1
|
Schlosser P, Schiwitza A, Klaus J, Hieke-Schulz S, Szic KSV, Duyster J, Trepel M, Zirlik K, Schumacher M, Claus R. Conditional survival to assess prognosis in patients with chronic lymphocytic leukemia. Ann Hematol 2024; 103:1613-1622. [PMID: 38308707 PMCID: PMC11009732 DOI: 10.1007/s00277-024-05627-w] [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: 09/13/2023] [Accepted: 01/13/2024] [Indexed: 02/05/2024]
Abstract
Biomarkers in chronic lymphocytic leukemia (CLL) allow assessment of prognosis. However, the validity of current prognostic biomarkers based on a single assessment point remains unclear for patients who have survived one or more years. Conditional survival (CS) studies that address how prognosis may change over time, especially in prognostic subgroups, are still rare. We performed CS analyses to estimate 5-year survival in 1-year increments, stratified by baseline disease characteristics and known risk factors in two community-based cohorts of CLL patients (Freiburg University Hospital (n = 316) and Augsburg University Hospital (n = 564)) diagnosed between 1984 and 2021. We demonstrate that 5-year CS probability is stable (app. 75%) for the entire CLL patient cohort over 10 years. While age, sex, and stage have no significant impact on CS, patients with high-risk disease features such as non-mutated IGHV, deletion 17p, and high-risk CLL-IPI have a significantly worse prognosis at diagnosis, and 5-year CS steadily decreases with each additional year survived. Our results confirm that CLL patients have a stable survival probability with excess mortality and that the prognosis of high-risk CLL patients declines over time. We infer that CS-based prognostic information is relevant for disease management and counseling of CLL patients.
Collapse
Affiliation(s)
- Pascal Schlosser
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Annett Schiwitza
- Hematology/Oncology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Jonas Klaus
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
| | - Stefanie Hieke-Schulz
- Institute of Medical Biometry and Medical Informatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
- Roche Pharma AG, Grenzach-Wyhlen, Germany
| | - Katarzyna Szarc Vel Szic
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
| | - Justus Duyster
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
| | - Martin Trepel
- Hematology/Oncology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Katja Zirlik
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
- Tumor- Und BrustZentrum Ostschweiz, Chur, Switzerland
| | - Martin Schumacher
- Institute of Medical Biometry and Medical Informatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Rainer Claus
- Hematology/Oncology, Faculty of Medicine, University of Augsburg, Augsburg, Germany.
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany.
- Pathology, Faculty of Medicine, University of Augsburg, Augsburg, Germany.
- Faculty of Medicine, Comprehensive Cancer Center, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany.
| |
Collapse
|
2
|
Wagner A, Rouleau M, Villeneuve L, Le T, Peltier C, Allain ÉP, Beaudoin C, Tremblay S, Courtier F, Nguyen Van Long F, Laverdière I, Lévesque É, Banerji V, Vanura K, Guillemette C. A Non-Canonical Role for the Glycosyltransferase Enzyme UGT2B17 as a Novel Constituent of the B Cell Receptor Signalosome. Cells 2023; 12:cells12091295. [PMID: 37174695 PMCID: PMC10177405 DOI: 10.3390/cells12091295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
In chronic lymphocytic leukemia (CLL), an elevated glycosyltransferase UGT2B17 expression (UGT2B17HI) identifies a subgroup of patients with shorter survival and poor drug response. We uncovered a mechanism, possibly independent of its enzymatic function, characterized by an enhanced expression and signaling of the proximal effectors of the pro-survival B cell receptor (BCR) pathway and elevated Bruton tyrosine kinase (BTK) phosphorylation in B-CLL cells from UGT2B17HI patients. A prominent feature of B-CLL cells is the strong correlation of UGT2B17 expression with the adverse marker ZAP70 encoding a tyrosine kinase that promotes B-CLL cell survival. Their combined high expression levels in the treatment of naïve patients further defined a prognostic group with the highest risk of poor survival. In leukemic cells, UGT2B17 knockout and repression of ZAP70 reduced proliferation, suggesting that the function of UGT2B17 might involve ZAP70. Mechanistically, UGT2B17 interacted with several kinases of the BCR pathway, including ZAP70, SYK, and BTK, revealing a potential therapeutic vulnerability. The dual SYK and JAK/STAT6 inhibitor cerdulatinib most effectively compromised the proliferative advantage conferred by UGT2B17 compared to the selective BTK inhibitor ibrutinib. Findings point to an oncogenic role for UGT2B17 as a novel constituent of BCR signalosome also connected with microenvironmental signaling.
Collapse
Affiliation(s)
- Antoine Wagner
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Michèle Rouleau
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Lyne Villeneuve
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Trang Le
- Department of Medicine I, Division of Haematology and Haemostaseology, Medical University of Vienna, 1090 Vienna, Austria
| | - Cheryl Peltier
- Department of Internal Medicine & Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- CancerCare Manitoba Research Institute, Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Éric P Allain
- Molecular Genetics Laboratory, Dr. Georges-L-Dumont University Hospital Center, Moncton, NB E1C 2Z3, Canada
| | - Caroline Beaudoin
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Sophie Tremblay
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Fréderic Courtier
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Flora Nguyen Van Long
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Isabelle Laverdière
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| | - Éric Lévesque
- CRCHUQc-UL, Faculty of Medicine, and CRC-UL, Université Laval, Québec, QC G1V 4G2, Canada
| | - Versha Banerji
- Department of Internal Medicine & Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- CancerCare Manitoba Research Institute, Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Katrina Vanura
- Department of Medicine I, Division of Haematology and Haemostaseology, Medical University of Vienna, 1090 Vienna, Austria
| | - Chantal Guillemette
- Centre Hospitalier Universitaire de Québec Research Center-Université Laval (CRCHUQc-UL), Faculty of Pharmacy, and Centre de Recherche sur le Cancer de l'Université Laval (CRC-UL), Université Laval, Québec, QC G1V 4G2, Canada
| |
Collapse
|
3
|
Panda D, Das N, Thakral D, Gupta R. Genomic landscape of mature B-cell non-Hodgkin lymphomas - an appraisal from lymphomagenesis to drug resistance. J Egypt Natl Canc Inst 2022; 34:52. [PMID: 36504392 DOI: 10.1186/s43046-022-00154-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Mature B-cell non-Hodgkin lymphomas are one of the most common hematological malignancies with a divergent clinical presentation, phenotype, and course of disease regulated by underlying genetic mechanism. MAIN BODY Genetic and molecular alterations are not only critical for lymphomagenesis but also largely responsible for differing therapeutic response in these neoplasms. In recent years, advanced molecular tools have provided a deeper understanding regarding these oncogenic drives for predicting progression as well as refractory behavior in these diseases. The prognostic models based on gene expression profiling have also been proved effective in various clinical scenarios. However, considerable overlap does exist between the genotypes of individual lymphomas and at the same time where additional molecular lesions may be associated with each entity apart from the key genetic event. Therefore, genomics is one of the cornerstones in the multimodality approach essential for classification and risk stratification of B-cell non-Hodgkin lymphomas. CONCLUSION We hereby in this review discuss the wide range of genetic aberrancies associated with tumorigenesis, immune escape, and chemoresistance in major B-cell non-Hodgkin lymphomas.
Collapse
Affiliation(s)
- Devasis Panda
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India
| | - Nupur Das
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India
| | - Deepshi Thakral
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India
| | - Ritu Gupta
- Department of Laboratory Oncology, Dr. BRAIRCH, AIIMS, New Delhi, 110029, India.
| |
Collapse
|
4
|
Gabusi A, Gissi DB, Grillini S, Stefanini M, Tarsitano A, Marchetti C, Foschini MP, Montebugnoli L, Morandi L. Shared epigenetic alterations between oral cancer and periodontitis: a preliminary study. Oral Dis 2022. [PMID: 35567390 DOI: 10.1111/odi.14251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 04/13/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
Abstract
INTRODUCTION We recently developed a non-invasive sampling procedure for oral squamous cell carcinoma (OSCC) detection based on DNA methylation analysis of a panel of 13 genes. Oral cancer, as well as acute and chronic inflammatory diseases, may influence the methylation level of several genes in the oral cavity. In the present study, we evaluated the presence of periodontal disease(PD) and the methylation status using our 13-gene panel. METHODS Oral brushing specimens were collected from three different patient groups: 23 gingival OSCC patients, 15 patients affected by PD, and 15 healthy volunteers lacking evidence of PD. DNA methylation analysis was performed and each sample was determined to be positive or negative based on a predefined cut-off value. RESULTS Positive results were found for 23/23 OSCC patients, 3/15 PD patients and 0/15 samples from healthy volunteers. The GP1BB and MIR193 genes in the PD group exhibited mean methylation levels similar to OSCC patients. ZAP70 showed different methylation levels among three groups. CONCLUSION Preliminary data identified shared epigenetic alterations between PD and OSCC patients in two inflammatory genes(GP1BB and MIR193). This study may help identify potential links between the two diseases and serve as a starting point for future research focused on pathogenesis.
Collapse
Affiliation(s)
- Andrea Gabusi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Davide B Gissi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Sara Grillini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Martina Stefanini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Achille Tarsitano
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.,Oral and Maxillo-facial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna
| | - Claudio Marchetti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.,Oral and Maxillo-facial Surgery Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna
| | - Maria Pia Foschini
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lucio Montebugnoli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy
| | - Luca Morandi
- Functional MR Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Department of Biomedical and Neuromotor Sciences, University of Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| |
Collapse
|
5
|
Ochoa E, Zuber V, Bottolo L. Accurate Measurement of DNA Methylation: Challenges and Bias Correction. Methods Mol Biol 2022; 2432:25-47. [PMID: 35505205 DOI: 10.1007/978-1-0716-1994-0_3] [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] [Indexed: 06/14/2023]
Abstract
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility is still not fully understood. As the cost of genome sequencing technologies continues to drop, it will soon become commonplace to perform genome-wide quantification of DNA methylation at a single base-pair resolution. However, the demand for its accurate quantification might vary across studies. When the scope of the analysis is to detect regions of the genome with different methylation patterns between two or more conditions, e.g., case vs control; treatments vs placebo, accuracy is not crucial. This is the case in epigenome-wide association studies used as genome-wide screening of methylation changes to detect new candidate genes and regions associated with a specific disease or condition. If the aim of the analysis is to use DNA methylation measurements as a biomarker for diseases diagnosis and treatment (Laird, Nat Rev Cancer 3:253-266, 2003; Bock, Epigenomics 1:99-110, 2009), it is instead recommended to produce accurate methylation measurements. Furthermore, if the objective is the detection of DNA methylation in subclonal tumor cell populations or in circulating tumor DNA or in any case of mosaicism, the importance of accuracy becomes critical. The aim of this chapter is to describe the factors that could affect the precise measurement of methylation levels and a recent Bayesian statistical method called MethylCal and its extension that have been proposed to minimize this problem.
