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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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Schiró M, Joshi C, Bordyuh M, Fazio R, Keeling J, Türeci HE. Exotic Attractors of the Nonequilibrium Rabi-Hubbard Model. Phys Rev Lett 2016; 116:143603. [PMID: 27104710 DOI: 10.1103/physrevlett.116.143603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Indexed: 06/05/2023]
Abstract
We explore the phase diagram of the dissipative Rabi-Hubbard model, as could be realized by a Raman-pumping scheme applied to a coupled cavity array. There exist various exotic attractors, including ferroelectric, antiferroelectric, and incommensurate fixed points, as well as regions of persistent oscillations. Many of these features can be understood analytically by truncating to the two lowest lying states of the Rabi model on each site. We also show that these features survive beyond mean field, using matrix product operator simulations.
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Affiliation(s)
- M Schiró
- Institut de Physique Théorique, Université Paris Saclay, CNRS, CEA, F-91191 Gif-sur-Yvette, France
| | - C Joshi
- Department of Physics, University of York, Heslington, York YO10 5DD, United Kingdom
- SUPA, School of Physics and Astronomy, University of St. Andrews, St. Andrews KY16 9SS, United Kingdom
| | - M Bordyuh
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - R Fazio
- ICTP, Strada Costiera 11, I-34151 Trieste, Italy
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, I-56127 Pisa, Italy
| | - J Keeling
- SUPA, School of Physics and Astronomy, University of St. Andrews, St. Andrews KY16 9SS, United Kingdom
| | - H E Türeci
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
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Abstract
Systems of strongly interacting atoms and photons, which can be realized wiring up individual cavity QED systems into lattices, are perceived as a new platform for quantum simulation. While sharing important properties with other systems of interacting quantum particles, here we argue that the nature of light-matter interaction gives rise to unique features with no analogs in condensed matter or atomic physics setups. By discussing the physics of a lattice model of delocalized photons coupled locally with two-level systems through the elementary light-matter interaction described by the Rabi model, we argue that the inclusion of counterrotating terms, so far neglected, is crucial to stabilize finite-density quantum phases of correlated photons out of the vacuum, with no need for an artificially engineered chemical potential. We show that the competition between photon delocalization and Rabi nonlinearity drives the system across a novel Z(2) parity symmetry-breaking quantum criticality between two gapped phases that share similarities with the Dicke transition of quantum optics and the Ising critical point of quantum magnetism. We discuss the phase diagram as well as the low-energy excitation spectrum and present analytic estimates for critical quantities.
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Affiliation(s)
- M Schiró
- Princeton Center for Theoretical Science, Joseph Henry Laboratories, Princeton University, New Jersey 08544, USA
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