Long Non-coding RNA Signature Research Articles

Significance of Long Noncoding RNAs in Regenerative Medicine

Significance of Long Noncoding RNAs in Regenerative Medicine

The Fusion Gene Landscape in Multiple Myeloma, with Clinical Impact

Background: Gene fusions play an important role in aberrant cellular biology as well as development and progression of cancer. Expression of fusion genes such as PML-RAR drives the transformation in APL and provides important targets for therapy. However, in multiple Myeloma (MM), a heterogeneous disease characterized by genomic instability, frequent gains and losses of DNA, and a diverse mutational landscape, only the well characterized MMSET-IGH fusion product has been reported. Here we investigate the fusion gene landscape in multiple myeloma, and its possible impact on survival.Method: Deep RNA-Seq was performed on purified MM cells from 430 newly-diagnosed MM patients, 20 normal individuals and 71 cell-lines; data were analyzed for gene expression profiles, long-non coding RNA signatures, and both novel and known fusion genes using two common algorithms: TopHat and MapSplice. MM characteristics, cytogenetic and FISH as well as clinical survival outcomes were also analyzed and correlated with genomic data.Results: After filtering candidate fusions linking genes belonging to the same family, we identified 416 different candidates in myeloma patients, 40 % of which identified either IGH or Kappa as a partner. IGH fusion partners included the previously described and validated WHSC1 and B2M genes, as well as over 50 new candidates, while more than 70 different partners were found to be fused with Kappa. These genes exhibit functional enrichment of positive regulators of the cytokine-mediated signaling pathway, negative regulation of myeloid cell differentiation, negative regulation of interleukin-6 production, as well as others. 31% of patients presented no fusions, and another 32% presented a single fusion event. The other 37% presented at least 2 fusion candidates, with up to 27 different candidates. Similar patterns were observed in cell-lines, with 196 unique candidates identified, only 16% of which involving IGH or kappa. However, all partners were found in at least one patient as well. Only 12% of cell-lines exhibited no fusion, and another 14% presented only one fusion. On average, 3 fusions were identified per cell-line, with a maximum of 10. Validation of some these fusion genes is required to understand their functional role. Importantly, although having IgH-or kappa-related fusions did not affect patient outcome by themselves, patients with high numbers of fusion candidates had worse event-free survival.Conclusion: Our data describes a diverse and rich fusion gene landscape in Multiple Myeloma. Similar to mutational profiles, there is no predominant fusion gene driving the disease process. Association of poor prognosis with a higher number of fusions may indicate that genomic instability plays an important role in the biology of Multiple Myeloma. DisclosuresNo relevant conflicts of interest to declare.

Functional significance of long non-coding RNAs in breast cancer.

Most of the genome is transcribed to transcripts of no protein-coding potential. However, these transcripts do not represent transcriptional 'noise', rather they play an important role in cellular metabolism and development. Non-coding transcripts of 200 bases to 100kb length are termed as long non-coding RNAs, majority of which are yet to be characterised thoroughly. Long non-coding RNAs (lncRNAs) play a significant role in cellular process ranging from transcriptional to post-transcriptional regulation. In this review, we highlight the recent efforts to characterise the major functions of lncRNAs in breast cancer. lncRNA expression is altered in several cancer types. Further, the aberrant regulation of lncRNAs promotes tumour development as they are involved in several cancer-associated pathways.

Guest editorial: noncoding RNA in hematopoietic system

Following the completion of the Human Genome Project, which revealed that the number of the protein-coding genes in human and mouse is nearly the same, many researchers began to be interested in non-coding RNAs, which are transcribed from so-called ‘‘junk DNA’’, a name suggesting these are no more than genomic garbage. This genomic region does not code protein, and shows considerable interspecies and inter-individual diversity, suggesting that it has the potential to be key to explaining the difference between human and mice, and between human individuals. Early studies focused on small RNAs including miRNAs, endo siRNAs, and piRNA, but more recently, the biological significance of long non-coding RNAs has begun to come into focus. In the hematopoietic system, Chang-Zheng Chen and Harvey Lodish first demonstrated that miR-181 affects B cell fate in 2004 [1]. Klaus Rajewsky subsequently established miR-155 deficient mice in 2006, showing that miR155 is critically important in B cell development and activation [2]. A body of work that accumulated thereafter clearly revealed that miRNAs are involved in this and other cellular biological systems. The study of long non-coding RNAs in the hematopoietic system thus remains in its early stages. However, a number of recent studies have yielded exciting new insights. This issue includes two excellent review articles [3, 4], in addition to one by our own groups [5]. Ikeda et al. who have long focused on the function of miRNAs in hematological malignancy, thoroughly review studies of miRNAs in T cell malignancy, including their recent new findings, as well as areas needing further investigation. This promises to be one of the most informative reviews on this important topic. The biological significance of long non-coding RNAs has long remained hidden due in part to its poor conservation. For the first time, Alvarez-Dominguez et al. [6] describe a number of characteristic features, including developmental stage-specific expression profiles, which suggest that long non-coding RNAs potentially have important biological functions in the hematopoietic system. The group, a leader in this field, reviews and discusses recent findings of long non-coding RNAs in hematopoietic system, with a special focus on phenotypes made possible by gene targeting technology, giving important new insights into the roles played by long non-coding RNAs in the hematopoietic system. Although still in its early days, this area of inquiry shows tremendous promise for the future. In the final review, our group focuses on recent developments involving cell fate-related miRNAs, non-canonical small RNAs, and secretory small RNAs in hematopoietic system. I hope that this month’s ‘‘Progress in Hematology’’ will help readers to understand recent progress in our understanding of the biological significance of noncoding RNAs in the hematopoietic system.

Long Non-Coding RNAs Involved in Cancer Development and Cell Fate Determination

The possible physiological significance of long non-coding RNAs (lncRNAs) has only recently been recognized. Technical innovations such as the super high-resolution tiling array and deep sequencing technology have indicated their importance. It has been proposed that lncRNAs such as HOTAIR are involved in the recruitment of chromatin modifiers to the target genes. The lncRNA ANRIL has been reported to be associated with a Polycomb complex, recruiting it to the target gene INK4 locus where it suppresses transcription via histone modification. Other lncRNAs such as Kcnq1ot1, AIR and Xist have also been found to recruit chromatin modifiers to their target loci. In this review, we discuss the function of lncRNAs such as HOTAIR, ANRIL, Kcnq1ot1, and Xist which recruit chromatin modifiers to target genes and discuss their involvement in cancer development and aggressiveness, and other cell fate determination.