Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq

被引:0
作者
Ruffle, Florence [1 ]
Reboul, Jerome [1 ]
Boureux, Anthony [1 ]
Guibert, Benoit [1 ]
Bessiere, Chloe [1 ,2 ]
Silva, Raissa [1 ]
Jourdan, Eric [3 ]
Gaillard, Jean-Baptiste [4 ]
Boland, Anne [5 ]
Deleuze, Jean-Francois [5 ]
Senamaud-Beaufort, Catherine [6 ]
Selimoglu-Buet, Dorothee [7 ]
Solary, Eric [7 ]
Gilbert, Nicolas [1 ]
Commes, Therese [1 ]
机构
[1] Univ Montpellier, IRMB, INSERM, 80 Rue Augustin Fliche, F-34295 Montpellier, France
[2] Univ Toulouse III Paul Sabatier, CRCT, Inserm, CNRS, F-31100 Toulouse, France
[3] Nimes Univ Hosp, Dept Hematol, F-30900 Nimes, France
[4] Montpellier Univ Hosp, Dept Mol Genet & Cytogen, F-34295 Montpellier, France
[5] Univ Paris Saclay, Ctr Natl Rech Genom Humaine, CEA, F-91057 Evry, France
[6] Univ PSL, Ecole Normale Super, Inst Biol ENS IBENS, Dept Biol,CNRS,INSERM,Genom ENS, F-75005 Paris, France
[7] Univ Paris Saclay, Gustave Roussy Canc Ctr, Dept Hematol, F-94805 Villejuif, France
关键词
GENE FUSIONS;
D O I
10.1093/nargab/lqae117
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
RNA sequencing technology combining short read and long read analysis can be used to detect chimeric RNAs in malignant cells. Here, we propose an integrated approach that uses k-mers to analyze indexed datasets. This approach is used to identify chimeric RNA in chronic myelomonocytic leukemia (CMML) cells, a myeloid malignancy that associates features of myelodysplastic and myeloproliferative neoplasms. In virtually every CMML patient, new generation sequencing identifies one or several somatic driver mutations, typically affecting epigenetic, splicing and signaling genes. In contrast, cytogenetic aberrations are currently detected in only one third of the cases. Nevertheless, chromosomal abnormalities contribute to patient stratification, some of them being associated with higher risk of poor outcome, e.g. through transformation into acute myeloid leukemia (AML). Our approach selects four chimeric RNAs that have been detected and validated in CMML cells. We further focus on NRIP1-MIR99AHG, as this fusion has also recently been detected in AML cells. We show that this fusion encodes three isoforms, including a novel one. Further studies will decipher the biological significance of such a fusion and its potential to improve disease stratification. Taken together, this report demonstrates the ability of a large-scale approach to detect chimeric RNAs in cancer cells. Graphical Abstract
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页数:14
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