1
|
Lin H, Chen H, Lin A, Liu X, Huang X, Zhou J, Yuan L, Zhuo Z. Associations between LMO1 gene polymorphisms and central nervous system tumor susceptibility. Pediatr Investig 2021; 5:281-287. [PMID: 34938970 PMCID: PMC8666933 DOI: 10.1002/ped4.12286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/04/2021] [Indexed: 11/17/2022] Open
Abstract
IMPORTANCE LIM domain only 1 (LMO1) gene polymorphisms were previously found to be implicated in the risk of several cancers. No available studies were performed regarding the predisposing effect of LMO1 gene single nucleotide polymorphisms (SNPs) on central nervous system (CNS) tumor risk. OBJECTIVE We aimed to determine whether the LMO1 gene SNPs were associated with the risk of CNS tumor by applying a case-control study with 191 cases and 248 controls in China. METHODS The contributions of LMO1 gene SNPs to the risk of CNS tumor was evaluated by multinomial logistic regression. RESULTS Based on the calculations of odds ratio (OR) and 95% confidence interval (CI), we failed to detect a significant relationship between each LMO1 gene SNP (rs110419 A>G, rs4758051 G>A, rs10840002 A>G, rs204938 A>G, and rs2168101 G>T) and CNS tumor risk, respectively. A negative association was also found in the combined effects on these five SNPs and CNS tumor risk. The stratification analysis further demonstrated the individuals with rs204938 AG/GG genotype confer to increased risk of CNS tumor compared with those with an AA genotype in males (OR: 1.74, 95% CI: 1.01-2.98, P = 0.046). INTERPRETATION We concluded that LMO1 gene SNPs may not strong enough to influence the risk of CNS tumor in Chinese children. More studies are required to verify this association.
Collapse
Affiliation(s)
- Huiran Lin
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children’s Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
- Faculty of MedicineMacau University of Science and TechnologyMacauChina
- Laboratory Animal Management OfficePublic Technology Service PlatformShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdongChina
| | - Huitong Chen
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children’s Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Ao Lin
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children’s Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Xiaoping Liu
- Department of HematologyGuangzhou Women and Children’s Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Xiaokai Huang
- Department of HematologyThe Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Jingying Zhou
- Department of HematologyThe Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Li Yuan
- Department of PathologyGuangzhou Women and Children’s Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Zhenjian Zhuo
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children’s Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| |
Collapse
|
2
|
LIM domain only 1: an oncogenic transcription cofactor contributing to the tumorigenesis of multiple cancer types. Chin Med J (Engl) 2021; 134:1017-1030. [PMID: 33870932 PMCID: PMC8116020 DOI: 10.1097/cm9.0000000000001487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
ABSTRACT The LIM domain only 1 (LMO1) gene belongs to the LMO family of genes that encodes a group of transcriptional cofactors. This group of transcriptional cofactors regulates gene transcription by acting as a key "connector" or "scaffold" in transcription complexes. All LMOs, including LMO1, are important players in the process of tumorigenesis. Unique biological features of LMO1 distinct from other LMO members, such as its tissue-specific expression patterns, interacting proteins, and transcriptional targets, have been increasingly recognized. Studies indicated that LMO1 plays a critical oncogenic role in various types of cancers, including T-cell acute lymphoblastic leukemia, neuroblastoma, gastric cancer, lung cancer, and prostate cancer. The molecular mechanisms underlying such functions of LMO1 have also been investigated, but they are currently far from being fully elucidated. Here, we focus on reviewing the current findings on the role of LMO1 in tumorigenesis, the mechanisms of its oncogenic action, and the mechanisms that drive its aberrant activation in cancers. We also briefly review its roles in the development process and non-cancer diseases. Finally, we discuss the remaining questions and future investigations required for promoting the translation of laboratory findings to clinical applications, including cancer diagnosis and treatment.