Collapse
Affiliation(s)
- Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Verena Zuber
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, UK.
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK.
- The Alan Turing Institute, London, UK.
| |
Collapse
|
6
|
Tariq F, Khan W, Ahmad W, Riaz SK, Khan M, Sherwani S, Haque S, Malik MFA, Iftikhar MJ, Khan S, Haq F. Effect of MHC Linked 7-Gene Signature on Delayed Hepatocellular Carcinoma Recurrence. J Pers Med 2021; 11:jpm11111129. [PMID: 34834481 PMCID: PMC8625636 DOI: 10.3390/jpm11111129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Dysregulated immune response significantly affects hepatocellular carcinoma's (HCC) prognosis. Human Leukocyte Antigens are key in devising immune responses against HCC. Here, we investigated how HLAs modulate HCC development at the transcriptomic level. RNA-seq data of 576 patients from two independent cohorts was retrieved. The clinicopathological relevance of all HLA genes was investigated using Fisher-Exact, correlation, and Kaplan-Meier and cox regression survival tests. Clustering of ~800 immune-related genes against HLAs was completed using a ward-agglomerative method. Networks were generated using 40 HLA associated unique genes and hub genes were investigated. HLAs including HLA-DMA, HLA-DMB, HLA-DOA and HLA-DRB6 were associated with delayed recurrence in both discovery (204 HCC cases) and validation (372 HCC cases) cohorts. Clustering analyses revealed 40 genes associated with these four HLAs in both cohorts. A set of seven genes (NCF4, TYROBP, LCP2, ZAP70, PTPRC, FYN and WAS) was found co-expressed at gene-gene interaction level in both cohorts. Furthermore, survival analysis revealed seven HLA-linked genes as predictors of delayed recurrence. Multivariate analysis also predicted that mean expression of 7-gene is an independent predictor of delayed recurrence in both cohorts. We conclude that the expression of 7-gene signature may lead to improved patient prognosis. Further studies are required for consideration in clinical practice.
Collapse
Affiliation(s)
- Fomaz Tariq
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | - Walizeb Khan
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | - Washaakh Ahmad
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | - Syeda Kiran Riaz
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan
- College of Medicine, Texas A&M University, College Station, TX 77840-77845, USA
| | - Mahvish Khan
- Department of Biology, College of Science, Ha’il University, Ha’il 55211, Saudi Arabia; (M.K.); (S.S.)
| | - Subuhi Sherwani
- Department of Biology, College of Science, Ha’il University, Ha’il 55211, Saudi Arabia; (M.K.); (S.S.)
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Bursa 16059, Turkey
| | - Muhammad Faraz Arshad Malik
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
| | | | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha’il University, Ha’il 55211, Saudi Arabia
- Correspondence: (S.K.); (F.H.)
| | - Farhan Haq
- Department of Biosciences, COMSATS University, Islamabad 44000, Pakistan; (F.T.); (W.K.); (W.A.); (S.K.R.); (M.F.A.M.)
- Correspondence: (S.K.); (F.H.)
| |
Collapse
|
7
|
Chen J, Moore A, Ringshausen I. ZAP-70 Shapes the Immune Microenvironment in B Cell Malignancies. Front Oncol 2020; 10:595832. [PMID: 33194762 PMCID: PMC7653097 DOI: 10.3389/fonc.2020.595832] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Zeta-chain-associated protein kinase-70 (ZAP-70) is a tyrosine kinase mainly expressed in T cells, NK cells and a subset of B cells. Primarily it functions in T cell receptor (TCR) activation through its tyrosine kinase activity. Aberrant expression of ZAP-70 has been evidenced in different B cell malignancies, with high expression of ZAP-70 in a subset of patients with Chronic Lymphocytic Leukemia (CLL), associating with unfavorable disease outcomes. Previous studies to understand the mechanisms underlying this correlation have been focused on tumor intrinsic mechanisms, including the activation of B cell receptor (BCR) signaling. Recent evidence also suggests that ZAP-70, intrinsically expressed in tumor cells, can modulate the cross-talk between malignant B cells and the immune environment, implying a more complex role of ZAP-70 in the pathogenesis of B cell malignancies. Meanwhile, the indispensible roles of ZAP-70 in T cell and NK cell activation also demonstrate that the autologous expression of ZAP-70 in the immune environment can be a central target in modulation of tumor immunity. Here we review the evidences of the link between ZAP-70 and tumor immunology in the microenvironment in B cell malignancies. Considering an emerging role of immunotherapies in treating these conditions, understanding the distinct molecular functions of ZAP-70 in a broader cellular context could ultimately benefit patient care.
Collapse
Affiliation(s)
| | | | - Ingo Ringshausen
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Wellcome Trust/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
8
|
SOHO State of the Art Updates and Next Questions: Clonal Evolution in Chronic Lymphocytic Leukemia. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2020; 20:779-784. [PMID: 33039357 DOI: 10.1016/j.clml.2020.08.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 12/27/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is an indolent disease with a long-lasting clinical course, with indication for treatment only when symptomatic. Its clinical heterogeneity is widely reported, with some patients requiring treatment soon after diagnosis because of development of cytopenia or bulky lymphadenopathy, and others showing a stable or a slowly progressive disease not requiring treatment for decades. Longitudinal sampling of peripheral blood, with accessible tumor cells and circulating tumor DNA, enabled the analysis of disease growing dynamics and the characterization of clonal evolution. Here we describe the main known features of CLL genomics and its shaping upon treatment, which can lead to progression, treatment refractoriness, or transformation into an aggressive lymphoma.
Collapse
|
9
|
Kreuzberger N, Damen JA, Trivella M, Estcourt LJ, Aldin A, Umlauff L, Vazquez-Montes MD, Wolff R, Moons KG, Monsef I, Foroutan F, Kreuzer KA, Skoetz N. Prognostic models for newly-diagnosed chronic lymphocytic leukaemia in adults: a systematic review and meta-analysis. Cochrane Database Syst Rev 2020; 7:CD012022. [PMID: 32735048 PMCID: PMC8078230 DOI: 10.1002/14651858.cd012022.pub2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Chronic lymphocytic leukaemia (CLL) is the most common cancer of the lymphatic system in Western countries. Several clinical and biological factors for CLL have been identified. However, it remains unclear which of the available prognostic models combining those factors can be used in clinical practice to predict long-term outcome in people newly-diagnosed with CLL. OBJECTIVES To identify, describe and appraise all prognostic models developed to predict overall survival (OS), progression-free survival (PFS) or treatment-free survival (TFS) in newly-diagnosed (previously untreated) adults with CLL, and meta-analyse their predictive performances. SEARCH METHODS We searched MEDLINE (from January 1950 to June 2019 via Ovid), Embase (from 1974 to June 2019) and registries of ongoing trials (to 5 March 2020) for development and validation studies of prognostic models for untreated adults with CLL. In addition, we screened the reference lists and citation indices of included studies. SELECTION CRITERIA We included all prognostic models developed for CLL which predict OS, PFS, or TFS, provided they combined prognostic factors known before treatment initiation, and any studies that tested the performance of these models in individuals other than the ones included in model development (i.e. 'external model validation studies'). We included studies of adults with confirmed B-cell CLL who had not received treatment prior to the start of the study. We did not restrict the search based on study design. DATA COLLECTION AND ANALYSIS We developed a data extraction form to collect information based on the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies (CHARMS). Independent pairs of review authors screened references, extracted data and assessed risk of bias according to the Prediction model Risk Of Bias ASsessment Tool (PROBAST). For models that were externally validated at least three times, we aimed to perform a quantitative meta-analysis of their predictive performance, notably their calibration (proportion of people predicted to experience the outcome who do so) and discrimination (ability to differentiate between people with and without the event) using a random-effects model. When a model categorised individuals into risk categories, we pooled outcome frequencies per risk group (low, intermediate, high and very high). We did not apply GRADE as guidance is not yet available for reviews of prognostic models. MAIN RESULTS From 52 eligible studies, we identified 12 externally validated models: six were developed for OS, one for PFS and five for TFS. In general, reporting of the studies was poor, especially predictive performance measures for calibration and discrimination; but also basic information, such as eligibility criteria and the recruitment period of participants was often missing. We rated almost all studies at high or unclear risk of bias according to PROBAST. Overall, the applicability of the models and their validation studies was low or unclear; the most common reasons were inappropriate handling of missing data and serious reporting deficiencies concerning eligibility criteria, recruitment period, observation time and prediction performance measures. We report the results for three models predicting OS, which had available data from more than three external validation studies: CLL International Prognostic Index (CLL-IPI) This score includes five prognostic factors: age, clinical stage, IgHV mutational status, B2-microglobulin and TP53 status. Calibration: for the low-, intermediate- and high-risk groups, the pooled five-year survival per risk group from validation studies corresponded to the frequencies observed in the model development study. In the very high-risk group, predicted survival from CLL-IPI was lower than observed from external validation studies. Discrimination: the pooled c-statistic of seven external validation studies (3307 participants, 917 events) was 0.72 (95% confidence interval (CI) 0.67 to 0.77). The 95% prediction interval (PI) of this model for the c-statistic, which describes the expected interval for the model's discriminative ability in a new external validation study, ranged from 0.59 to 0.83. Barcelona-Brno score Aimed at simplifying the CLL-IPI, this score includes three prognostic factors: IgHV mutational status, del(17p) and del(11q). Calibration: for the low- and intermediate-risk group, the pooled survival per risk group corresponded to the frequencies observed in the model development study, although the score seems to overestimate survival for the high-risk group. Discrimination: the pooled c-statistic of four external validation studies (1755 participants, 416 events) was 0.64 (95% CI 0.60 to 0.67); 95% PI 0.59 to 0.68. MDACC 2007 index score The authors presented two versions of this model including six prognostic factors to predict OS: age, B2-microglobulin, absolute lymphocyte count, gender, clinical stage and number of nodal groups. Only one validation study was available for the more comprehensive version of the model, a formula with a nomogram, while seven studies (5127 participants, 994 events) validated the simplified version of the model, the index score. Calibration: for the low- and intermediate-risk groups, the pooled survival per risk group corresponded to the frequencies observed in the model development study, although the score seems to overestimate survival for the high-risk group. Discrimination: the pooled c-statistic of the seven external validation studies for the index score was 0.65 (95% CI 0.60 to 0.70); 95% PI 0.51 to 0.77. AUTHORS' CONCLUSIONS Despite the large number of published studies of prognostic models for OS, PFS or TFS for newly-diagnosed, untreated adults with CLL, only a minority of these (N = 12) have been externally validated for their respective primary outcome. Three models have undergone sufficient external validation to enable meta-analysis of the model's ability to predict survival outcomes. Lack of reporting prevented us from summarising calibration as recommended. Of the three models, the CLL-IPI shows the best discrimination, despite overestimation. However, performance of the models may change for individuals with CLL who receive improved treatment options, as the models included in this review were tested mostly on retrospective cohorts receiving a traditional treatment regimen. In conclusion, this review shows a clear need to improve the conducting and reporting of both prognostic model development and external validation studies. For prognostic models to be used as tools in clinical practice, the development of the models (and their subsequent validation studies) should adapt to include the latest therapy options to accurately predict performance. Adaptations should be timely.
