1
|
Bryant D, Smith L, Rogers-Broadway KR, Karydis L, Woo J, Blunt MD, Forconi F, Stevenson FK, Goodnow C, Russell A, Humburg P, Packham G, Steele AJ, Strefford JC. Network analysis reveals a major role for 14q32 cluster miRNAs in determining transcriptional differences between IGHV-mutated and unmutated CLL. Leukemia 2023; 37:1454-1463. [PMID: 37169950 PMCID: PMC10317834 DOI: 10.1038/s41375-023-01918-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) cells can express unmutated (U-CLL) or mutated (M-CLL) immunoglobulin heavy chain (IGHV) genes with differing clinical behaviours, variable B cell receptor (BCR) signalling capacity and distinct transcriptional profiles. As it remains unclear how these differences reflect the tumour cells' innate pre/post germinal centre origin or their BCR signalling competence, we applied mRNA/miRNA sequencing to 38 CLL cases categorised into three subsets by IGHV mutational status and BCR signalling capacity. We identified 492 mRNAs and 38 miRNAs differentially expressed between U-CLL and M-CLL, but only 9 mRNAs and 0 miRNAs associated with BCR competence within M-CLL. Of the IGHV-associated miRNAs, (14/38 (37%)) derived from chr14q32 clusters where all miRNAs were co-expressed with the MEG3 lncRNA from a cancer associated imprinted locus. Integrative analysis of miRNA/mRNA data revealed pronounced regulatory potential for the 14q32 miRNAs, potentially accounting for up to 25% of the IGHV-related transcriptome signature. GAB1, a positive regulator of BCR signalling, was potentially regulated by five 14q32 miRNAs and we confirmed that two of these (miR-409-3p and miR-411-3p) significantly repressed activity of the GAB1 3'UTR. Our analysis demonstrates a potential key role of the 14q32 miRNA locus in the regulation of CLL-related gene regulation.
Collapse
Affiliation(s)
- Dean Bryant
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lindsay Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Laura Karydis
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jeongmin Woo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthew D Blunt
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Francesco Forconi
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Freda K Stevenson
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Christopher Goodnow
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Amanda Russell
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Peter Humburg
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Graham Packham
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew J Steele
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jonathan C Strefford
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
| |
Collapse
|
2
|
Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in Chronic Lymphocytic Leukemia. Cancers (Basel) 2023; 15:cancers15041294. [PMID: 36831635 PMCID: PMC9953986 DOI: 10.3390/cancers15041294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/08/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The fluorescence in situ hybridization (FISH) technique plays an important role in the risk stratification and clinical management of patients with chronic lymphocytic leukemia (CLL). For genome-wide analysis, FISH needs to be complemented with other cytogenetic methods, including karyotyping and/or chromosomal microarrays. However, this is often not feasible in a diagnostic setup. Optical genome mapping (OGM) is a novel technique for high-resolution genome-wide detection of structural variants (SVs), and previous studies have indicated that OGM could serve as a generic cytogenetic tool for hematological malignancies. Herein, we report the results from our study evaluating the concordance of OGM and standard-of-care FISH in 18 CLL samples. The results were fully concordant between these two techniques in the blinded comparison. Using in silico dilution series, the lowest limit of detection with OGM was determined to range between 3 and 9% variant allele fractions. Genome-wide analysis by OGM revealed additional (>1 Mb) aberrations in 78% of the samples, including both unbalanced and balanced SVs. Importantly, OGM also enabled the detection of clinically relevant complex karyotypes, undetectable by FISH, in three samples. Overall, this study demonstrates the potential of OGM as a first-tier cytogenetic test for CLL and as a powerful tool for genome-wide SV analysis.
Collapse
|
3
|
Sha Y, Jiang R, Miao Y, Qin S, Wu W, Xia Y, Wang L, Fan L, Jin H, Xu W, Li J, Zhu H. The pyroptosis-related gene signature predicts prognosis and indicates the immune microenvironment status of chronic lymphocytic leukemia. Front Immunol 2022; 13:939978. [PMID: 36177050 PMCID: PMC9513039 DOI: 10.3389/fimmu.2022.939978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world with great heterogeneity. Pyroptosis has recently been recognized as an inflammatory form of programmed cell death (PCD) and shares a close relationship with apoptosis. Although the role of apoptosis in CLL was comprehensively studied and successfully applied in clinical treatment, the relationship between pyroptosis genes and CLL remained largely unknown. In this study, eight differentially expressed pyroptosis-related genes (PRGs) were identified between CLL and normal B cells. In order to screen out the prognostic value of differentially expressed PRGs, univariate and multivariate Cox regression analyses were conducted and a risk model with three PRG signatures (GSDME, NLRP3, and PLCG1) was constructed. All CLL samples were stratified into high- and low-risk subgroups according to risk scores. The risk model showed high efficacy in predicting both overall survival (OS) and time to first treatment (TTFT). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) showed the dysregulation of immune and inflammatory response in the high-risk group. Single-sample GSEA (ssGSEA) of immune cell infiltration and the activity of immune-related pathways also displayed decreased antitumor immunity in the high-risk group. In conclusion, PRGs are of prognostic value in CLL and may play important roles in tumor immunity, and the underlying relationship between PRGs and CLL needs to be explored further.