Collapse
|
3
|
Yap L, Wang JW, Moreno-Moral A, Chong LY, Sun Y, Harmston N, Wang X, Chong SY, Vanezis K, Öhman MK, Wei H, Bunte R, Gosh S, Cook S, Hovatta O, de Kleijn DPV, Petretto E, Tryggvason K. In Vivo Generation of Post-infarct Human Cardiac Muscle by Laminin-Promoted Cardiovascular Progenitors. Cell Rep 2020; 26:3231-3245.e9. [PMID: 30893597 DOI: 10.1016/j.celrep.2019.02.083] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/15/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
Regeneration of injured human heart muscle is limited and an unmet clinical need. There are no methods for the reproducible generation of clinical-quality stem cell-derived cardiovascular progenitors (CVPs). We identified laminin-221 (LN-221) as the most likely expressed cardiac laminin. We produced it as human recombinant protein and showed that LN-221 promotes differentiation of pluripotent human embryonic stem cells (hESCs) toward cardiomyocyte lineage and downregulates pluripotency and teratoma-associated genes. We developed a chemically defined, xeno-free laminin-based differentiation protocol to generate CVPs. We show high reproducibility of the differentiation protocol using time-course bulk RNA sequencing developed from different hESC lines. Single-cell RNA sequencing of CVPs derived from hESC lines supported reproducibility and identified three main progenitor subpopulations. These CVPs were transplanted into myocardial infarction mice, where heart function was measured by echocardiogram and human heart muscle bundle formation was identified histologically. This method may provide clinical-quality cells for use in regenerative cardiology.
Collapse
Affiliation(s)
- Lynn Yap
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Aida Moreno-Moral
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Li Yen Chong
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yi Sun
- BioLamina AB, Löfströms Allé 5A, Sundbyberg 17266, Sweden
| | - Nathan Harmston
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Xiaoyuan Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Suet Yen Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore
| | - Konstantinos Vanezis
- Cardiovascular Genetics and Genomics Group MRC London Institute of Medical Sciences, Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Miina K Öhman
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Heming Wei
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
| | - Ralph Bunte
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Sujoy Gosh
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Stuart Cook
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore; National Heart & Lung Institute, Imperial College London, Cale Street, London SW3 6LY, UK
| | - Outi Hovatta
- Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Dominique P V de Kleijn
- Cardiovascular Research Institute, National University Heart Centre, Singapore 117599, Singapore; University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Enrico Petretto
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Cardiovascular & Metabolic Disorders Program, Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore; Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden.
| |
Collapse
|
4
|
Hashemi M, Sarabandi S, Karami S, Śmieja J, Moazeni-Roodi A, Ghavami S, Łos MJ. LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta-analysis of case-control studies. J Cell Mol Med 2019; 24:1160-1168. [PMID: 31830377 PMCID: PMC6991665 DOI: 10.1111/jcmm.14836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022] Open
Abstract
Neuroblastoma (NB), a neuroendocrine tumour, is one of the most prevalent cancers in children. The link between LMO1 polymorphisms and NB has been investigated by several groups, rendering inconclusive results. Here, with this comprehensive systematic review and up‐to‐date meta‐analysis, we aim to distinctively elucidate the possible correlation between LMO1 polymorphisms and NB susceptibility. Eligible studies were systematically researched and identified using PubMed, Web of Science and Scopus databases up to 10 February 2019. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of the associations. Our findings revealed that rs110419 and rs2168101 polymorphisms were significantly associated with a decreased risk of NB in all genetic models. In addition, the rs4758051 variant appeared protective against NB in homozygous, dominant and allele genetic models, whereas the rs10840002 variant markedly decreased the risk of NB in the allele model. In contrast, the rs204938 polymorphism showed a positive association with NB susceptibility in allele genetic models. In summary, our meta‐analysis is the first to provide clear evidence of an association between specific polymorphisms of LMO1 and susceptibility to NB. Of note, additional larger well‐designed studies would be helpful to further evaluate and confirm this association.