Collapse
MESH Headings
- Adult
- Age Factors
- Bias
- Biomarkers, Tumor
- Calibration
- Confidence Intervals
- Discriminant Analysis
- Disease-Free Survival
- Female
- Genes, p53/genetics
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Models, Theoretical
- Neoplasm Staging
- Prognosis
- Progression-Free Survival
- Receptors, Antigen, B-Cell/genetics
- Reproducibility of Results
- Tumor Suppressor Protein p53/genetics
Collapse
Affiliation(s)
- Nina Kreuzberger
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Johanna Aag Damen
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | | | - Lise J Estcourt
- Haematology/Transfusion Medicine, NHS Blood and Transplant, Oxford, UK
| | - Angela Aldin
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lisa Umlauff
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | | | - Karel Gm Moons
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ina Monsef
- Cochrane Haematology, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Farid Foroutan
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Karl-Anton Kreuzer
- Center of Integrated Oncology Cologne-Bonn, Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Nicole Skoetz
- Cochrane Cancer, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| |
Collapse
|
10
|
Lundh S, Maji S, Melenhorst JJ. Next-generation CAR T cells to overcome current drawbacks. Int J Hematol 2020; 114:532-543. [PMID: 32594314 DOI: 10.1007/s12185-020-02923-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 06/11/2020] [Indexed: 12/26/2022]
Abstract
As a rapidly emerging treatment in the oncology field, adoptive transfer of autologous, genetically modified chimeric antigen receptor (CAR) T cells has shown striking efficacy and is curative in certain relapsed/refractory patients with hematologic malignancy. This treatment modality of using a "living drug" offers many tantalizing and novel therapeutic strategies for cancer patients whose remaining treatment options may have otherwise been limited. Despite the early success of CAR T cells in hematologic malignancies, many barriers remain for widespread adoption. General barriers include cellular manufacturing limitations, baseline quality of the T cells, adverse events post-infusion such as cytokine release syndrome (CRS) and neurotoxicity, and host rejection of non-human CARs. Additionally, each hematologic disease presents unique mechanisms of relapse which have to be addressed in future clinical trials if we are to augment the efficacy of CAR T treatment. In this review, we will describe current barriers to hindering efficacy of CAR T-cell treatment for hematologic malignancies in a disease-specific manner and review recent innovations aimed at enhancing the potency and applicability of CAR T cells, with the overall goal of building a framework to begin incorporating this form of therapy into the standard medical management of blood cancers.
Collapse
Affiliation(s)
- Stefan Lundh
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sayantan Maji
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Joseph Melenhorst
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA. .,Parker Institute for Cancer Immunotherapy, University of Pennsylvania, South Pavilion Expansion, Room 9-105, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA, 19104, USA.
| |
Collapse
|
11
|
Wierzbinska JA, Toth R, Ishaque N, Rippe K, Mallm JP, Klett LC, Mertens D, Zenz T, Hielscher T, Seifert M, Küppers R, Assenov Y, Lutsik P, Stilgenbauer S, Roessner PM, Seiffert M, Byrd J, Oakes CC, Plass C, Lipka DB. Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL. Genome Med 2020; 12:29. [PMID: 32188505 PMCID: PMC7081711 DOI: 10.1186/s13073-020-00724-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
Background In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset, and progression. The cancer epigenome is composed of the epigenetic patterns present in the tumor-initiating cell at the time of transformation, and the tumor-specific epigenetic alterations that are acquired during tumor initiation and progression. The precise dissection of these two components of the tumor epigenome will facilitate a better understanding of the biological mechanisms underlying malignant transformation. Chronic lymphocytic leukemia (CLL) originates from differentiating B cells, which undergo extensive epigenetic programming. This poses the challenge to precisely determine the epigenomic ground state of the cell-of-origin in order to identify CLL-specific epigenetic aberrations. Methods We developed a linear regression model, methylome-based cell-of-origin modeling (Methyl-COOM), to map the cell-of-origin for individual CLL patients based on the continuum of epigenomic changes during normal B cell differentiation. Results Methyl-COOM accurately maps the cell-of-origin of CLL and identifies CLL-specific aberrant DNA methylation events that are not confounded by physiologic epigenetic B cell programming. Furthermore, Methyl-COOM unmasks abnormal action of transcription factors, altered super-enhancer activities, and aberrant transcript expression in CLL. Among the aberrantly regulated transcripts were many genes that have previously been implicated in T cell biology. Flow cytometry analysis of these markers confirmed their aberrant expression on malignant B cells at the protein level. Conclusions Methyl-COOM analysis of CLL identified disease-specific aberrant gene regulation. The aberrantly expressed genes identified in this study might play a role in immune-evasion in CLL and might serve as novel targets for immunotherapy approaches. In summary, we propose a novel framework for in silico modeling of reference DNA methylomes and for the identification of cancer-specific epigenetic changes, a concept that can be broadly applied to other human malignancies. Electronic supplementary material Supplementary information accompanies this paper at 10.1186/s13073-020-00724-7.
Collapse
Affiliation(s)
- Justyna A Wierzbinska
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,The German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Reka Toth
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Naveed Ishaque
- The German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Karsten Rippe
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Jan-Philipp Mallm
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Lara C Klett
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Division of Chromatin Networks, DKFZ, Heidelberg, Germany
| | - Daniel Mertens
- The German Cancer Consortium (DKTK), Heidelberg, Germany.,Mechanisms of Leukemogenesis, DKFZ, Heidelberg, Germany
| | - Thorsten Zenz
- Experimental Hematology Lab, University Hospital Zurich, Zurich, Switzerland
| | | | - Marc Seifert
- Group Molecular Genetics, Essen University Hospital, Essen, Germany
| | - Ralf Küppers
- Group Molecular Genetics, Essen University Hospital, Essen, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | | | | | | | - John Byrd
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, USA
| | - Christopher C Oakes
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, USA
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,The German Cancer Consortium (DKTK), Heidelberg, Germany.
| | - Daniel B Lipka
- The German Cancer Consortium (DKTK), Heidelberg, Germany. .,Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Faculty of Medicine, Medical Center, Otto-von-Guericke-University, 39120, Magdeburg, Germany.
| |
Collapse
|
12
|
Gissi DB, Tarsitano A, Gabusi A, Rossi R, Attardo G, Lenzi J, Marchetti C, Montebugnoli L, Foschini MP, Morandi L. 13-gene DNA Methylation Analysis from Oral Brushing: A Promising Non Invasive Tool in the Follow-up of Oral Cancer Patients. J Clin Med 2019; 8:jcm8122107. [PMID: 31810211 PMCID: PMC6947392 DOI: 10.3390/jcm8122107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
Background: This study aimed to evaluate the prognostic value of a non-invasive sampling procedure based on 13-gene DNA methylation analysis in the follow-up of patients previously treated for oral squamous cell carcinoma (OSCC). Methods: The study population included 49 consecutive patients treated for OSCC. Oral brushing sample collection was performed at two different times: before any cancer treatment in the tumor mass and during patient follow-up almost 6 months after OSCC treatment, within the regenerative area after OSCC resection. Each sample was considered positive or negative in relation to a predefined cut-off value. Results: Before any cancer treatment, 47/49 specimens exceeded the score and were considered as positive. Six months after OSCC resection, 16/49 specimens also had positive scores in the samples collected from the regenerative area. During the follow-up period, 7/49 patients developed locoregional relapse: 6/7 patients had a positive score in the regenerative area after OSCC resection. The presence of a positive score after oral cancer treatment was the most powerful variable related to the appearance of locoregional relapse. Conclusion: 13-gene DNA methylation analysis by oral brushing may have a clinical application as a prognostic non-invasive tool in the follow-up of patients surgically treated for OSCC.
Collapse
Affiliation(s)
- Davide B. Gissi
- Section of Oral Sciences, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (A.G.); (R.R.); (L.M.)
- Correspondence: ; Tel.: +39-0512088123
| | - Achille Tarsitano
- Section of Maxillo-Facial Surgery at Policlinico S. Orsola-Malpighi, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy; (A.T.); (C.M.)
| | - Andrea Gabusi
- Section of Oral Sciences, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (A.G.); (R.R.); (L.M.)
| | - Roberto Rossi
- Section of Oral Sciences, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (A.G.); (R.R.); (L.M.)
| | - Giuseppe Attardo
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy; (G.A.); (M.P.F.)
| | - Jacopo Lenzi
- Section of Hygiene, Department of Biomedical and Neuromotor Sciences, Public Health and Medical Statistics, University of Bologna, 40126 Bologna, Italy
| | - Claudio Marchetti
- Section of Maxillo-Facial Surgery at Policlinico S. Orsola-Malpighi, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy; (A.T.); (C.M.)
| | - Lucio Montebugnoli
- Section of Oral Sciences, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (A.G.); (R.R.); (L.M.)
| | - Maria P. Foschini
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy; (G.A.); (M.P.F.)
| | - Luca Morandi
- Functional MR Unit, IRCCS Istituto delle Scienze Neurologiche di Bologna, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy;
| |
Collapse
|
13
|
Xanthopoulos C, Kostareli E. Advances in Epigenetics and Epigenomics in Chronic Lymphocytic Leukemia. CURRENT GENETIC MEDICINE REPORTS 2019. [DOI: 10.1007/s40142-019-00178-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
Purpose of Review
The development and progression of chronic lymphocytic leukemia (CLL), a highly heterogenous B cell malignancy, are influenced by both genetic and environmental factors. Environmental factors, including pharmacological interventions, can affect the epigenetic landscape of CLL and thereby determine the CLL phenotype, clonal evolution, and clinical outcome. In this review, we critically present the latest advances in the field of CLL epigenomics/epigenetics in order to provide a systematic overview of to-date achievements and highlight the potential of epigenomics approaches in light of novel treatment therapies.