Collapse
MESH Headings
- Gene Ontology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein
- Prognosis
- Pyroptosis/genetics
- Tumor Microenvironment/genetics
Collapse
Affiliation(s)
- Yeqin Sha
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Rui Jiang
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Miao
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Shuchao Qin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Xia
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Lei Fan
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hui Jin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Xu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Wei Xu, ; Jianyong Li, ; Huayuan Zhu,
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Wei Xu, ; Jianyong Li, ; Huayuan Zhu,
| | - Huayuan Zhu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Wei Xu, ; Jianyong Li, ; Huayuan Zhu,
| |
Collapse
|
4
|
Morabito F, Tripepi G, Moia R, Recchia AG, Boggione P, Mauro FR, Bossio S, D'Arrigo G, Martino EA, Vigna E, Storino F, Fronza G, Di Raimondo F, Rossi D, Condoluci A, Colombo M, Fais F, Fabris S, Foa R, Cutrona G, Gentile M, Montserrat E, Gaidano G, Ferrarini M, Neri A. Lymphocyte Doubling Time As A Key Prognostic Factor To Predict Time To First Treatment In Early-Stage Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:684621. [PMID: 34408978 PMCID: PMC8366564 DOI: 10.3389/fonc.2021.684621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
The prognostic role of lymphocyte doubling time (LDT) in chronic lymphocytic leukemia (CLL) was recognized more than three decades ago when the neoplastic clone’s biology was almost unknown. LDT was defined as the time needed for the peripheral blood lymphocyte count to double the of the initial observed value. Herein, the LDT prognostic value for time to first treatment (TTFT) was explored in our prospective O-CLL cohort and validated in in two additional CLL cohorts. Specifically, newly diagnosed Binet stage A CLL patients from 40 Italian Institutions, representative of the whole country, were prospectively enrolled into the O-CLL1-GISL protocol (clinicaltrial.gov identifier: NCT00917540). Two independent cohorts of newly diagnosed CLL patients recruited respectively at the Division of Hematology in Novara, Italy, and at the Hospital Clinic in Barcelona, Spain, were utilized as validation cohorts. In the training cohort, TTFT of patients with LDT >12 months was significantly longer related to those with a shorter LDT. At Cox multivariate regression model, LDT ≤ 12 months maintained a significant independent relationship with shorter TTFT along with IGHV unmutated (IGHVunmut) status, 11q and 17p deletions, elevated β2M, Rai stage I-II, and NOTCH1 mutations. Based on these statistics, two regression models were constructed including the same prognostic factors with or without the LDT. The model with the LTD provided a significantly better data fitting (χ2 = 8.25, P=0.0041). The risk prediction developed including LDT had better prognostic accuracy than those without LDT. Moreover, the Harrell’C index for the scores including LDT were higher than those without LDT, although the accepted 0.70 threshold exceeded in both cases. These findings were also confirmed when the same analysis was carried out according to TTFT’s explained variation. When data were further analyzed based on the combination between LDT and IGHV mutational status in the training and validation cohorts, IGHVunmut and LDT>12months group showed a predominant prognostic role over IGHVmut LTD ≤ 12 months (P=0.006) in the O-CLL validation cohort. However, this predominance was of borden-line significance (P=0.06) in the Barcelona group, while the significant prognostic impact was definitely lost in the Novara group. Overall, in this study, we demonstrated that LDT could be re-utilized together with the more sophisticated prognostic factors to manage the follow-up plans for Binet stage A CLL patients.
Collapse
Affiliation(s)
- Fortunato Morabito
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy.,Department of Hematology and Bone Marrow Transplant Unit, Augusta Victoria Hospital, Jerusalem, Israel
| | - Giovanni Tripepi
- Centro Nazionale Ricerca Istituto di Fisiologia Clinica (CNR-IFC), Research Unit of Reggio Calabria, Reggio Calabria, Italy
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Anna Grazia Recchia
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy
| | - Paola Boggione
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Francesca Romana Mauro
- Hematology, Department of Translational and Precision Medicine, 'Sapienza' University, Rome, Italy
| | - Sabrina Bossio
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy
| | - Graziella D'Arrigo
- Centro Nazionale Ricerca Istituto di Fisiologia Clinica (CNR-IFC), Research Unit of Reggio Calabria, Reggio Calabria, Italy
| | | | - Ernesto Vigna
- Department of Onco-Hematology AO Cosenza, Hematology Unit AO of Cosenza, Cosenza, Italy
| | - Francesca Storino
- Department of Onco-Hematology Azienda Ospedaliera (AO) Cosenza, Biotechnology Research Unit, Cosenza, Italy
| | - Gilberto Fronza
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Francesco Di Raimondo
- Division of Hematology, Policlinico, Department of Surgery and Medical Specialties, University of Catania, Catania, Italy
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Adalgisa Condoluci
- Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Monica Colombo
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Franco Fais
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Robin Foa
- Hematology, Department of Translational and Precision Medicine, 'Sapienza' University, Rome, Italy
| | - Giovanna Cutrona
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Massimo Gentile
- Department of Onco-Hematology AO Cosenza, Hematology Unit AO of Cosenza, Cosenza, Italy
| | - Emili Montserrat
- Department of Hematology, Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Antonino Neri
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| |
Collapse
|
5
|
Miller CR, Huang Y, Ruppert AS, Labanowska J, Jaglowski SM, Maddocks KJ, Rogers KA, Bhat S, Kittai AS, Grever M, Lapalombella R, Abruzzo LV, Heerema NA, Byrd JC, Hertlein EK, Woyach JA. Significance of chromosome 2p gain in ibrutinib-treated chronic lymphocytic leukemia patients. Leukemia 2021; 35:3287-3290. [PMID: 33820961 DOI: 10.1038/s41375-021-01237-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Cecelia R Miller
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Ying Huang
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Amy S Ruppert
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jadwiga Labanowska
