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Raponi S, Del Giudice I, Marinelli M, Wang J, Cafforio L, Ilari C, Piciocchi A, Messina M, Bonina S, Tavolaro S, Bordyuh M, Mariglia P, Peragine N, Mauro FR, Chiaretti S, Molica S, Gentile M, Visentin A, Trentin L, Rigolin GM, Cuneo A, Diop F, Rossi D, Gaidano G, Guarini A, Rabadan R, Foà R. Genetic landscape of ultra-stable chronic lymphocytic leukemia patients. Ann Oncol 2019; 29:966-972. [PMID: 29365086 DOI: 10.1093/annonc/mdy021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) has a heterogeneous clinical course. Beside patients requiring immediate treatment, others show an initial indolent phase followed by progression and others do not progress for decades. The latter two subgroups usually display mutated IGHV genes and a favorable FISH profile. Patients and methods Patients with absence of disease progression for over 10 years (10-34) from diagnosis were defined as ultra-stable CLL (US-CLL). Forty US-CLL underwent extensive characterization including whole exome sequencing (WES), ultra-deep sequencing and copy number aberration (CNA) analysis to define their unexplored genetic landscape. Microarray analysis, comparing US-CLL with non-US-CLL with similar immunogenetic features (mutated IGHV/favorable FISH), was also carried out to recognize US-CLL at diagnosis. Results WES was carried out in 20 US-CLL and 84 non-silent somatic mutations in 78 genes were found. When re-tested in a validation cohort of 20 further US-CLL, no recurrent lesion was identified. No clonal mutations of NOTCH1, BIRC3, SF3B1 and TP53 were found, including ATM and other potential progression driving mutations. CNA analysis identified 31 lesions, none with known poor prognostic impact. No novel recurrent lesion was identified: most cases showed no lesions (38%) or an isolated del(13q) (31%). The expression of 6 genes, selected from a gene expression profile analysis by microarray and quantified by droplet digital PCR on a cohort of 79 CLL (58 US-CLL and 21 non-US-CLL), allowed to build a decision-tree capable of recognizing at diagnosis US-CLL patients. Conclusions The genetic landscape of US-CLL is characterized by the absence of known unfavorable driver mutations/CNA and of novel recurrent genetic lesions. Among CLL patients with favorable immunogenetics, a decision-tree based on the expression of 6 genes may identify at diagnosis patients who are likely to maintain an indolent disease for decades.
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Affiliation(s)
- S Raponi
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - I Del Giudice
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - M Marinelli
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - J Wang
- Division of Life Science and Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - L Cafforio
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - C Ilari
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - A Piciocchi
- GIMEMA Data Centre, GIMEMA Foundation, Rome, Italy
| | - M Messina
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Bonina
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Tavolaro
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - M Bordyuh
- Department of Systems Biology, Columbia University, New York, USA; Department of, Biomedical Informatics, Columbia University, New York, USA
| | - P Mariglia
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - N Peragine
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - F R Mauro
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Chiaretti
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Molica
- Department of Hematology-Oncology, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - M Gentile
- Hematology Uni, Department of Hemato-Oncology, Ospedale Annunziata, Cosenza, Italy
| | - A Visentin
- Hematology Sectio, Department of Clinical and Experimental Medicine, University of Padova, Padova, Italy
| | - L Trentin
- Hematology Sectio, Department of Clinical and Experimental Medicine, University of Padova, Padova, Italy
| | - G M Rigolin
- Hematology Sectio, Azienda Ospedaliero Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - A Cuneo
- Hematology Sectio, Azienda Ospedaliero Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - F Diop
- Division of Hematolog, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - D Rossi
- Department of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Institute of Oncology Research, Bellinzona, Switzerland
| | - G Gaidano
- Division of Hematolog, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - A Guarini
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - R Rabadan
- Department of Systems Biology, Columbia University, New York, USA; Department of, Biomedical Informatics, Columbia University, New York, USA
| | - R Foà
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy.
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Giudice ID, Rigolin GM, Raponi S, Cafforio L, Ilari C, Wang J, Bordyuh M, Piciocchi A, Marinelli M, Nanni M, Tavolaro S, Filetti M, Bardi A, Tammiso E, Volta E, Negrini M, Saccenti E, Mauro FR, Rossi D, Gaidano G, Guarini A, Rabadan R, Cuneo A, Foà R. Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile. Leukemia 2017; 32:543-546. [PMID: 28924243 DOI: 10.1038/leu.2017.292] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- I Del Giudice
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - G M Rigolin
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - S Raponi
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - L Cafforio
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - C Ilari
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - J Wang
- Divisions of Life Science and Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - M Bordyuh
- Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - A Piciocchi
- GIMEMA Data Centre, GIMEMA Foundation, Rome, Italy
| | - M Marinelli
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - M Nanni
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - S Tavolaro
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - M Filetti
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - A Bardi
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - E Tammiso
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - E Volta
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - M Negrini
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - E Saccenti
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - F R Mauro
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
| | - D Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - G Gaidano
- Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - A Guarini
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - R Rabadan
- Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - A Cuneo
- Hematology Section, Azienda Ospedaliera Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - R Foà
- Hematology, Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Rome, Italy
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