Recent Findings
Recent technological advances have enabled broad and precise mapping of the CLL epigenome. The identification of CLL-specific DNA methylation patterns has allowed for accurate CLL subtype definition, a better understanding of clonal origin and evolution, and the discovery of reliable biomarkers. More recently, studies have started to unravel the prognostic, predictive, and therapeutic potential of mapping chromatin dynamics and histone modifications in CLL. Finally, analysis of non-coding RNA expression has indicated their contribution to disease pathogenesis and helped to define prognostic subsets in CLL.
Summary
Overall, the potential of CLL epigenomics for predicting treatment response and resistance is mounting, especially with the advent of novel targeted CLL therapies.
Collapse
|
14
|
Developmental subtypes assessed by DNA methylation-iPLEX forecast the natural history of chronic lymphocytic leukemia. Blood 2019; 134:688-698. [PMID: 31292113 DOI: 10.1182/blood.2019000490] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/03/2019] [Indexed: 12/26/2022] Open
Abstract
Alterations in global DNA methylation patterns are a major hallmark of cancer and represent attractive biomarkers for personalized risk stratification. Chronic lymphocytic leukemia (CLL) risk stratification studies typically focus on time to first treatment (TTFT), time to progression (TTP) after treatment, and overall survival (OS). Whereas TTFT risk stratification remains similar over time, TTP and OS have changed dramatically with the introduction of targeted therapies, such as the Bruton tyrosine kinase inhibitor ibrutinib. We have shown that genome-wide DNA methylation patterns in CLL are strongly associated with phenotypic differentiation and patient outcomes. Here, we developed a novel assay, termed methylation-iPLEX (Me-iPLEX), for high-throughput quantification of targeted panels of single cytosine guanine dinucleotides from multiple independent loci. Me-iPLEX was used to classify CLL samples into 1 of 3 known epigenetic subtypes (epitypes). We examined the impact of epitype in 1286 CLL patients from 4 independent cohorts representing a comprehensive view of CLL disease course and therapies. We found that epitype significantly predicted TTFT and OS among newly diagnosed CLL patients. Additionally, epitype predicted TTP and OS with 2 common CLL therapies: chemoimmunotherapy and ibrutinib. Epitype retained significance after stratifying by biologically related biomarkers, immunoglobulin heavy chain mutational status, and ZAP70 expression, as well as other common prognostic markers. Furthermore, among several biological traits enriched between epitypes, we found highly biased immunogenetic features, including IGLV3-21 usage in the poorly characterized intermediate-programmed CLL epitype. In summary, Me-iPLEX is an elegant method to assess epigenetic signatures, including robust classification of CLL epitypes that independently stratify patient risk at diagnosis and time of treatment.
Collapse
|
15
|
Sridhar K, Singh A, Butzmann A, Jangam D, Ohgami RS. Molecular genetic testing methodologies in hematopoietic diseases: current and future methods. Int J Lab Hematol 2019; 41 Suppl 1:102-116. [PMID: 31069972 DOI: 10.1111/ijlh.13024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Rapid technological advancements in clinical molecular genetics have increased our diagnostic and prognostic capabilities in health care. Understanding these assays, as well as how they may change over time, is critical for pathologists, clinicians, and translational researchers alike. METHODS This review provides a practical summary and basic reference for current molecular genetic technologies, as well as new testing methodologies that are in use, gaining momentum, or anticipated to contribute more broadly in the future. RESULTS Here, we discuss DNA and RNA based methodologies including classic assays such as the polymerase chain reaction (PCR), Sanger sequencing, and microarrays, to more cutting-edge next-generation sequencing (NGS) based assays and emerging molecular technologies such as cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA), and NGS-based detection of infectious disease organisms. CONCLUSION This review serves as a basic foundation for knowledge in current and emerging clinical molecular genetic technologies.
Collapse
Affiliation(s)
- Kaushik Sridhar
- Department of Pathology, Stanford University, Stanford, California
| | - Amol Singh
- Department of Pathology, Stanford University, Stanford, California
| | | | - Diwash Jangam
- Department of Pathology, Stanford University, Stanford, California
| | - Robert S Ohgami
- Department of Pathology, Stanford University, Stanford, California.,Department of Pathology, University of California, San Francisco, CA
| |
Collapse
|
16
|
Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K. Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Syst Biol 2019; 15:e8339. [PMID: 31118277 PMCID: PMC6529931 DOI: 10.15252/msb.20188339] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In chronic lymphocytic leukemia (CLL), a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin features, we mapped DNA methylation, seven histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF, as well as the transcriptome of B cells from CLL patients and healthy donors. A globally increased histone deacetylase activity was detected and half of the genome comprised transcriptionally downregulated partially DNA methylated domains demarcated by CTCF. CLL samples displayed a H3K4me3 redistribution and nucleosome gain at promoters as well as changes of enhancer activity and enhancer linkage to target genes. A DNA binding motif analysis identified transcription factors that gained or lost binding in CLL at sites with aberrant chromatin features. These findings were integrated into a gene regulatory enhancer containing network enriched for B‐cell receptor signaling pathway components. Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.
Collapse
Affiliation(s)
- Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics and Heidelberg Center for Personalized Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lara C Klett
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sabrina J Kugler
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Jose M Muino
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Vladimir B Teif
- School of Biological Sciences, University of Essex, Colchester, UK
| | - Alexandra M Poos
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Jena, Germany
| | - Sebastian Großmann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.,Centre de Biologie Intégrative (CBI), CNRS, UPS, Toulouse, France
| | - Daniele Tavernari
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Sandra D Koser
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Jena, Germany
| | - Daniel Remondini
- Department of Physics and Astronomy, Bologna University, Bologna, Italy
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Mertens
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany .,Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| |
Collapse
|
17
|
Kittai AS, Lunning M, Danilov AV. Relevance of Prognostic Factors in the Era of Targeted Therapies in CLL. Curr Hematol Malig Rep 2019; 14:302-309. [DOI: 10.1007/s11899-019-00511-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
18
|
Daugaard I, Hussmann D, Kristensen L, Kristensen T, Kjeldsen TE, Nyvold CG, Larsen TS, Møller MB, Hansen LL, Wojdacz TK. Chronic lymphocytic leukemia patients with heterogeneously or fully methylated LPL promotor display longer time to treatment. Epigenomics 2018; 10:1155-1166. [PMID: 30182737 DOI: 10.2217/epi-2018-0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIM We investigated whether DNA methylation regulates expression of LPL and PI3K complex genes in chronic lymphocytic leukemia (CLL) and evaluated the prognostic significance of LPL promoter methylation in CLL patients. Patients & methods: Methylation of LPL promoter was assessed in 112 patients using methylation-sensitive high-resolution melting (MS-HRM). RESULTS Patients with a fully or heterogeneously methylated LPL promoter had significantly longer median time to treatment (p < 0.001) and 75% lower (hazard ratio: 0.25; 95% CI: 0.15-0.42; p < 0.001) risk of requirement for treatment as opposed to patients with nonmethylated promoter. Multivariate modeling confirmed independent prognostic value of these findings. CONCLUSION Chronic lymphocytic leukemia patients with a fully or heterogeneously methylated LPL gene promoter display indolent disease course and acquisition of heterogeneous methylation of LPL promoter is insufficient to induce gene expression.
Collapse
Affiliation(s)
- Iben Daugaard
- Department of Biomedicine, Aarhus University, Bartholins Allé 6, DK-8000 Aarhus C, Denmark
| | - Dianna Hussmann
- Department of Biomedicine, Aarhus University, Bartholins Allé 6, DK-8000 Aarhus C, Denmark
| | - Louise Kristensen
- Department of Pathology, Odense University Hospital, J. B. Winsløws Vej 15, 5000 Odense C, Denmark
| | - Thomas Kristensen
- Department of Pathology, Odense University Hospital, J. B. Winsløws Vej 15, 5000 Odense C, Denmark
| | - Tina E Kjeldsen
- Department of Biomedicine, Aarhus University, Bartholins Allé 6, DK-8000 Aarhus C, Denmark
| | - Charlotte G Nyvold
- Department of Haematology, Odense University Hospital, Sdr. Bouldvard 29, 5000 Odense C, Denmark
| | - Thomas S Larsen
- Department of Haematology, Odense University Hospital, Sdr. Bouldvard 29, 5000 Odense C, Denmark
| | - Michael B Møller
- Department of Pathology, Odense University Hospital, J. B. Winsløws Vej 15, 5000 Odense C, Denmark
| | - Lise Lotte Hansen
- Department of Biomedicine, Aarhus University, Bartholins Allé 6, DK-8000 Aarhus C, Denmark
| | - Tomasz K Wojdacz
- Department of Biomedicine, Aarhus University, Bartholins Allé 6, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
| |
Collapse
|
19
|
Insight into origins, mechanisms, and utility of DNA methylation in B-cell malignancies. Blood 2018; 132:999-1006. [PMID: 30037886 DOI: 10.1182/blood-2018-02-692970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/15/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding how tumor cells fundamentally alter their identity is critical to identify specific vulnerabilities for use in precision medicine. In B-cell malignancy, knowledge of genetic changes has resulted in great gains in our understanding of the biology of tumor cells, impacting diagnosis, prognosis, and treatment. Despite this knowledge, much remains to be explained as genetic events do not completely explain clinical behavior and outcomes. Many patients lack recurrent driver mutations, and said drivers can persist in nonmalignant cells of healthy individuals remaining cancer-free for decades. Epigenetics has emerged as a valuable avenue to further explain tumor phenotypes. The epigenetic landscape is the software that powers and stabilizes cellular identity by abridging a broad genome into the essential information required per cell. A genome-level view of B-cell malignancies reveals complex but recurrent epigenetic patterns that define tumor types and subtypes, permitting high-resolution classification and novel insight into tumor-specific mechanisms. Epigenetic alterations are guided by distinct cellular processes, such as polycomb-based silencing, transcription, signaling pathways, and transcription factor activity, and involve B-cell-specific aspects, such as activation-induced cytidine deaminase activity and germinal center-specific events. Armed with a detailed knowledge of the epigenetic events that occur across the spectrum of B-cell differentiation, B-cell tumor-specific aberrations can be detected with improved accuracy and serve as a model for identification of tumor-specific events in cancer. Insight gained through recent efforts may prove valuable in guiding the use of both epigenetic- and nonepigenetic-based therapies.