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Samantha M Jaglowski
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Kami J Maddocks
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Kerry A Rogers
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Seema Bhat
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Adam S Kittai
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Michael Grever
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Rosa Lapalombella
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Lynne V Abruzzo
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Nyla A Heerema
- Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Erin K Hertlein
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jennifer A Woyach
- Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
6
|
Guo C, Gao YY, Ju QQ, Zhang CX, Gong M, Li ZL. HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. J Transl Med 2021; 19:42. [PMID: 33485349 PMCID: PMC7825181 DOI: 10.1186/s12967-021-02708-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/16/2021] [Indexed: 11/16/2022] Open
Abstract
Background IGHV mutation status is a crucial prognostic biomarker for CLL. In the present study, we investigated the transcriptomic signatures associating with IGHV mutation status and CLL prognosis. Methods The co-expression modules and hub genes correlating with IGHV status, were identified using the GSE28654, by ‘WGCNA’ package and R software (version 4.0.2). The over-representation analysis was performed to reveal enriched cell pathways for genes of correlating modules. Then 9 external cohorts were used to validate the correlation of hub genes expression with IGHV status or clinical features (treatment response, transformation to Richter syndrome, etc.). Moreover, to elucidate the significance of hub genes on disease course and prognosis of CLL patients, the Kaplan–Meier analysis for the OS and TTFT of were performed between subgroups dichotomized by the median expression value of individual hub genes. Results 2 co-expression modules and 9 hub genes ((FCRL1/FCRL2/HELQ/EGR3LPL/LDOC1/ZNF667/SOWAHC/SEPTIN10) correlating with IGHV status were identified by WGCNA, and validated by external datasets. The modules were found to be enriched in NF-kappaB, HIF-1 and other important pathways, involving cell proliferation and apoptosis. The expression of hub genes was revealed to be significantly different, not only between CLL and normal B cell, but also between various types of lymphoid neoplasms. HELQ expression was found to be related with response of immunochemotherapy treatment significantly (p = 0.0413), while HELQ and ZNF667 were expressed differently between stable CLL and Richter syndrome patients (p < 0.0001 and p = 0.0278, respectively). By survival analysis of subgroups, EGR3 expression was indicated to be significantly associated with TTFT by 2 independent cohorts (GSE39671, p = 0.0311; GSE22762, p = 0.0135). While the expression of HELQ and EGR3 was found to be associated with OS (p = 0.0291 and 0.0114 respectively).The Kras, Hedgehog and IL6-JAK-STAT3 pathways were found to be associating with the expression of hub genes, resulting from GSEA. Conclusions The expression of HELQ and EGR3 were correlated with IGHV mutation status in CLL patients. Additionally, the expression of HELQ/EGR3 were prognostic markers for CLL associating with targetable cell signaling pathways.
Collapse
Affiliation(s)
- Chao Guo
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Ya-Yue Gao
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Qian-Qian Ju
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Chun-Xia Zhang
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Ming Gong
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Zhen-Ling Li
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China.
| |
Collapse
|
7
|
Complex karyotype as a predictor of high-risk chronic lymphocytic leukemia: A single center experience over 12 years. Leuk Res 2019; 85:106218. [PMID: 31476701 DOI: 10.1016/j.leukres.2019.106218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVES A complex karyotype (CK) is considered a poor prognostic marker in chronic lymphocytic leukemia (CLL). METHODS The study analyzed 644 untreated CLL patients (pts) using conventional/molecular cytogenetics to reveal the presence of a CK and its composition and to assess its predictive value. The mutational status ofTP53 was detected by next generation sequencing. RESULTS A CK was detected in 79 pts (12.3%). Patients with a CK showed shorter overall survival (OS) compared to those without a CK (77 months vs. 115 months, p < 0.0001). Chromosomes most frequently included in a CK were 13, 11, 17, 8, 2, and 6. The most common aberrations in a CK were translocations, numerical changes and dicentric chromosomes (with no effect on OS). Patients with aberrations ofTP53 and ATM were shown to have adverse prognosis comparable to patients with a CK without these abnormalities. A stronger impact of a CK on OS of female and older CLL patients was observed. CONCLUSIONS The determining of the presence of a CK is essential in modern clinical CLL practice. According to recent studies, the presence of a CK affects clinical and treatment decision-making.
Collapse
|
8
|
Maitre E, Troussard X. Monoclonal B-cell lymphocytosis. Best Pract Res Clin Haematol 2019; 32:229-238. [PMID: 31585623 DOI: 10.1016/j.beha.2019.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
Abstract
Flow cytometry diagnostic practices can detect very low levels of clonal B cells in the peripheral blood. In the absence of clinical symptoms, cytopenia or organomegaly, the small clones may correspond to monoclonal B-cell leukemia (MBL) diagnosis. Most MBLs harbor a chronic lymphocytic leukemia (CLL) phenotype (e.g., CD5+, CD23+) and are referred to as CLL-type MBL. The two other types are atypical CLL-type MBL and non-CLL-type MBL. In addition to the phenotypical classification, the clonal B count is a major issue because of the impact on the prognosis and the risk of progression in CLL. It allows for the discrimination of two distinct types: high-count (HC) MBL and low-count (LC)-MBL based on a cutoff value of 0.5 × 109/L clonal B cells. LC MBL appears to be very stable over time and is probably related to immunosenescence. Conversely, HC MBL could be a premalignant state before the occurrence of CLL.
Collapse
Affiliation(s)
- Elsa Maitre
- Laboratoire d'hématologie biologique, CHU de Caen Normandie, Caen, 14033, CEDEX 9, France.
| | - Xavier Troussard
- Laboratoire d'hématologie biologique, CHU de Caen Normandie, Caen, 14033, CEDEX 9, France.
