.3
  • 37
    • 79952816655 scopus 로고    scopus 로고
    • MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers
    • Steidl C, Shah SP, Woolcock BW, et al. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature. 2011;471(7338):377-381.
    • (2011) Nature , vol.471 , Issue.7338 , pp. 377-381
    • Steidl, C.1    Shah, S.P.2    Woolcock, B.W.3
  • 39
    • 33947581390 scopus 로고    scopus 로고
    • The impact of translocations and gene fusions on cancer causation
    • DOI 10.1038/nrc2091, PII NRC2091
    • Mitelman F, Johansson B, Mertens F. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007;7(4):233-245. (Pubitemid 46480968)
    • (2007) Nature Reviews Cancer , vol.7 , Issue.4 , pp. 233-245
    • Mitelman, F.1    Johansson, B.2    Mertens, F.3
  • 40
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Web server issue
    • Kong L, Zhang Y, Ye Z-Q, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35(Web server issue):W345-W349.
    • (2007) Nucleic Acids Res. , vol.35
    • Kong, L.1    Zhang, Y.2    Ye, Z.-Q.3
  • 41
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Database issue
    • Finn RD, Mistry J, Tate J, et al. The Pfam protein families database. Nucleic Acids Res. 2010;38(Database issue):D211-D222.
    • (2010) Nucleic Acids Res. , vol.38
    • Finn, R.D.1    Mistry, J.2    Tate, J.3
  • 43
    • 77957096339 scopus 로고    scopus 로고
    • Notch1 as a potential therapeutic target in cutaneous T-cell lymphoma
    • Kamstrup MR, Gjerdrum LMR, Biskup E, et al. Notch1 as a potential therapeutic target in cutaneous T-cell lymphoma. Blood. 2010;116(14):2504-2512.
    • (2010) Blood , vol.116 , Issue.14 , pp. 2504-2512
    • Kamstrup, M.R.1    Gjerdrum, L.M.R.2    Biskup, E.3
  • 44
    • 76549083562 scopus 로고    scopus 로고
    • Inhibition of the K+ channel KCa3.1 ameliorates T cellmediated colitis
    • Di L, Srivastava S, Zhdanova O, et al. Inhibition of the K+ channel KCa3.1 ameliorates T cellmediated colitis. Proc Natl Acad Sci U S A. 2010;107(4):1541-1546.
    • (2010) Proc Natl Acad Sci U S A. , vol.107 , Issue.4 , pp. 1541-1546
    • Di, L.1    Srivastava, S.2    Zhdanova, O.3
  • 45
    • 78650478671 scopus 로고    scopus 로고
    • Increased programmed death-1 expression on CD4+ T cells in cutaneous T-cell lymphoma: Implications for immune suppression
    • Samimi S, Benoit B, Evans K, et al. Increased programmed death-1 expression on CD4+ T cells in cutaneous T-cell lymphoma: implications for immune suppression. Arch Dermatol. 2010;146(12):1382-1388.
    • (2010) Arch Dermatol. , vol.146 , Issue.12 , pp. 1382-1388
    • Samimi, S.1    Benoit, B.2    Evans, K.3
  • 46
    • 80054790597 scopus 로고    scopus 로고
    • Absence of TCR loci chromosomal translocations in cutaneous T-cell lymphomas
    • Salgado R, Gallardo F, Servitje O, et al. Absence of TCR loci chromosomal translocations in cutaneous T-cell lymphomas. Cancer Genet. 2011;204(7):405-409.
    • (2011) Cancer Genet. , vol.204 , Issue.7 , pp. 405-409
    • Salgado, R.1    Gallardo, F.2    Servitje, O.3
  • 47
    • 77954786287 scopus 로고    scopus 로고
    • Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis
    • Kondo T, Plaza S, Zanet J, et al. Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science. 2010;329(5989):336-339.
    • (2010) Science , vol.329 , Issue.5989 , pp. 336-339
    • Kondo, T.1    Plaza, S.2    Zanet, J.3
  • 48
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011;147(4):789-802.
    • (2011) Cell , vol.147 , Issue.4 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 49
    • 33746493350 scopus 로고    scopus 로고
    • A survey of mRNA sequences with a non-AUG start codon in RefSeq database
    • Tikole S, Sankararamakrishnan R. A survey of mRNA sequences with a non-AUG start codon in RefSeq database. J Biomol Struct Dyn. 2006;24(1):33-42.
    • (2006) J Biomol Struct Dyn. , vol.24 , Issue.1 , pp. 33-42
    • Tikole, S.1    Sankararamakrishnan, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.