Collapse
|
20
|
Strati P, Jain N, O'Brien S. Chronic Lymphocytic Leukemia: Diagnosis and Treatment. Mayo Clin Proc 2018; 93:651-664. [PMID: 29728204 DOI: 10.1016/j.mayocp.2018.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/30/2018] [Accepted: 03/02/2018] [Indexed: 12/27/2022]
Abstract
The complexity of the treatment of patients with chronic lymphocytic leukemia has increased substantially over the past several years as a consequence of the advent of novel biological agents such as ibrutinib, idelalisib, and venetoclax, as well as increasingly potent anti-CD20 monoclonal antibodies. In addition, the identification of molecular predictive markers and the introduction of more sensitive and sophisticated techniques to assess minimal residual disease have allowed optimization of the use of chemoimmunotherapy and targeted therapies and may become standard of care in the future. This review summarizes the diagnosis, prognostication, and treatment of patients with chronic lymphocytic leukemia with emphasis on new prognostic and predictive factors and novel treatment strategies.
Collapse
MESH Headings
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Humans
- Immunotherapy/methods
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
Collapse
Affiliation(s)
- Paolo Strati
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nitin Jain
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Susan O'Brien
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Orange, CA.
| |
Collapse
|
21
|
Affiliation(s)
- Byron B. Au-Yeung
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Lin Shen
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, California 94143, USA;,
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, California 94143, USA;,
- Howard Hughes Medical Institute, University of California, San Francisco, California 94143, USA
| |
Collapse
|
22
|
Liu Y, Wang Y, Yang J, Bi Y, Wang H. ZAP-70 in chronic lymphocytic leukemia: A meta-analysis. Clin Chim Acta 2018; 483:82-88. [PMID: 29680229 DOI: 10.1016/j.cca.2018.04.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/14/2018] [Accepted: 04/16/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND Recent studies have reported that zeta-chain-associated protein kinase 70 (ZAP-70) expression plays a prognostic role in chronic lymphocytic leukemia (CLL). However, these results remain controversial. Thus, we performed a meta-analysis to clarify the prognostic value of ZAP-70 expression in CLL. MATERIALS AND METHODS Relevant studies were searched in PubMed, Embase, Cochrane library, and Web of Science up to January 2018. Clinicopathological features and prognostic data were extracted from the studies. We pooled estimates and 95% confidence intervals (CIs) and estimated the heterogeneity of studies using Mantel-Haenszel or DerSimonian and Laird method. RESULTS Twelve studies that included 1956 patients with CLL were eligible for inclusion. The pooled results revealed that increased ZAP-70 expression was significantly associated with poor overall survival (hazard ratio [HR] = 2.48, 95% CI: 1.72-3.59, P = 0.019, I2 = 53.0%) and event-free survival (HR = 4.17, 95% CI: 2.17-8.01, P = 0.014, I2 = 68.2%) in a random-effects model with significant heterogeneity. Clinicopathological analysis demonstrated that ZAP-70 expression was significantly associated with unmutated immunoglobulin heavy-chain genes, CD38 expression, serum β-2 microglobulin, and lymphocyte doubling time. CONCLUSIONS Our findings indicated that ZAP-70 was a strong prognostic biomarker for patients with CLL.
Collapse
Affiliation(s)
- Yini Liu
- Department of Occupational and Environmental Health, School of Health Sciences, Wuhan University, Donghu Road 115, Wuhan 430071, China
| | - Yangfeng Wang
- Department of Occupational and Environmental Health, School of Health Sciences, Wuhan University, Donghu Road 115, Wuhan 430071, China
| | - Jule Yang
- Department of Occupational and Environmental Health, School of Health Sciences, Wuhan University, Donghu Road 115, Wuhan 430071, China
| | - Yongyi Bi
- Department of Occupational and Environmental Health, School of Health Sciences, Wuhan University, Donghu Road 115, Wuhan 430071, China
| | - Hong Wang
- Department of Occupational and Environmental Health, School of Health Sciences, Wuhan University, Donghu Road 115, Wuhan 430071, China.
| |
Collapse
|
23
|
Ozer HG, El-Gamal D, Powell B, Hing ZA, Blachly JS, Harrington B, Mitchell S, Grieselhuber NR, Williams K, Lai TH, Alinari L, Baiocchi RA, Brinton L, Baskin E, Cannon M, Beaver L, Goettl VM, Lucas DM, Woyach JA, Sampath D, Lehman AM, Yu L, Zhang J, Ma Y, Zhang Y, Spevak W, Shi S, Severson P, Shellooe R, Carias H, Tsang G, Dong K, Ewing T, Marimuthu A, Tantoy C, Walters J, Sanftner L, Rezaei H, Nespi M, Matusow B, Habets G, Ibrahim P, Zhang C, Mathé EA, Bollag G, Byrd JC, Lapalombella R. BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor. Cancer Discov 2018; 8:458-477. [PMID: 29386193 PMCID: PMC5882533 DOI: 10.1158/2159-8290.cd-17-0902] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/12/2017] [Accepted: 01/26/2018] [Indexed: 11/16/2022]
Abstract
Bromodomain and extra-terminal (BET) family proteins are key regulators of gene expression in cancer. Herein, we utilize BRD4 profiling to identify critical pathways involved in pathogenesis of chronic lymphocytic leukemia (CLL). BRD4 is overexpressed in CLL and is enriched proximal to genes upregulated or de novo expressed in CLL with known functions in disease pathogenesis and progression. These genes, including key members of the B-cell receptor (BCR) signaling pathway, provide a rationale for this therapeutic approach to identify new targets in alternative types of cancer. Additionally, we describe PLX51107, a structurally distinct BET inhibitor with novel in vitro and in vivo pharmacologic properties that emulates or exceeds the efficacy of BCR signaling agents in preclinical models of CLL. Herein, the discovery of the involvement of BRD4 in the core CLL transcriptional program provides a compelling rationale for clinical investigation of PLX51107 as epigenetic therapy in CLL and application of BRD4 profiling in other cancers.Significance: To date, functional studies of BRD4 in CLL are lacking. Through integrated genomic, functional, and pharmacologic analyses, we uncover the existence of BRD4-regulated core CLL transcriptional programs and present preclinical proof-of-concept studies validating BET inhibition as an epigenetic approach to target BCR signaling in CLL. Cancer Discov; 8(4); 458-77. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 371.
Collapse
MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Cell Cycle Proteins
- Cell Line, Tumor
- Cell Proliferation
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Humans
- Isoxazoles/pharmacology
- Isoxazoles/therapeutic use
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/physiopathology
- Mice
- Mice, SCID
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Pyridines/pharmacology
- Pyridines/therapeutic use
- Pyrroles/pharmacology
- Pyrroles/therapeutic use
- Signal Transduction
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Hatice Gulcin Ozer
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Dalia El-Gamal
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | | | - Zachary A Hing
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - James S Blachly
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Bonnie Harrington
- College of Veterinary Medicine, The Ohio State University, Columbus, Ohio
| | - Shaneice Mitchell
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Nicole R Grieselhuber
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Katie Williams
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Tzung-Huei Lai
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Lapo Alinari
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Robert A Baiocchi
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Lindsey Brinton
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Elizabeth Baskin
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Matthew Cannon
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Larry Beaver
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Virginia M Goettl
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - David M Lucas
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Jennifer A Woyach
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Deepa Sampath
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio
| | - Amy M Lehman
- Center for Biostatistics, The Ohio State University, Columbus, Ohio
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University, Columbus, Ohio
| | | | - Yan Ma
- Plexxikon Inc., Berkeley, California
| | | | | | | | | | | | | | | | - Ken Dong
- Plexxikon Inc., Berkeley, California
| | | | | | | | | | | | | | | | | | | | | | | | - Ewy A Mathé
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | | | - John C Byrd
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio.
| | - Rosa Lapalombella
- Division of Hematology, Department of Medicine, The Ohio State University, Columbus, Ohio.
| |
Collapse
|
24
|
Ioannidou A, Zachaki S, Karakosta M, Daraki A, Roussou P, Manola KN. Cohesin RAD21 Gene Promoter Methylation in Patients with Chronic Lymphocytic Leukemia. Cytogenet Genome Res 2018; 154:126-131. [PMID: 29587287 DOI: 10.1159/000487868] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2018] [Indexed: 12/23/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common type of leukemia in adults and is characterized by the presence of specific cytogenetic abnormalities. CLL research has been focused on epigenetic processes like gene promoter methylation of CpG islands. In the present study, the methylation status of the RAD21 gene is studied and associated with cytogenetic findings in CLL patients in order to investigate its possible implication in CLL pathogenesis and the formation of CLL chromosomal abnormalities.
Collapse
|
25
|
Schliesser MG, Claus R, Hielscher T, Grimm C, Weichenhan D, Blaes J, Wiestler B, Hau P, Schramm J, Sahm F, Weiß EK, Weiler M, Baer C, Schmidt-Graf F, Schackert G, Westphal M, Hertenstein A, Roth P, Galldiks N, Hartmann C, Pietsch T, Felsberg J, Reifenberger G, Sabel MC, Winkler F, von Deimling A, Meisner C, Vajkoczy P, Platten M, Weller M, Plass C, Wick W. Prognostic relevance of miRNA-155 methylation in anaplastic glioma. Oncotarget 2018; 7:82028-82045. [PMID: 27880937 PMCID: PMC5347671 DOI: 10.18632/oncotarget.13452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/13/2016] [Indexed: 02/03/2023] Open
Abstract
The outcome of patients with anaplastic gliomas varies considerably depending on single molecular markers, such as mutations of the isocitrate dehydrogenase (IDH) genes, as well as molecular classifications based on epigenetic or genetic profiles. Remarkably, 98% of the RNA within a cell is not translated into proteins. Of those, especially microRNAs (miRNAs) have been shown not only to have a major influence on physiologic processes but also to be deregulated and prognostic in malignancies.To find novel survival markers and treatment options we performed unbiased DNA methylation screens that revealed 12 putative miRNA promoter regions with differential DNA methylation in anaplastic gliomas. Methylation of these candidate regions was validated in different independent patient cohorts revealing a set of miRNA promoter regions with prognostic relevance across data sets. Of those, miR-155 promoter methylation and miR-155 expression were negatively correlated and especially the methylation showed superior correlation with patient survival compared to established biomarkers.Functional examinations in malignant glioma cells further cemented the relevance of miR-155 for tumor cell viability with transient and stable modifications indicating an onco-miRNA activity. MiR-155 also conferred resistance towards alkylating temozolomide and radiotherapy as consequence of nuclear factor (NF)κB activation.Preconditioning glioma cells with an NFκB inhibitor reduced therapy resistance of miR-155 overexpressing cells. These cells resembled tumors with a low methylation of the miR-155 promoter and thus mir-155 or NFκB inhibition may provide treatment options with a special focus on patients with IDH wild type tumors.