| |
Collapse
|
9
|
Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia. Cancer Genet 2018; 228-229:236-250. [DOI: 10.1016/j.cancergen.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 01/18/2023]
|
10
|
Biray Avci C, Goker Bagca B, Tetik Vardarli A, Saydam G, Gunduz C. Epigenetic modifications in chronic myeloid leukemia cells through ruxolitinib treatment. J Cell Biochem 2018; 120:4555-4563. [PMID: 30260022 DOI: 10.1002/jcb.27744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 12/28/2022]
Abstract
Chronic myeloid leukemia is a clonal malignancy of hematopoietic stem cell that is characterized by the occurrence of t(9;22)(q34;q11.2) translocation, named Philadelphia chromosome. Ruxolitinib is a powerful Janus tyrosine kinase 1 and 2 inhibitor that is used for myelofibrosis treatment. DNA-histone connection mediates a wide range of genes that code methylation, demethylation, acetylation, deacetylation, ubiquitination, and phosphorylation enzymes. Epigenetic modifications regulate chromatin compactness, which plays pivotal roles in critical biological processes including the transcriptional activity and cell proliferation as well as various pathological mechanisms, including CML. This study is aimed to determine the alterations of the expression levels of epigenetic modification-related genes after ruxolitinib treatment. Total RNA was isolated from K-562 cells treated with the IC50 value of ruxolitinib and untreated K-562 control cells. A reverse transcription procedure was performed for complementary DNA synthesis, and gene expressions were detected by real-time polymerase chain reaction compared with the untreated cells. Ruxolitinib treatment caused a significant alteration in the expression levels of epigenetic regulation-related genes in K-562 cells. Our novel results suggested that ruxolitinib has inhibitor effects on epigenetic modification-regulator genes.
Collapse
Affiliation(s)
- Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| | - Bakiye Goker Bagca
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| | - Asli Tetik Vardarli
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| | - Guray Saydam
- Department of Internal Medicine, Division of Haematology, Medical Faculty, Ege University, Izmir, Turkey
| | - Cumhur Gunduz
- Department of Medical Biology, Medical Faculty, Ege University, Izmir, Turkey
| |
Collapse
|
11
|
Clarisse D, Thommis J, Van Wesemael K, Houtman R, Ratman D, Tavernier J, Offner F, Beck I, De Bosscher K. Coregulator profiling of the glucocorticoid receptor in lymphoid malignancies. Oncotarget 2017; 8:109675-109691. [PMID: 29312638 PMCID: PMC5752551 DOI: 10.18632/oncotarget.22764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022] Open
Abstract
Coregulators cooperate with nuclear receptors, such as the glucocorticoid receptor (GR), to enhance or repress transcription. These regulatory proteins are implicated in cancer, yet, their role in lymphoid malignancies, including multiple myeloma (MM) and acute lymphoblastic leukemia (ALL), is largely unknown. Here, we report the use and extension of the microarray assay for real-time nuclear receptor coregulator interactions (MARCoNI) technology to detect coregulator associations with endogenous GR in cell lysates. We use MARCoNI to determine the GR coregulator profile of glucocorticoid-sensitive (MM and ALL) and glucocorticoid-resistant (ALL) cells, and identify common and unique coregulators for different cell line comparisons. Overall, we identify SRC-1/2/3, PGC-1α, RIP140 and DAX-1 as the strongest interacting coregulators of GR in MM and ALL cells and show that the interaction strength does not correlate with GR protein levels. Lastly, as a step towards patient samples, we determine the GR coregulator profile of peripheral blood mononuclear cells. We profile the interactions between GR and coregulators in MM and ALL cells and suggest to further explore the GR coregulator profile in hematological patient samples.
Collapse
Affiliation(s)
- Dorien Clarisse
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jonathan Thommis
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Karlien Van Wesemael
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - René Houtman
- PamGene International B.V., 's Hertogenbosch, The Netherlands
| | - Dariusz Ratman
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Current/Present address: Roche Global IT Solutions, Roche-Polska, Warsaw, Poland
| | - Jan Tavernier
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Fritz Offner
- Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ilse Beck
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Department of Health Sciences, Odisee University College, Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| |
Collapse
|
12
|
Li L, Xu-Monette ZY, Ok CY, Tzankov A, Manyam GC, Sun R, Visco C, Zhang M, Montes-Moreno S, Dybkaer K, Chiu A, Orazi A, Zu Y, Bhagat G, Richards KL, Hsi ED, Choi WWL, van Krieken JH, Huh J, Ponzoni M, Ferreri AJM, Møller MB, Wang J, Parsons BM, Winter JN, Piris MA, Pham LV, Medeiros LJ, Young KH. Prognostic impact of c-Rel nuclear expression and REL amplification and crosstalk between c-Rel and the p53 pathway in diffuse large B-cell lymphoma. Oncotarget 2016; 6:23157-80. [PMID: 26324762 PMCID: PMC4695110 DOI: 10.18632/oncotarget.4319] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 06/16/2015] [Indexed: 02/06/2023] Open
Abstract
Dysregulated NF-κB signaling is critical for lymphomagenesis. The regulation, function, and clinical relevance of c-Rel/NF-κB activation in diffuse large B-cell lymphoma (DLBCL) have not been well studied. In this study we analyzed the prognostic significance and gene-expression signature of c-Rel nuclear expression as surrogate of c-Rel activation in 460 patients with de novo DLBCL. Nuclear c-Rel expression, observed in 137 (26.3%) DLBCL patients frequently associated with extranoal origin, did not show significantly prognostic impact in the overall- or germinal center B-like-DLBCL cohort, likely due to decreased pAKT and Myc levels, up-regulation of FOXP3, FOXO3, MEG3 and other tumor suppressors coincided with c-Rel nuclear expression, as well as the complicated relationships between NF-κB members and their overlapping function. However, c-Rel nuclear expression correlated with significantly poorer survival in p63+ and BCL-2− activated B-cell-like-DLBCL, and in DLBCL patients with TP53 mutations. Multivariate analysis indicated that after adjusting clinical parameters, c-Rel positivity was a significantly adverse prognostic factor in DLBCL patients with wild type TP53. Gene expression profiling suggested dysregulations of cell cycle, metabolism, adhesion, and migration associated with c-Rel activation. In contrast, REL amplification did not correlate with c-Rel nuclear expression and patient survival, likely due to co-amplification of genes that negatively regulate NF-κB activation. These insights into the expression, prognostic impact, regulation and function of c-Rel as well as its crosstalk with the p53 pathway underscore the importance of c-Rel and have significant therapeutic implications.
