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On the way towards a 'CLL prognostic index': focus on TP53, BIRC3, SF3B1, NOTCH1 and MYD88 in a population-based cohort.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
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2014 (English)In: Leukemia, ISSN 0887-6924, E-ISSN 1476-5551, Vol. 28, no 3, 710-713 p.Article in journal, Letter (Refereed) Published
Place, publisher, year, edition, pages
2014. Vol. 28, no 3, 710-713 p.
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-214248DOI: 10.1038/leu.2013.333ISI: 000332845700029PubMedID: 24217197OAI: oai:DiVA.org:uu-214248DiVA: diva2:684510
Note

Mansouri and Rosenquist contributed equally as senior authors to this work.

Available from: 2014-01-08 Created: 2014-01-08 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Genomic and transcriptomic sequencing in chronic lymphocytic leukemia
Open this publication in new window or tab >>Genomic and transcriptomic sequencing in chronic lymphocytic leukemia
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Identification of recurrent mutations through next-generation sequencing (NGS) has given us a deeper understanding of the molecular mechanisms involved in chronic lymphocytic leukemia (CLL) development and progression and provided novel means for risk assessment in this clinically heterogeneous disease. In paper I, we screened a population-based cohort of CLL patients (n=364) for TP53, NOTCH1, SF3B1, BIRC3 and MYD88 mutations using Sanger sequencing, and confirmed the negative prognostic impact of TP53, SF3B1 or NOTCH1 aberrations, though at lower frequencies compared to previous studies. In paper II, we assessed the feasibility of targeted NGS using a gene panel including 9 CLL-related genes in a large patient cohort (n=188). We could validate 93% (144/155) of mutations with Sanger sequencing; the remaining were at the detection limit of the latter technique, and technical replication showed a high concordance (77/82 mutations, 94%). In paper III, we performed a longitudinal study of CLL patients (n=41) relapsing after fludarabine, cyclophosphamide and rituximab (FCR) therapy using whole-exome sequencing. In addition to known poor-prognostic mutations (NOTCH1, TP53, ATM, SF3B1, BIRC3, and NFKBIE), we detected mutations in a ribosomal gene, RPS15, in almost 20% of cases (8/41). In extended patient series, RPS15-mutant cases had a poor survival similar to patients with NOTCH1, SF3B1, or 11q aberrations. In vitro studies revealed that RPS15mut cases displayed reduced p53 stabilization compared to cases wildtype for RPS15. In paper IV, we performed RNA-sequencing in CLL patients (n=50) assigned to 3 clinically and biologically distinct subsets carrying stereotyped B-cell receptors (i.e. subsets #1, #2 and #4) and revealed unique gene expression profiles for each subset. Analysis of SF3B1-mutated versus wildtype subset #2 patients revealed a large number of splice variants (n=187) in genes involved in chromatin remodeling and ribosome biogenesis. Taken together, this thesis confirms the prognostic impact of recurrent mutations and provides data supporting implementation of targeted NGS in clinical routine practice. Moreover, we provide evidence for the involvement of novel players, such as RPS15, in disease progression and present transcriptome data highlighting the potential of global approaches for the identification of molecular mechanisms contributing to CLL development within prognostically relevant subgroups.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 63 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1259
Keyword
chronic, lymphocytic, leukemia, CLL, genomics, transcriptomics, DNA, RNA, mutations, NGS, whole-exome, sequencing, prognostic, markers, TP53, SF3B1, RPS15, relapse, stereotyped, subsets.
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-303703 (URN)978-91-554-9702-6 (ISBN)
Public defence
2016-11-11, Rudbecksalen, Dag Hammarskjölds väg 20, 75237 Uppsala University, Uppsala, 09:15 (English)
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Available from: 2016-10-20 Created: 2016-09-22 Last updated: 2016-11-22

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Cortese, DiegoSutton, Lesley AnnMansouri, LarryRosenquist, Richard

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