Collapse
Affiliation(s)
- Maximilian Georg Schliesser
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer Claus
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Diagnostic and Interventional Neuroradiology, Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christiane Grimm
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas Blaes
- Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Wiestler
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Hau
- Neurology Clinic, Regensburg University, Regensburg, Germany
| | - Johannes Schramm
- Neurosurgery Clinic, University of Bonn Medical Center, TU Munich, Munich, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elisa K Weiß
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Markus Weiler
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of General Neurology, University Hospital Tübingen, Germany
| | - Constance Baer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Friederike Schmidt-Graf
- Department of General Neurology, University Hospital Tübingen, Germany.,Neurology Clinic, TU Munich, Munich, Germany
| | | | - Manfred Westphal
- Neurosurgery Clinic, University Clinic Hamburg, Eppendorf, Germany
| | - Anne Hertenstein
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Roth
- Department of General Neurology, University Hospital Tübingen, Germany.,Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | | | - Christian Hartmann
- Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany
| | - Torsten Pietsch
- Department of Neuropathology, Heinrich-Heine-University, Germany
| | - Joerg Felsberg
- Department of Neurosurgery, Heinrich-Heine-University, Germany.,Neurosurgery Clinic, Charité, Berlin, Germany
| | - Guido Reifenberger
- Department of Neurosurgery, Heinrich-Heine-University, Germany.,Neurosurgery Clinic, Charité, Berlin, Germany
| | | | - Frank Winkler
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Peter Vajkoczy
- Department Hematology, Oncology and Stem Cell Transplantation, University Hospital Freiburg, Germany
| | - Michael Platten
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of General Neurology, University Hospital Tübingen, Germany
| | - Michael Weller
- Department of General Neurology, University Hospital Tübingen, Germany.,Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital and German Cancer Consortium, Clinical Cooperation Units, Germany.,Clinical Cooperation Unit of Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of General Neurology, University Hospital Tübingen, Germany
| |
Collapse
|
26
|
Wang ZR, Wei JH, Zhou JC, Haddad A, Zhao LY, Kapur P, Wu KJ, Wang B, Yu YH, Liao B, He DL, Chen W, Margulis V, Hsieh JT, Luo JH. Validation of DAB2IP methylation and its relative significance in predicting outcome in renal cell carcinoma. Oncotarget 2017; 7:31508-19. [PMID: 27129174 PMCID: PMC5058774 DOI: 10.18632/oncotarget.8971] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/02/2016] [Indexed: 12/21/2022] Open
Abstract
We have recently reported tumor suppressive role of DAB2IP in RCC development. In this study, We identified one CpG methylation biomarker (DAB2IP CpG1) located UTSS of DAB2IP that was associated with poor overall survival in a cohort of 318 ccRCC patients from the Cancer Genome Atlas (TCGA). We further validated the prognostic accuracy of DAB2IP CpG methylation by pyrosequencing quantitative methylation assay in 224 ccRCC patients from multiple Chinese centers (MCHC set), and 239 patients from University of Texas Southwestern Medical Center at Dallas (UTSW set) by using FFPE samples. DAB2IP CpG1 can predict the overall survival of patients in TCGA, MCHC, and UTSW sets independent of patient age, Fuhrman grade and TNM stage (all p<0.05). DAB2IP CpG1 successfully categorized patients into high-risk and low-risk groups with significant differences of clinical outcome in respective clinical subsets, regardless of age, sex, grade, stage, or race (HR: 1.63-7.83; all p<0.05). The detection of DAB2IP CpG1 methylation was minimally affected by ITH in ccRCC. DAB2IP mRNA expression was regulated by DNA methylation in vitro. DAB2IP CpG1 methylation is a practical and repeatable biomarker for ccRCC, which can provide prognostic value that complements the current staging system.
Collapse
Affiliation(s)
- Zong-Ren Wang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China.,Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jin-Huan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Jian-Cheng Zhou
- Department of Urology, Shaanxi Provincial People's Hospital, Shaanxi, China
| | - Ahmed Haddad
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Liang-Yun Zhao
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, Yunnan, China
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Kai-Jie Wu
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Bin Wang
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Yan-Hong Yu
- Department of Urology, Affiliated Hospital of Kunming University of Science and Technology, Yunnan, China
| | - Bing Liao
- Department of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Da-Lin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Wei Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jun-Hang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| |
Collapse
|
27
|
Mina A, Sandoval Sus J, Sleiman E, Pinilla-Ibarz J, Awan FT, Kharfan-Dabaja MA. Using prognostic models in CLL to personalize approach to clinical care: Are we there yet? Blood Rev 2017; 32:159-166. [PMID: 29122300 DOI: 10.1016/j.blre.2017.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/14/2017] [Accepted: 10/27/2017] [Indexed: 01/14/2023]
Abstract
Four decades ago, two staging systems were developed to help stratify CLL into different prognostic categories. These systems, the Rai and the Binet staging, depended entirely on abnormal exam findings and evidence of anemia and thrombocytopenia. Better understanding of biologic, genetic, and molecular characteristics of CLL have contributed to better appreciating its clinical heterogeneity. New prognostic models, the GCLLSG prognostic index and the CLL-IPI, emerged. They incorporate biologic and genetic information related to CLL and are capable of predicting survival outcomes and cases anticipated to need therapy earlier in the disease course. Accordingly, these newer models are helping develop better informed surveillance strategies and ultimately tailor treatment intensity according to presence (or lack thereof) of certain prognostic markers. This represents a step towards personalizing care of CLL patients. We anticipate that as more prognostic factors continue to be identified, the GCLLSG prognostic index and CLL-IPI models will undergo further revisions.
Collapse
Affiliation(s)
- Alain Mina
- Dept. of Internal Medicine, Kansas University Medical Ctr, Kansas City, KS, USA
| | | | - Elsa Sleiman
- Faculty of Medicine, American Univ. of Beirut, Beirut, Lebanon
| | - Javier Pinilla-Ibarz
- Dept. of Malignant Hematology, Moffitt Cancer Ctr, Tampa, FL, USA; Department of Oncologic Sciences, Moffitt Cancer Ctr, Univ. of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Farrukh T Awan
- Div. of Hematology, Dept. of Internal Medicine, The Ohio State Univ. Comprehensive Cancer Ctr, Columbus, OH, USA
| | - Mohamed A Kharfan-Dabaja
- Department of Oncologic Sciences, Moffitt Cancer Ctr, Univ. of South Florida Morsani College of Medicine, Tampa, FL, USA; Dept. of Blood and Marrow Transplantation and Cellular Immunotherapy, Moffitt Cancer Ctr, Tampa, FL, USA.
| |
Collapse
|
28
|
Morandi L, Gissi D, Tarsitano A, Asioli S, Gabusi A, Marchetti C, Montebugnoli L, Foschini MP. CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel. Clin Epigenetics 2017; 9:85. [PMID: 28814981 PMCID: PMC5558660 DOI: 10.1186/s13148-017-0386-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/07/2017] [Indexed: 02/08/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is usually diagnosed at an advanced stage and is commonly preceded by oral premalignant lesions. The mortality rates have remained unchanged (50% within 5 years after diagnosis), and it is related to tobacco smoking and alcohol intake. Novel molecular markers for early diagnosis are urgently needed. The purpose of this study was to evaluate the diagnostic value of methylation level in a set of 18 genes by bisulfite next-generation sequencing. Methods With minimally invasive oral brushing, 28 consecutive OSCC, one squamous cell carcinoma with sarcomatoid features, six high-grade squamous intraepithelial lesions (HGSIL), 30 normal contralateral mucosa from the same patients, and 65 healthy donors were evaluated for DNA methylation analyzing 18 target genes by quantitative bisulfite next-generation sequencing. We further evaluated an independent cohort (validation dataset) made of 20 normal donors, one oral fibroma, 14 oral lichen planus (OLP), three proliferative verrucous leukoplakia (PVL), and two OSCC. Results Comparing OSCC with normal healthy donors and contralateral mucosa in 355 CpGs, we identified the following epigenetically altered genes: ZAP70, ITGA4, KIF1A, PARP15, EPHX3, NTM, LRRTM1, FLI1, MIR193, LINC00599, PAX1, and MIR137HG showing hypermethylation and MIR296, TERT, and GP1BB showing hypomethylation. The behavior of ZAP70, GP1BB, H19, EPHX3, and MIR193 fluctuated among different interrogated CpGs. The gap between normal and OSCC samples remained mostly the same (Kruskal-Wallis P values < 0.05), but the absolute values changed conspicuously. ROC curve analysis identified the most informative CpGs, and we correctly stratified OSCC and HGSIL from normal donors using a multiclass linear discriminant analysis in a 13-gene panel (AUC 0.981). Only the OSCC with sarcomatoid features was negative. Three contralateral mucosa were positive, a sign of a possible field cancerization. Among imprinted genes, only MIR296 showed loss of imprinting. DNMT1, TERC, and H19 together with the global methylation of long interspersed element 1 were unchanged. In the validation dataset, values over the threshold were detected in 2/2 OSCC, in 3/3 PVL, and in 2/14 OLP. Conclusions Our data highlight the importance of CpG location and correct estimation of DNA methylation level for highly accurate early diagnosis of OSCC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0386-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luca Morandi
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| | - Davide Gissi
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Achille Tarsitano
- Unit of Maxillofacial Surgery, S. Orsola Hospital Bologna, Bologna, Italy
| | - Sofia Asioli
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| | - Andrea Gabusi
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Claudio Marchetti
- Unit of Maxillofacial Surgery, S. Orsola Hospital Bologna, Bologna, Italy
| | - Lucio Montebugnoli
- Section of Oral Science, Department of Biomedical and Neuromuscular Sciences, University of Bologna, Bologna, Italy
| | - Maria Pia Foschini
- "M. Malpighi" Section of Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, Bellaria Hospital, University of Bologna, via Altura n.3, 40137 Bologna, Italy
| |
Collapse
|
29
|
Das Tumorepigenom – von der Genregulation über die Tumorklassifikation zum Therapietarget. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-016-0115-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zusammenfassung
Epigenetische Regulationsmechanismen sind essenziell für den koordinierten Ablauf zahlreicher zellulärer Prozesse wie die Differenzierung und Entwicklung oder auch die Anpassung der Genaktivität an die herrschenden Umweltbedingungen. Insbesondere Tumorerkrankungen gehen mit oftmals umfangreichen Alterationen im Epigenom einher. Diese Veränderungen sind dabei vielfach charakteristisch entweder für die Tumorentität, das Stadium der Erkrankung oder aber das klinische Ansprechen des Tumors auf eine Therapie und damit die individuelle Prognose des Patienten. Nach einer kurzen Darstellung epigenetischer Marker und ihrer Bedeutung bei malignen Erkrankungen werden in diesem Artikel Alterationen im Tumorepigenom und ihre Nutzbarkeit im Rahmen einer individualisierten Medizin exemplarisch vorgestellt.