Collapse
Affiliation(s)
- Ling Li
- Zhengzhou University, The First Affiliated University Hospital, Zhengzhou, China.,Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zijun Y Xu-Monette
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi Young Ok
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Ganiraju C Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruifang Sun
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mingzhi Zhang
- Zhengzhou University, The First Affiliated University Hospital, Zhengzhou, China
| | | | | | - April Chiu
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Attilio Orazi
- Weill Medical College of Cornell University, New York, NY, USA
| | - Youli Zu
- The Methodist Hospital, Houston, TX, USA
| | - Govind Bhagat
- Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, USA
| | - Kristy L Richards
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - William W L Choi
- University of Hong Kong Li Ka Shing Faculty of Medicine, Hong Kong, China
| | | | - Jooryung Huh
- Asan Medical Center, Ulsan University College of Medicine, Seoul, Korea
| | | | | | | | | | | | - Jane N Winter
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miguel A Piris
- Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Lan V Pham
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas School of Medicine, Graduate School of Biomedical Sciences, Houston, Texas, USA
| |
Collapse
|
13
|
Yepes S, Torres MM, López-Kleine L. Regulatory network reconstruction reveals genes with prognostic value for chronic lymphocytic leukemia. BMC Genomics 2015; 16:1002. [PMID: 26606983 PMCID: PMC4659237 DOI: 10.1186/s12864-015-2189-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
Background The clinical course of chronic lymphocytic leukemia (CLL) is highly variable; some patients follow an indolent course, but others progress to a more advanced stage. The mutational status of rearranged immunoglobulin heavy chain variable (IGVH) genes in CLL is a feature that is widely recognized for dividing patients into groups that are related to their prognoses. However, the regulatory programs associated with the IGVH statuses are poorly understood, and markers that can precisely predict survival outcomes have yet to be identified. Methods In this study, (i) we reconstructed gene regulatory networks in CLL by applying an information-theoretic approach to the expression profiles of 5 cohorts. (ii) We applied master regulator analysis (MRA) to these networks to identify transcription factors (TFs) that regulate an IGVH mutational status signature. The IGVH mutational status signature was developed by searching for differentially expressed genes between the IGVH mutational statuses in numerous CLL cohorts. (iii) To evaluate the biological implication of the inferred regulators, prognostic values were determined using time to treatment (TTT) and overall survival (OS) in two different cohorts. Results A robust IGVH expression signature was obtained, and various TFs emerged as regulators of the signature in most of the reconstructed networks. The TF targets expression profiles exhibited significant differences with respect to survival, which allowed the definition of a reduced profile with a high value for OS. TCF7 and its targets stood out for their roles in progression. Conclusion TFs and their targets, which were obtained merely from inferred regulatory associations, have prognostic implications and reflect a regulatory context for prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2189-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sally Yepes
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Maria Mercedes Torres
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Liliana López-Kleine
- Departamento de Estadística, Universidad Nacional de Colombia, Bogotá D.C., Colombia.
| |
Collapse
|
14
|
Yepes S, Torres MM, Andrade RE. Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions. PLoS One 2015; 10:e0137132. [PMID: 26355846 PMCID: PMC4565688 DOI: 10.1371/journal.pone.0137132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 08/12/2015] [Indexed: 12/18/2022] Open
Abstract
Although the identification of inherent structure in chronic lymphocytic leukemia (CLL) gene expression data using class discovery approaches has not been extensively explored, the natural clustering of patient samples can reveal molecular subdivisions that have biological and clinical implications. To explore this, we preprocessed raw gene expression data from two published studies, combined the data to increase the statistical power, and performed unsupervised clustering analysis. The clustering analysis was replicated in 4 independent cohorts. To assess the biological significance of the resultant clusters, we evaluated their prognostic value and identified cluster-specific markers. The clustering analysis revealed two robust and stable subgroups of CLL patients in the pooled dataset. The subgroups were confirmed by different methodological approaches (non-negative matrix factorization NMF clustering and hierarchical clustering) and validated in different cohorts. The subdivisions were related with differential clinical outcomes and markers associated with the microenvironment and the MAPK and BCR signaling pathways. It was also found that the cluster markers were independent of the immunoglobulin heavy chain variable (IGVH) genes mutational status. These findings suggest that the microenvironment can influence the clinical behavior of CLL, contributing to prognostic differences. The workflow followed here provides a new perspective on differences in prognosis and highlights new markers that should be explored in this context.
Collapse
MESH Headings
- Biomarkers, Tumor/metabolism
- Cluster Analysis
- Cohort Studies
- Gene Expression Regulation, Leukemic
- Genes, Neoplasm
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Survival Analysis
- Transcription, Genetic
- Treatment Outcome
- Tumor Microenvironment/genetics
- Up-Regulation/genetics
Collapse
Affiliation(s)
- Sally Yepes
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia
- * E-mail:
| | - Maria Mercedes Torres
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia
| | - Rafael E. Andrade
- Facultad de Medicina, Universidad de los Andes, Departamento de Patología, Hospital Universitario, Fundación Santa Fe de Bogotá, Bogotá D.C., Colombia
| |
Collapse
|
15
|
Morabito F, Cutrona G, Mosca L, D'Anca M, Matis S, Gentile M, Vigna E, Colombo M, Recchia AG, Bossio S, De Stefano L, Maura F, Manzoni M, Ilariucci F, Consoli U, Vincelli I, Musolino C, Cortelezzi A, Molica S, Ferrarini M, Neri A. Surrogate molecular markers for IGHV mutational status in chronic lymphocytic leukemia for predicting time to first treatment. Leuk Res 2015; 39:840-5. [PMID: 26038121 DOI: 10.1016/j.leukres.2015.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
Abstract
ZAP-70 is a marker of clinical outcome in chronic lymphocytic leukemia (CLL), however its assessment suffers from a lack of standardization consensus. To identify novel markers able to surrogate IGHV mutational status, CD19(+)CD5(+)-B-lymphocytes from 216 patients enrolled in a prospective study (ClinicalTrial.gov Identifier:NCT00917540), underwent gene expression profiling. Samples were split into CLL-Training (n=102) and CLL-Validation (n=114) sets, and an independent supervised analysis for IGHV mutational status was performed considering all genes with gene expression equal or above that of ZAP-70. Thirty-one genes (23 up- and 8 down-regulated) and 23 genes (18 up- and 5 down-regulated) satisfied these criteria in the CLL-Training and CLL-Validation sets, respectively, and 20 common genes (15 up and 5 down) were found to be differentially regulated in both sets. Two (SNORA70F, NRIP1) of the down-regulated and 6 (SEPT10, ZNF667, TGFBR3, MBOAT1, LPL, CRY1) of the up-regulated genes were significantly associated with a reduced risk of disease progression in both sets. Forcing the afore-mentioned genes in a Cox multivariate model together with IGHV mutational status, only CRY1 (HR=2.3, 95% CI: 1.1-4.9, P=.027) and MBOAT1 (HR=2.1, 95% CI: 1.1-3.7, P=.018) retained their independent prognostic impact, supporting the hypothesis that these genes may potentially act as surrogates for predicting IGHV mutational status.