Collapse
Affiliation(s)
- Mohammad Hashemi
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sahel Sarabandi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shima Karami
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Jarosław Śmieja
- Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland
| | | | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada.,CancerCare Manitoba, Research Institute in Oncology and Hematology, University of Manitoba, Winnipeg, MB, Canada
| | - Marek J Łos
- Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| |
Collapse
|
5
|
Stanulovic VS, Cauchy P, Assi SA, Hoogenkamp M. LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage. Nucleic Acids Res 2017; 45:9874-9888. [PMID: 28973433 PMCID: PMC5622341 DOI: 10.1093/nar/gkx573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
LMO2 is a bridging factor within a DNA binding complex and is required for definitive haematopoiesis to occur. The developmental stage of the block in haematopoietic specification is not known. We show that Lmo2−/− mouse embryonic stem cells differentiated to Flk-1+ haemangioblasts, but less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. Genome-wide approaches indicated that LMO2 is required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, the target site recognition of TAL1 is impaired. The lack of LMO2 resulted in altered gene expression levels already at the haemangioblast stage, with transcription factor genes accounting for ∼15% of affected genes. Comparison of Lmo2−/− with Tal1−/− Flk-1+ cells further showed that TAL1 was required to initiate or sustain Lmo2 expression.
Collapse
Affiliation(s)
- Vesna S Stanulovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Maarten Hoogenkamp
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
6
|
Li Z, Abraham BJ, Berezovskaya A, Farah N, Liu Y, Leon T, Fielding A, Tan SH, Sanda T, Weintraub AS, Li B, Shen S, Zhang J, Mansour MR, Young RA, Look AT. APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL. Leukemia 2017; 31:2057-2064. [PMID: 28260788 PMCID: PMC5629363 DOI: 10.1038/leu.2017.75] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/27/2017] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
Abstract
Oncogenic driver mutations are those that provide a proliferative or survival advantage to neoplastic cells, resulting in clonal selection. Although most cancer-causing mutations have been detected in the protein-coding regions of the cancer genome; driver mutations have recently also been discovered within noncoding genomic sequences. Thus, a current challenge is to gain precise understanding of how these unique genomic elements function in cancer pathogenesis, while clarifying mechanisms of gene regulation and identifying new targets for therapeutic intervention. Here we report a C-to-T single nucleotide transition that occurs as a somatic mutation in noncoding sequences 4 kb upstream of the transcriptional start site of the LMO1 oncogene in primary samples from patients with T-cell acute lymphoblastic leukaemia. This single nucleotide alteration conforms to an APOBEC-like cytidine deaminase mutational signature, and generates a new binding site for the MYB transcription factor, leading to the formation of an aberrant transcriptional enhancer complex that drives high levels of expression of the LMO1 oncogene. Since APOBEC-signature mutations are common in a broad spectrum of human cancers, we suggest that noncoding nucleotide transitions such as the one described here may activate potent oncogenic enhancers not only in T-lymphoid cells but in other cell lineages as well.