Collapse
|
30
|
Genetic evolution in chronic lymphocytic leukaemia. Best Pract Res Clin Haematol 2016; 29:67-78. [PMID: 27742073 DOI: 10.1016/j.beha.2016.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 06/30/2016] [Accepted: 08/04/2016] [Indexed: 11/21/2022]
Abstract
Next-generation sequencing provides a comprehensive understanding of the genomic, epigenomic and transcriptomic underpinnings of chronic lymphocytic leukaemia. Recent studies have uncovered new drivers, including mutations in non-coding regions, and signalling pathways whose role in cancer was previously unknown or poorly understood. Moreover, massive scale epigenomics and transcriptomics have supplied the foundations for the cellular origin of the disease. Some drivers could be targeted pharmacologically, and the ability to detect mutations present in minority subclones might even allow treatment before clonal selection occurs, thus preventing disease refractoriness. As our understanding broadens and ongoing technological innovation propels new achievements, we will certainly learn how to apply it in our daily practice.
Collapse
|
31
|
Surface IgM expression and function are associated with clinical behavior, genetic abnormalities, and DNA methylation in CLL. Blood 2016; 128:816-26. [DOI: 10.1182/blood-2016-03-707786] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023] Open
Abstract
Key Points
High sIgM level is a potential key factor associated with poorer clinical outcome in CLL. Genetic and epigenetic features influence sIgM levels and function in CLL.
Collapse
|
32
|
Rathi P, Maurer S, Kubik G, Summerer D. Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity. J Am Chem Soc 2016; 138:9910-8. [PMID: 27429302 DOI: 10.1021/jacs.6b04807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the direct isolation of user-defined DNA sequences from the human genome with programmable selectivity for both canonical and epigenetic nucleobases. This is enabled by the use of engineered transcription-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment. The approach provides the direct quantification of 5-methylcytosine (5mC) levels at single genomic nucleotide positions in a strand-specific manner. We demonstrate the simple, multiplexed typing of a variety of epigenetic cancer biomarker 5mC with custom TALE mixes. Compared to antibodies as the most widely used affinity probes for 5mC analysis, i.e., employed in the methylated DNA immunoprecipitation (MeDIP) protocol, TALEs provide superior sensitivity, resolution and technical ease. We engineer a range of size-reduced TALE repeats and establish full selectivity profiles for their binding to all five human cytosine nucleobases. These provide insights into their nucleobase recognition mechanisms and reveal the ability of TALEs to isolate genomic target sequences with selectivity for single 5-hydroxymethylcytosine and, in combination with sodium borohydride reduction, single 5-formylcytosine nucleobases.
Collapse
Affiliation(s)
- Preeti Rathi
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Sara Maurer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Grzegorz Kubik
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund , Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| |
Collapse
|
33
|
Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; 34:726-37. [PMID: 27347756 DOI: 10.1038/nbt.3605] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
Collapse
|
34
|
Bhoi S, Ljungström V, Baliakas P, Mattsson M, Smedby KE, Juliusson G, Rosenquist R, Mansouri L. Prognostic impact of epigenetic classification in chronic lymphocytic leukemia: The case of subset #2. Epigenetics 2016; 11:449-55. [PMID: 27128508 DOI: 10.1080/15592294.2016.1178432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Based on the methylation status of 5 single CpG sites, a novel epigenetic classification of chronic lymphocytic leukemia (CLL) was recently proposed, classifying CLL patients into 3 clinico-biological subgroups with different outcome, termed memory like CLL (m-CLL), naïve like CLL (n-CLL), and a third intermediate CLL subgroup (i-CLL). While m-CLL and n-CLL patients at large corresponded to patients carrying mutated and unmutated IGHV genes, respectively, limited information exists regarding the less defined i-CLL group. Using pyrosequencing, we investigated the prognostic impact of the proposed 5 CpG signature in a well-characterized CLL cohort (135 cases), including IGHV-mutated and unmutated patients as well as clinically aggressive stereotyped subset #2 patients. Overall, we confirmed the signature's association with established prognostic markers. Moreover, in the presence of the IGHV mutational status, the epigenetic signature remained independently associated with both time-to-first-treatment and overall survival in multivariate analyses. As a prime finding, we observed that subset #2 patients were predominantly classified as i-CLL, probably reflecting their borderline IGHV mutational status (97-99% germline identity), though having a similarly poor prognosis as n-CLL patients. In summary, we validated the epigenetic classifier as an independent factor in CLL prognostication and provide further evidence that subset #2 is a member of the i-CLL group, hence supporting the existence of a third, intermediate epigenetic subgroup.
Collapse
Affiliation(s)
- Sujata Bhoi
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Viktor Ljungström
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Panagiotis Baliakas
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Mattias Mattsson
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden.,b Department of Medical Sciences , Uppsala University , Uppsala , Sweden
| | - Karin E Smedby
- c Department of Medicine Solna , Clinical Epidemiology Unit, Karolinska Institutet , Stockholm , Sweden
| | - Gunnar Juliusson
- d Department of Laboratory Medicine , Stem Cell Center, Hematology and Transplantation, Lund University , Lund , Sweden
| | - Richard Rosenquist
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| | - Larry Mansouri
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Sweden
| |
Collapse
|
35
|
Bogusz AM, Bagg A. Genetic aberrations in small B-cell lymphomas and leukemias: molecular pathology, clinical relevance and therapeutic targets. Leuk Lymphoma 2016; 57:1991-2013. [PMID: 27121112 DOI: 10.3109/10428194.2016.1173212] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Small B-cell lymphomas and leukemias (SBCLs) are a clinically, morphologically, immunophenotypically and genetically heterogeneous group of clonal lymphoid neoplasms, including entities such as chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), follicular lymphoma (FL), lymphoplasmacytic lymphoma (LPL), marginal zone lymphoma (MZL) and hairy cell leukemia (HCL). The pathogenesis of some of these lymphoid malignancies is characterized by distinct translocations, for example t(11;14) in the majority of cases of MCL and t(14;18) in most cases of FL, whereas other entities are associated with a variety of recurrent but nonspecific numeric chromosomal abnormalities, as exemplified by del(13q14), del(11q22), and +12 in CLL, and yet others such as LPL and HCL that lack recurrent or specific cytogenetic aberrations. The recent surge in next generation sequencing (NGS) technology has shed more light on the genetic landscape of SBCLs through characterization of numerous driver mutations including SF3B1 and NOTCH1 in CLL, ATM and CCND1 in MCL, KMT2D and EPHA7 in FL, MYD88 (L265P) in LPL, KLF2 and NOTCH2 in splenic MZL (SMZL) and BRAF (V600E) in HCL. The identification of distinct genetic lesions not only provides greater insight into the molecular pathogenesis of these disorders but also identifies potential valuable biomarkers for prognostic stratification, as well as specific targets for directed therapy. This review discusses the well-established and recently identified molecular lesions underlying the pathogenesis of SBCLs, highlights their clinical relevance and summarizes novel targeted therapies.
Collapse
Affiliation(s)
- Agata M Bogusz
- a Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Adam Bagg
- a Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| |
Collapse
|
36
|
Van Dyke DL, Werner L, Rassenti LZ, Neuberg D, Ghia E, Heerema NA, Dal Cin P, Dell Aquila M, Sreekantaiah C, Greaves AW, Kipps TJ, Kay NE. The Dohner fluorescence in situ hybridization prognostic classification of chronic lymphocytic leukaemia (CLL): the CLL Research Consortium experience. Br J Haematol 2016; 173:105-13. [PMID: 26848054 PMCID: PMC4963001 DOI: 10.1111/bjh.13933] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/19/2015] [Indexed: 12/23/2022]
Abstract
This study revisited the Dohner prognostic hierarchy in a cohort of 1585 well-documented patients with chronic lymphocytic leukaemia. The duration of both time to first treatment (TTFT) and overall survival (OS) were significantly longer than observed previously, and this is at least partly due to improved therapeutic options. Deletion 13q remains the most favourable prognostic group with median TTFT and OS from fluorescence in situ hybridization (FISH) testing of 72 months and >12 years, respectively. Deletion 11q had the poorest median TTFT (22 months) and 17p deletion the poorest median OS (5 years). The percentages of abnormal nuclei were significantly associated with differential TTFT for the trisomy 12, 13q and 17p deletion cohorts but not for the 11q deletion cohort. From the date of the first FISH study, patients with >85% 13q deletion nuclei had a notably shorter TTFT (24 months). Patients with ≤20% 17p deletion nuclei had longer median TTFT and OS from the date of the first FISH study (44 months and 11 years), and were more likely to be IGHV mutated.