Collapse
Affiliation(s)
- Fortunato Morabito
- Hematology Unit, AO, Cosenza, Italy; Biotecnology Research Unit, Aprigliano, Cosenza, Italy.
| | - Giovanna Cutrona
- SS di Diagnostica Molecolare IRCCS S. Martino-IST, Genova, Italy
| | - Laura Mosca
- Department of Clinical and Community Science, University of Milan, Milano, Italy
| | - Marianna D'Anca
- Department of Clinical and Community Science, University of Milan, Milano, Italy
| | - Serena Matis
- Scientific Division, IRCCS S. Martino-National Cancer Institute, Genova, Italy
| | | | | | - Monica Colombo
- Scientific Division, IRCCS S. Martino-National Cancer Institute, Genova, Italy
| | | | | | | | - Francesco Maura
- Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| | - Martina Manzoni
- Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| | | | - Ugo Consoli
- Hematology-Oncology Unit, Garibaldi-Nesima Hospital, Catania, Italy
| | | | | | - Agostino Cortelezzi
- Department of Clinical and Community Science, University of Milan, Milano, Italy; Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| | | | - Manlio Ferrarini
- Scientific Division, IRCCS S. Martino-National Cancer Institute, Genova, Italy
| | - Antonino Neri
- Department of Clinical and Community Science, University of Milan, Milano, Italy; Hematology Division, IRCCS Foundation Cà Granda, Policlinico Hospital, Milan, Italy
| |
Collapse
|
16
|
Maura F, Cutrona G, Mosca L, Matis S, Lionetti M, Fabris S, Agnelli L, Colombo M, Massucco C, Ferracin M, Zagatti B, Reverberi D, Gentile M, Recchia AG, Bossio S, Rossi D, Gaidano G, Molica S, Cortelezzi A, Di Raimondo F, Negrini M, Tassone P, Morabito F, Ferrarini M, Neri A. Association between gene and miRNA expression profiles and stereotyped subset #4 B-cell receptor in chronic lymphocytic leukemia. Leuk Lymphoma 2015; 56:3150-8. [PMID: 25860243 DOI: 10.3109/10428194.2015.1028051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study we investigated specific biological and clinical features associated with chronic lymphocytic leukemia (CLL) patients carrying stereotyped BCR subset #4 (IGHV4-34) among a prospective cohort of 462 CLL/MBL patients in early stage (Binet A). All subset #4 patients (n = 16) were characterized by the IGHV mutated gene configuration, and absence of unfavorable cytogenetic lesions, NOTCH1 or SF3B1 mutations. Gene and miRNA expression profiling evidenced that the leukemic cells of subset #4 cases showed significant downregulation of WDFY4, MF2A and upregulation of PDGFA, FGFR1 and TFEC gene transcripts, as well as the upregulation of miR-497 and miR-29c. The transfection of miR-497 mimic in primary leukemic CLL cells induced a downregulation of BCL2, a known validated target of this miRNA. Our data identify biological characteristics associated with subset #4 patients, providing further evidence for the putative role of BCR in shaping the features of the tumor cells in CLL.