Collapse
Affiliation(s)
- Z Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - B J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - A Berezovskaya
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - N Farah
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Y Liu
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - T Leon
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - A Fielding
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - S H Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - T Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, Singapore, Singapore
| | - A S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - B Li
- Department of Hematology and Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - S Shen
- Department of Hematology and Oncology, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - J Zhang
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - M R Mansour
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - R A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - A T Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Division of Hematology/Oncology, Children’s Hospital, Boston, MA, USA
| |
Collapse
|
7
|
|
8
|
A Novel Cryptic Three-Way Translocation t(2;9;18)(p23.2;p21.3;q21.33) with Deletion of Tumor Suppressor Genes in 9p21.3 and 13q14 in a T-Cell Acute Lymphoblastic Leukemia. LEUKEMIA RESEARCH AND TREATMENT 2014; 2014:357123. [PMID: 25374696 PMCID: PMC4206928 DOI: 10.1155/2014/357123] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/18/2014] [Accepted: 09/20/2014] [Indexed: 11/18/2022]
Abstract
Acute leukemia often presents with pure chromosomal resolution; thus, aberrations may not be detected by banding cytogenetics. Here, a case of 26-year-old male diagnosed with T-cell acute lymphoblastic leukemia (T-ALL) and a normal karyotype after standard GTG-banding was studied retrospectively in detail by molecular cytogenetic and molecular approaches. Besides fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and high resolution array-comparative genomic hybridization (aCGH) were applied. Thus, cryptic chromosomal aberrations not observed before were detected: three chromosomes were involved in a cytogenetically balanced occurring translocation t(2;9;18)(p23.2;p21.3;q21.33). Besides a translocation t(10;14)(q24;q11) was identified, an aberration known to be common in T-ALL. Due to the three-way translocation deletion of tumor suppressor genes CDKN2A/INK4A/p16, CDKN2B/INK4B/p15, and MTAP/ARF/p14 in 9p21.3 took place. Additionally RB1 in 13q14 was deleted. This patient, considered to have a normal karyotype after low resolution banding cytogenetics, was treated according to general protocol of anticancer therapy (ALL-BFM 95).
Collapse
|
9
|
Kalender Atak Z, Gianfelici V, Hulselmans G, De Keersmaecker K, Devasia AG, Geerdens E, Mentens N, Chiaretti S, Durinck K, Uyttebroeck A, Vandenberghe P, Wlodarska I, Cloos J, Foà R, Speleman F, Cools J, Aerts S. Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia. PLoS Genet 2013; 9:e1003997. [PMID: 24367274 PMCID: PMC3868543 DOI: 10.1371/journal.pgen.1003997] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/16/2013] [Indexed: 12/22/2022] Open
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. The quest for somatic mutations underlying oncogenic processes is a central theme in today's cancer research. High-throughput genomics approaches including amplicon re-sequencing, exome re-sequencing, full genome re-sequencing, and SNP arrays have contributed to cataloguing driver genes across cancer types. Thus far transcriptome sequencing by RNA-seq has been mainly used for the detection of fusion genes, while few studies have assessed its value for the combined detection of SNPs, INDELs, fusions, gene expression changes, and alternative transcript events. Here we apply RNA-seq to 49 T-ALL samples and perform a critical assessment of the bioinformatics pipelines and filters to identify each type of aberration. By comparing to exome re-sequencing, and by exploiting the catalogues of known cancer drivers, we identified many known and several novel driver genes in T-ALL. We also determined an optimal normalization strategy to obtain accurate gene expression levels and used these to identify over-expressed transcription factors that characterize different T-ALL subtypes. Finally, by PCR, cloning, and in vitro cellular assays we uncover new fusion genes that have consequences at the level of gene expression, oncogenic chimaeras, and tumor suppressor inactivation. In conclusion, we present the first RNA-seq data set across T-ALL patients and identify new driver events.
Collapse
Affiliation(s)
- Zeynep Kalender Atak
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Valentina Gianfelici
- 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
| | - Gert Hulselmans
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Kim De Keersmaecker
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Arun George Devasia
- 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
| | - Ellen Geerdens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Nicole Mentens
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Sabina Chiaretti
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Anne Uyttebroeck
- Pediatric Hemato-Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Iwona Wlodarska
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
| | - Jacqueline Cloos
- Pediatric Oncology/Hematology and Hematology, VU Medical Center, Amsterdam, The Netherlands
| | - Robin Foà
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, ‘Sapienza’ University of Rome, Rome, Italy
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Jan Cools
- Laboratory for the Molecular Biology of Leukemia, Center for Human Genetics, KU Leuven and Center for the Biology of Disease, VIB, Leuven, Belgium
- * E-mail: (JC); (SA)
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail: (JC); (SA)
| |
Collapse
|