title: Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia.
abstract: RNA-seq is a promising technology to re-sequence protein coding genes for the identification of single nucleotide variants (SNV), while simultaneously obtaining information on structural variations and gene expression perturbations. We asked whether RNA-seq is suitable for the detection of driver mutations in T-cell acute lymphoblastic leukemia (T-ALL). These leukemias are caused by a combination of gene fusions, over-expression of transcription factors and cooperative point mutations in oncogenes and tumor suppressor genes. We analyzed 31 T-ALL patient samples and 18 T-ALL cell lines by high-coverage paired-end RNA-seq. First, we optimized the detection of SNVs in RNA-seq data by comparing the results with exome re-sequencing data. We identified known driver genes with recurrent protein altering variations, as well as several new candidates including H3F3A, PTK2B, and STAT5B. Next, we determined accurate gene expression levels from the RNA-seq data through normalizations and batch effect removal, and used these to classify patients into T-ALL subtypes. Finally, we detected gene fusions, of which several can explain the over-expression of key driver genes such as TLX1, PLAG1, LMO1, or NKX2-1; and others result in novel fusion transcripts encoding activated kinases (SSBP2-FER and TPM3-JAK2) or involving MLLT10. In conclusion, we present novel analysis pipelines for variant calling, variant filtering, and expression normalization on RNA-seq data, and successfully applied these for the detection of translocations, point mutations, INDELs, exon-skipping events, and expression perturbations in T-ALL.
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Zeynep Kalender
authors.initials: ZK
authors.lastname: Atak
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium ; Division of Hematology, Department of Cellular Biotechnologies and Hematology, 'Sapienza' University of Rome, Rome, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Gianfelici
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Gert
authors.initials: G
authors.lastname: Hulselmans
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Kim
authors.initials: K
authors.lastname: De Keersmaecker
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium ; Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Arun George
authors.initials: AG
authors.lastname: Devasia
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Ellen
authors.initials: E
authors.lastname: Geerdens
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Nicole
authors.initials: N
authors.lastname: Mentens
authors.affiliation: Division of Hematology, Department of Cellular Biotechnologies and Hematology, 'Sapienza' University of Rome, Rome, Italy.
authors.forename: Sabina
authors.initials: S
authors.lastname: Chiaretti
authors.affiliation: Center for Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Kaat
authors.initials: K
authors.lastname: Durinck
authors.affiliation: Pediatric Hemato-Oncology, University Hospitals Leuven, Leuven, Belgium.
authors.forename: Anne
authors.initials: A
authors.lastname: Uyttebroeck
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Vandenberghe
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Iwona
authors.initials: I
authors.lastname: Wlodarska
authors.affiliation: Pediatric Oncology/Hematology and Hematology, VU Medical Center, Amsterdam, The Netherlands.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Cloos
authors.affiliation: Division of Hematology, Department of Cellular Biotechnologies and Hematology, 'Sapienza' University of Rome, Rome, Italy.
authors.forename: Robin
authors.initials: R
authors.lastname: Foà
authors.affiliation: Center for Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Frank
authors.initials: F
authors.lastname: Speleman
authors.affiliation: Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Cools
authors.affiliation: Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium.
authors.forename: Stein
authors.initials: S
authors.lastname: Aerts
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D001483:Base Sequence / Q000235:genetics*; D045744:Cell Line, Tumor; D002648:Child; D002675:Child, Preschool; D059472:Exome / Q000235:genetics; D005260:Female; D015973:Gene Expression Regulation, Leukemic; D050939:Gene Fusion; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D007223:Infant; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide; D054218:Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / Q000209:etiology / Q000235:genetics* / Q000473:pathology; D059467:Transcriptome / Q000235:genetics*