Collapse
Affiliation(s)
- Francesco Maura
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| | - Giovanna Cutrona
- b SS Molecular Diagnostics, IRCCS S. Martino-IST , Genova , Italy
| | - Laura Mosca
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| | - Serena Matis
- c Scientific Direction IRCCS S. Martino-IST , Genova , Italy
| | - Marta Lionetti
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| | - Sonia Fabris
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| | - Luca Agnelli
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| | - Monica Colombo
- c Scientific Direction IRCCS S. Martino-IST , Genova , Italy
| | | | - Manuela Ferracin
- d Department of Morphology , Surgery and Experimental Medicine and Laboratory for the Technologies of Advanced Therapies (LTTA), University of Ferrara , Genova , Italy
| | - Barbara Zagatti
- d Department of Morphology , Surgery and Experimental Medicine and Laboratory for the Technologies of Advanced Therapies (LTTA), University of Ferrara , Genova , Italy
| | | | - Massimo Gentile
- f U.O.C. di Ematologia, Azienda Ospedaliera di Cosenza , Cosenza , Italy
| | | | - Sabrina Bossio
- f U.O.C. di Ematologia, Azienda Ospedaliera di Cosenza , Cosenza , Italy
| | - Davide Rossi
- g Division of Hematology, Department of Translational Medicine , Amedeo Avogadro University of Eastern Piedmont , Novara , Italy
| | - Gianluca Gaidano
- g Division of Hematology, Department of Translational Medicine , Amedeo Avogadro University of Eastern Piedmont , Novara , Italy
| | - Stefano Molica
- h Department of Oncology and Hematology , Pugliese-Ciaccio Hospital , Catanzaro , Italy
| | - Agostino Cortelezzi
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| | - Francesco Di Raimondo
- i University of Catania and Ferrarotto Hospital, Catania, Department of Biomedical Sciences , Division of Hematology , Catanzaro , Italy
| | - Massimo Negrini
- d Department of Morphology , Surgery and Experimental Medicine and Laboratory for the Technologies of Advanced Therapies (LTTA), University of Ferrara , Genova , Italy
| | - Pierfrancesco Tassone
- j Department of Experimental and Clinical Medicine , Magna Graecia University , Catanzaro , Italy
| | - Fortunato Morabito
- f U.O.C. di Ematologia, Azienda Ospedaliera di Cosenza , Cosenza , Italy
| | | | - Antonino Neri
- a Department of Clinical Sciences and Community Health , University of Milano and Hematology 1 CTMO, Foundation IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milano , Italy
| |
Collapse
|
17
|
Comprehensive chronic lymphocytic leukemia diagnostics by combined multiplex ligation dependent probe amplification (MLPA) and interphase fluorescence in situ hybridization (iFISH). Mol Cytogenet 2014; 7:79. [PMID: 25435911 PMCID: PMC4247644 DOI: 10.1186/s13039-014-0079-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
Background Banding-karyotyping and metaphase-directed-fluorescence-in-situhybridization (FISH) may be hampered by low mitotic index in leukemia. Interphase FISH (iFISH) is a way out here, however, testing many probes at the same time is protracted and expensive. Here multiplex-ligation-dependent-probe-amplification (MLPA) was used retrospectively in chronic lymphocytic leukemia (CLL) samples initially studied by banding cytogenetics and iFISH. Detection rates of iFISH and MLPA were compared and thus a cost-efficient scheme for routine diagnostics is proposed. Results Banding cytogenetics was done successfully in 67/85 samples. DNA was extracted from all 85 CLL samples. A commercially available MLPA probe set directed against 37 loci prone to be affected in hematological malignancies was applied. Besides, routine iFISH was done by commercially available probes for following regions: 11q22.3, 12p11.2-q11.1, 13q14.3, 13q34, 14q32.33 and 17p13.1. MLPA results were substantiated by iFISH using corresponding locus-specific probes. Aberrations were detected in 67 of 85 samples (~79%) applying banding cytogenetics, iFISH and MLPA. A maximum of 8 aberrations was detected per sample; however, one aberration per sample was found most frequently. Overall 163 aberrations were identified. 15 of those (~9%) were exclusively detected by banding cytogenetics, 95 were found by MLPA (~58%) and 100 (~61%) by routine iFISH. MLPA was not able to distinguish reliably between mono- and biallelic del(13)(q14.3q14.3), which could be easily identified as well as quantified by routine iFISH. Also iFISH was superior to MLPA in samples with low tumor cell load. On the other hand MLPA detected additional aberrations in 22 samples, two of them being without any findings after routine iFISH. Conclusions Both MLPA and routine iFISH have comparable detection rates for aberrations being typically present in CLL. As MLPA can detect also rare chromosomal aberrations it should be used as an initial test if routine cytogenetics is not possible or non-informative. Still iFISH should be used additionally to distinguish mono- from biallelic deletions and also to determine rate of mosaicism for 13q14.2 to 13q14.3. In case MLPA is negative the corresponding CLL samples should be tested at least by iFISH using the standard probe set to. Electronic supplementary material The online version of this article (doi:10.1186/s13039-014-0079-2) contains supplementary material, which is available to authorized users.
Collapse
|
18
|
Szedlak A, Paternostro G, Piermarocchi C. Control of asymmetric Hopfield networks and application to cancer attractors. PLoS One 2014; 9:e105842. [PMID: 25170874 PMCID: PMC4149479 DOI: 10.1371/journal.pone.0105842] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/24/2014] [Indexed: 12/20/2022] Open
Abstract
The asymmetric Hopfield model is used to simulate signaling dynamics in gene regulatory networks. The model allows for a direct mapping of a gene expression pattern into attractor states. We analyze different control strategies aimed at disrupting attractor patterns using selective local fields representing therapeutic interventions. The control strategies are based on the identification of signaling bottlenecks, which are single nodes or strongly connected clusters of nodes that have a large impact on the signaling. We provide a theorem with bounds on the minimum number of nodes that guarantee control of bottlenecks consisting of strongly connected components. The control strategies are applied to the identification of sets of proteins that, when inhibited, selectively disrupt the signaling of cancer cells while preserving the signaling of normal cells. We use an experimentally validated non-specific and an algorithmically-assembled specific B cell gene regulatory network reconstructed from gene expression data to model cancer signaling in lung and B cells, respectively. Among the potential targets identified here are TP53, FOXM1, BCL6 and SRC. This model could help in the rational design of novel robust therapeutic interventions based on our increasing knowledge of complex gene signaling networks.
