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

Lee, Carolyn; Ungewickell, Alexander; Bhaduri, Aparna; Qu, Kun; Webster, Dan E.; Armstrong, Randall; Weng, Wei; Aros, Cody J.; Mah, Angela; Chen, Richard; Lin, Meihong; Sundram, Uma; Chang, Howard Y.; Kretz, Markus; Kim, Youn H.; Khavari, Paul A.

doi:10.1182/blood-2012-04-423061

Cited by 80 publications

(74 citation statements)

References 51 publications

(68 reference statements)

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“…2H). These observations are consistent with the weak expression of lncRNAs in several vertebrates and biological systems [23,27,29,73]. We calculated an expression specificity score based on the Shannon (information theoretic measure) entropy Q value to estimate the abundance specificity in the various testicular cell types [74] as previously suggested [23,29].…”

Section: Genomic Characterization Of Tuts Confirmed Lncrna Features Amentioning

confidence: 68%

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

Chalmel

Lardenois

Evrard

et al. 2014

Biology of Reproduction

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Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-encoding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in rat, using next-generation sequencing technology and highly enriched testicular cell populations. Among 20 424 high-confidence transcripts reconstructed, we defined a stringent set of 1419 long multi-exonic unannotated transcripts expressed in the testis (testis-expressed unannotated transcripts [TUTs]). TUTs were divided into 7 groups with different expression patterns. Most TUTs share many of the characteristics of vertebrate long noncoding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of noncoding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource for novel loci expressed during spermatogenesis that significantly contributes to rat genome annotation.

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Section: Genomic Characterization Of Tuts Confirmed Lncrna Features Amentioning

confidence: 68%

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

Chalmel

Lardenois

Evrard

et al. 2014

Biology of Reproduction

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“…Aberrations in signal transducers and transcription factors have been reported in SS studies, such as Jun B, JunD, TGFBR2, STAT3, STAT4, CDKN1C, CTLA-4, GATA3, AHI-1, SATB1, PDCD10, and NOTCH1. 4,16,17,[32][33][34][35][36] Several of these dysregulated genes (TGFBR2, GATA3, STAT3, SATB1, and NOTCH1) are involved in the signal cascades governing T-cell development. [37][38][39][40][41] Our recent observation of aberrant TOX upregulation in MF, subsequently confirmed by McGirt et al, 10 prompted us to ask whether TOX is also upregulated in SS, the advanced CTCL, and whether TOX contributes to the development of CTCL.…”

Section: Discussionmentioning

confidence: 99%

Evidence of an oncogenic role of aberrant TOX activation in cutaneous T-cell lymphoma

Huang

Jiang

et al. 2015

Blood

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“…In general, lncRNAs are a heterogeneous class of transcripts without any single unifying feature except for an arbitrary minimum length of 200 nucleotides and an apparent lack of protein-coding potential (Guttman et al, 2013; Rinn and Chang, 2012; Ulitsky and Bartel, 2013). Despite this, lncRNAs have been shown to be important in development (Boumil and Lee, 2001; Grote et al, 2013; Guttman et al, 2011; Klattenhoff et al, 2013; Kretz et al, 2013; Loewer et al, 2010; Rinn et al, 2007) and disease (Gomez et al, 2013; Gupta et al, 2010; Huarte et al, 2010; Lee et al, 2012; Yildirim et al, 2013) in many different cell types, suggesting a ubiquitous role in regulation of cellular state. Although the molecular mechanisms by which lncRNAs act are poorly understood, they have been implicated as regulators of diverse cellular processes including regulation of cell cycle (Hung et al, 2011), RNA stability (Kretz et al, 2013), and chromatin structure (Gupta et al, 2010; Lee, 2012; Tsai et al, 2010; Wang et al, 2011b; Yang et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

Trimarchi

Bilal

Ntziachristos

et al. 2014

Cell

391

332

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Accumulating evidence demonstrated that while a small minority of the human genome encodes proteins a large portion of the genome encodes non-protein coding transcripts. Thus it has been suggested that such RNAs, including the recently described family of long non-coding RNAs (lncRNA) are key regulators of cellular homeostasis and transformation leading to tumorigenesis. Here we tested this hypothesis focusing on the role of lncRNAs in T cell leukemia (T-ALL), a pediatric blood cancer, characterized by Notch pathway activation. Using RNA-Sequencing we identified and catalogued a large number of T-ALL-specific lncRNAs targeted by the NOTCH pathway. We further focused on a single such transcript, LUNAR1 (LeUkemia-induced Non-coding Activator RNA-1), and demonstrated that through chromosomal looping it is able to control the expression of the IGF1R gene, IGF1 signaling and growth of T-ALL, providing evidence that suggests that lncRNAs could be used as biomarkers as well as therapy targets in human cancer.

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

Abstract: Sé zary syndrome (SS) is an aggressive cutaneous T-cell lymphoma (CTCL

Cited by 80 publications

References 51 publications

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

Evidence of an oncogenic role of aberrant TOX activation in cutaneous T-cell lymphoma

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

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