Collapse
Affiliation(s)
- Anthony Szedlak
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
| | - Giovanni Paternostro
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- Salgomed Inc., Del Mar, California, United States of America
| | - Carlo Piermarocchi
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, United States of America
- Salgomed Inc., Del Mar, California, United States of America
| |
Collapse
|
19
|
Hoxha M, Fabris S, Agnelli L, Bollati V, Cutrona G, Matis S, Recchia AG, Gentile M, Cortelezzi A, Morabito F, Bertazzi PA, Ferrarini M, Neri A. Relevance of telomere/telomerase system impairment in early stage chronic lymphocytic leukemia. Genes Chromosomes Cancer 2014; 53:612-21. [PMID: 24706380 DOI: 10.1002/gcc.22171] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/18/2014] [Indexed: 01/10/2023] Open
Abstract
Several studies have proposed telomere length and telomerase activity as prognostic factors in chronic lymphocytic leukemia (CLL), whereas information addressing the role of telomere-associated genes is limited. We measured relative telomere length (RTL) and TERT expression levels in purified peripheral CD19(+) B-cells from seven healthy donors and 77 untreated CLLs in early stage disease (Binet A). Data were correlated with the major biological and cytogenetic markers, global DNA methylation (Alu and LINE-1), and clinical outcome. The expression profiles of telomere-associated genes were also investigated. RTL was decreased in CLLs as compared with controls (P < 0.001); within CLL, a progressive and significant RTL shortening was observed in patients from 13q- through +12, 11q-, and 17p- alterations; short telomeres were significantly associated with unmutated IGHV configuration and global DNA hypomethylation. Decreased RTL was associated with a shorter time to first treatment. A significant upregulation of POT1, TRF1, RAP1, MRE11A, RAD50, and RPA1 transcript levels was observed in CLLs compared with controls. Our study suggests that impairment of telomere/telomerase system represents an early event in CLL pathogenesis. Moreover, the correlation between telomere shortening and global DNA hypomethylation supports the involvement of DNA hypomethylation to increase chromosome instability. © 2014 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Mirjam Hoxha
- Department of Clinical Sciences and Community Health, Center of Molecular and Genetic Epidemiology, University of Milan, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Lionetti M, Fabris S, Cutrona G, Agnelli L, Ciardullo C, Matis S, Ciceri G, Colombo M, Maura F, Mosca L, Gentile M, Recchia AG, Ilariucci F, Musolino C, Molica S, Di Raimondo F, Cortelezzi A, Rossi D, Gaidano G, Morabito F, Ferrarini M, Neri A. High-throughput sequencing for the identification of NOTCH1 mutations in early stage chronic lymphocytic leukaemia: biological and clinical implications. Br J Haematol 2014; 165:629-39. [PMID: 24579978 DOI: 10.1111/bjh.12800] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/16/2014] [Indexed: 01/21/2023]
Abstract
NOTCH1 mutations have recently emerged as new genetic lesions significantly correlated with survival in chronic lymphocytic leukaemia (CLL). We performed deep next generation sequencing of the NOTCH1 mutation hotspot in 384 cases at diagnosis, including 100 monoclonal B cell lymphocytosis (MBL) and 284 Binet stage A CLL cases, enrolled in the Gruppo Italiano Studio Linfomi O-CLL1 multicentre trial. The NOTCH1 c.7541_7542delCT dinucleotide deletion was detected and confirmed by an extremely sensitive polymerase chain reaction-based approach in 11% of MBL and 13·4% of CLL patients. Remarkably, the NOTCH1 mutation was often observed at low clonal level, mainly in MBL patients. Sequential analyses in a fraction of cases showed that the NOTCH1 mutation generally does not occur during the disease course and that the mutational load in positive cases tends to be stable over time. NOTCH1-mutated cases, even at low clonal level, displayed a significant reduction in median progression-free survival, although NOTCH1 mutation lost its prognostic impact in a multivariate analysis including 11q and/or 17p deletion, IGHV mutational status, and MBL or CLL status. Our data highlight the importance of using highly sensitive methods to measure NOTCH1 mutations, in order to improve prognostic stratification and obtain useful information for potential therapeutic approaches.
Collapse
Affiliation(s)
- Marta Lionetti
- Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy; Haematology 1 CTMO, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Houldsworth J, Guttapalli A, Thodima V, Yan XJ, Mendiratta G, Zielonka T, Nanjangud G, Chen W, Patil S, Mato A, Brown JR, Rai K, Chiorazzi N, Chaganti RSK. Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia. Leuk Lymphoma 2013; 55:920-8. [PMID: 24047479 DOI: 10.3109/10428194.2013.845882] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Array comparative genomic hybridization (aCGH) has yet to be fully leveraged in a prognostic setting in chronic lymphocytic leukemia (CLL). Genomic imbalance was assessed in 288 CLL specimens using a targeted array. Based on 20 aberrations in a hierarchical manner, all 228 treatment-naive specimens were classified into a group with poor outcome (20.6%) exhibiting at least one aberration that was univariately associated with adverse outcome (gain: 2p, 3q, 8q, 17q, loss: 7q, 8p, 11q, 17p, 18p), good outcome (32.5%) showing 13q14 loss without any of the other 10 aberrations (gain: 1p, 7p, 12, 18p, 18q, 19, loss: 4p, 5p, 6q, 7p) or intermediate outcome (remainder). The three groups were significantly separated with respect to time to first treatment and overall survival (p < 0.001), and validation of the stratification scheme was performed in two independent datasets. Gain of 3q and 8q, and 17p loss were determined to be independent unfavorable prognostic biomarkers. TP53, NOTCH1 and SF3B1 mutations correlated with the presence of one poor outcome aCGH marker, at a considerably higher frequency than when only considering poor risk aberrations routinely detected by fluorescence in situ hybridization (FISH). These data support genomic imbalance evaluation in CLL by aCGH to assist in risk stratification.
Collapse
|
22
|
Dasgupta S, Lonard DM, O'Malley BW. Nuclear receptor coactivators: master regulators of human health and disease. Annu Rev Med 2013; 65:279-92. [PMID: 24111892 DOI: 10.1146/annurev-med-051812-145316] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transcriptional coregulators (coactivators and corepressors) have emerged as the principal modulators of the functions of nuclear receptors and other transcription factors. During the decade since the discovery of steroid receptor coactivator-1 (SRC-1), the first authentic coregulator, more than 400 coregulators have been identified and characterized, and deciphering their function has contributed significantly to our understanding of their role in human physiology. Deregulated expression of coregulators has been implicated in diverse disease states and related pathologies. The advancement of molecular technologies has enabled us to better characterize the molecular associations of the SRC family of coactivators with other protein complexes in the context of gene regulation. These continuing discoveries not only expand our knowledge of the roles of coactivators in various human diseases but allow us to discover novel coactivator-targeting strategies for therapeutic intervention in these diseases.
Collapse
Affiliation(s)
- Subhamoy Dasgupta
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030;
| | | | | |
Collapse
|