Collapse
MESH Headings
- Chromosome Deletion
- Chromosomes, Human/genetics
- Disease-Free Survival
- Female
- Follow-Up Studies
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Survival Rate
Collapse
Affiliation(s)
- Daniel L. Van Dyke
- Departments of Laboratory Medicine and Pathology and Internal MedicineMayo ClinicRochesterMNUSA
| | - Lillian Werner
- Biostatistics and Computational BiologyDana‐Farber Cancer InstituteBostonMAUSA
| | - Laura Z. Rassenti
- Moores University of California San Diego Cancer CenterLa JollaCAUSA
| | - Donna Neuberg
- Biostatistics and Computational BiologyDana‐Farber Cancer InstituteBostonMAUSA
| | - Emanuella Ghia
- Moores University of California San Diego Cancer CenterLa JollaCAUSA
| | - Nyla A. Heerema
- Department of PathologyThe Ohio State UniversityColumbusOHUSA
| | - Paola Dal Cin
- Brigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Marie Dell Aquila
- Moores University of California San Diego Cancer CenterLa JollaCAUSA
| | | | - Andrew W. Greaves
- Moores University of California San Diego Cancer CenterLa JollaCAUSA
| | - Thomas J. Kipps
- Moores University of California San Diego Cancer CenterLa JollaCAUSA
| | - Neil E. Kay
- Departments of Laboratory Medicine and Pathology and Internal MedicineMayo ClinicRochesterMNUSA
| |
Collapse
|
37
|
|
38
|
Kostareli E, Hielscher T, Zucknick M, Baboci L, Wichmann G, Holzinger D, Mücke O, Pawlita M, Del Mistro A, Boscolo-Rizzo P, Da Mosto MC, Tirelli G, Plinkert P, Dietz A, Plass C, Weichenhan D, Hess J. Gene promoter methylation signature predicts survival of head and neck squamous cell carcinoma patients. Epigenetics 2016; 11:61-73. [PMID: 26786582 DOI: 10.1080/15592294.2015.1137414] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Infection with high-risk types of human papilloma virus (HPV) is currently the best-established prognostic marker for head and neck squamous cell carcinoma (HNSCC), one of the most common and lethal human malignancies worldwide. Clinical trials have been launched to address the concept of treatment de-escalation for HPV-positive HNSCC with the final aim to reduce treatment related toxicity and debilitating long-term impacts on the quality of life. However, HPV-related tumors are mainly restricted to oropharyngeal SCC (OPSCC) and there is an urgent need to establish reliable biomarkers for all patients at high risk for treatment failure. A patient cohort (n = 295) with mainly non-OPSCC (72.9%) and a low prevalence of HPV16-related tumors (8.8%) was analyzed by MassARRAY to determine a previously established prognostic methylation score (MS). Kaplan-Meier revealed a highly significant correlation between a high MS and a favorable survival for OPSCC (P = 0.0004) and for non-OPSCC (P<0.0001), which was confirmed for all HNSCC by multivariate Cox regression models (HR: 9.67, 95% CI [4.61-20.30], P<0.0001). Next, we established a minimal methylation signature score (MMSS), which consists of ten most informative of the originally 62 CpG units used for the MS. The prognostic value of the MMSS was confirmed by Kaplan-Meier analysis for all HNSCC (P<0.0001) and non-OPSCC (P = 0.0002), and was supported by multivariate Cox regression models for all HNSCC (HR: 2.15, 95% CI [1.36-3.41], P = 0.001). In summary, the MS and the MMSS exhibit an excellent performance as prognosticators for survival, which is not limited by the anatomical site, and both could be implemented in future clinical trials.
Collapse
Affiliation(s)
- Efterpi Kostareli
- a Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany.,b Department of Otolaryngology , Head and Neck Surgery, University Hospital , Heidelberg, Heidelberg , Germany
| | - Thomas Hielscher
- c Division of Biostatistics, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Manuela Zucknick
- c Division of Biostatistics, German Cancer Research Center (DKFZ) , Heidelberg , Germany.,d Oslo Center for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo , Norway
| | - Lorena Baboci
- e Veneto Institute of Oncology IOV - IRCCS, Immunology and Molecular Oncology Unit , Padua , Italy.,f Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Gunnar Wichmann
- g Department of Otorhinolaryngology , University Hospital Leipzig , Germany
| | - Dana Holzinger
- f Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Oliver Mücke
- a Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Michael Pawlita
- f Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Annarosa Del Mistro
- e Veneto Institute of Oncology IOV - IRCCS, Immunology and Molecular Oncology Unit , Padua , Italy
| | - Paolo Boscolo-Rizzo
- h Department of Neurosciences , ENT Clinic and Regional Center for Head and Neck Cancer, University of Padua, School of Medicine, Treviso Regional Hospital , Treviso , Italy
| | - Maria Cristina Da Mosto
- h Department of Neurosciences , ENT Clinic and Regional Center for Head and Neck Cancer, University of Padua, School of Medicine, Treviso Regional Hospital , Treviso , Italy
| | - Giancarlo Tirelli
- i Head and Neck Department, Hospital of Cattinara, University of Trieste , Trieste , Italy
| | - Peter Plinkert
- b Department of Otolaryngology , Head and Neck Surgery, University Hospital , Heidelberg, Heidelberg , Germany
| | - Andreas Dietz
- g Department of Otorhinolaryngology , University Hospital Leipzig , Germany
| | - Christoph Plass
- a Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Dieter Weichenhan
- a Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jochen Hess
- b Department of Otolaryngology , Head and Neck Surgery, University Hospital , Heidelberg, Heidelberg , Germany.,j Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| |
Collapse
|
39
|
DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet 2016; 48:253-64. [PMID: 26780610 DOI: 10.1038/ng.3488] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022]
Abstract
Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.
Collapse
|
40
|
|
41
|
Skoetz N, Trivella M, Kreuzer KA, Collins G, Köhler N, Wolff R, Moons K, Estcourt LJ. Prognostic models for chronic lymphocytic leukaemia: an exemplar systematic review and meta-analysis. Hippokratia 2016. [DOI: 10.1002/14651858.cd012022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nicole Skoetz
- University Hospital of Cologne; Cochrane Haematological Malignancies Group, Department I of Internal Medicine; Kerpener Str. 62 Cologne Germany 50937
| | - Marialena Trivella
- University of Oxford; Centre for Statistics in Medicine; Botnar Research Centre Windmill Road Oxford UK OX3 7LD
| | - Karl-Anton Kreuzer
- University Hospital of Cologne; Department I of Internal Medicine; Cologne Germany
| | - Gary Collins
- University of Oxford; Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences; Windmill Road Oxford UK OX3 7LD
| | - Nicola Köhler
- University Hospital of Cologne; Cochrane Haematological Malignancies Group, Department I of Internal Medicine; Kerpener Str. 62 Cologne Germany 50937
| | - Robert Wolff
- Kleijnen Systematic Reviews Ltd; Unit 6 Escrick Business Park Riccall Road, Escrick York North Yorkshire UK YO19 6FD
| | - Karel Moons
- University Medical Center Utrecht; Julius Center for Health Sciences and Primary Care; PO Box 85500 Utrecht Netherlands 3508 GA
| | - Lise J Estcourt
- NHS Blood and Transplant; Haematology/Transfusion Medicine; Level 2, John Radcliffe Hospital Headington Oxford UK OX3 9BQ
| |
Collapse
|
42
|
DNA methylation analysis by bisulfite next-generation sequencing for early detection of oral squamous cell carcinoma and high-grade squamous intraepithelial lesion from oral brushing. J Craniomaxillofac Surg 2015; 43:1494-500. [DOI: 10.1016/j.jcms.2015.07.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/19/2015] [Accepted: 07/27/2015] [Indexed: 12/28/2022] Open
|
43
|
Guièze R, Wu CJ. Genomic and epigenomic heterogeneity in chronic lymphocytic leukemia. Blood 2015; 126:445-53. [PMID: 26065654 PMCID: PMC4513249 DOI: 10.1182/blood-2015-02-585042] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/01/2015] [Indexed: 12/15/2022] Open
Abstract
Defining features of chronic lymphocytic leukemia (CLL) are not only its immunophenotype of CD19(+)CD5(+)CD23(+)sIgdim expressing clonal mature B cells but also its highly variable clinical course. In recent years, advances in massively parallel sequencing technologies have led to rapid progress in our understanding of the CLL genome and epigenome. Overall, these studies have clearly demarcated not only the vast degree of genetic and epigenetic heterogeneity among individuals with CLL but also even within individual patient leukemias. We herein review the rapidly growing series of studies assessing the genetic and epigenetic features of CLL within clinically defined periods of its growth. These studies strongly suggest an evolving spectrum of lesions over time and that these features may have clinical impact.
Collapse
Affiliation(s)
- Romain Guièze
- CHU Clermont-Ferrand, Service d'Hématologie Clinique Adulte et de Thérapie Cellulaire, and Université d'Auvergne, Clermont-Ferrand, France; Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute, Cambridge, MA; and Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Catherine J Wu
- Division of Hematologic Neoplasia, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute, Cambridge, MA; and Division of Medical Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| |
Collapse
|
44
|
Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CHM, Carson DA, Kipps TJ, Frazer KA. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J 2015; 5:e303. [PMID: 25860294 PMCID: PMC4450323 DOI: 10.1038/bcj.2015.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023] Open
Abstract
We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.
Collapse
Affiliation(s)
- E N Smith
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - E M Ghia
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - C M DeBoever
- Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA
| | - L Z Rassenti
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K Jepsen
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K-A Yoon
- Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA
| | - H Matsui
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - S Rozenzhak
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - H Alakus
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - P J Shepard
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Y Dai
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - M Khosroheidari
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - M Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - K L Gunderson
- Illumina, Inc., 5200 Illumina Way, San Diego, CA, USA
| | - K Messer
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - L Muthuswamy
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - T J Hudson
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - O Harismendy
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C L Barrett
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C H M Jamieson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA [3] Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - D A Carson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - T J Kipps
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K A Frazer
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [3] Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA [4] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| |
Collapse
|
45
|
Lucas DM, Ruppert AS, Lozanski G, Dewald GW, Lozanski A, Claus R, Plass C, Flinn IW, Neuberg DS, Paietta EM, Bennett JM, Jelinek DF, Gribben JG, Hussein MA, Appelbaum FR, Larson RA, Moore DF, Tallman MS, Byrd JC, Grever MR. Cytogenetic prioritization with inclusion of molecular markers predicts outcome in previously untreated patients with chronic lymphocytic leukemia treated with fludarabine or fludarabine plus cyclophosphamide: a long-term follow-up study of the US intergroup phase III trial E2997. Leuk Lymphoma 2015; 56:3031-7. [PMID: 25721902 DOI: 10.3109/10428194.2015.1023800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fludarabine (F) and cyclophosphamide (C) remain backbones of up-front chemotherapy regimens for chronic lymphocytic leukemia (CLL). We report long-term follow-up of a randomized F vs. FC trial in untreated CLL (#) . With median follow-up of 88 months, estimated median progression-free survival (PFS) was 19.3 vs. 48.1 months for F (n = 109) and FC (n = 118), respectively (p < 0.0001), and median overall survival (OS) was 88.0 vs. 79.1 months (p = 0.96). In multivariable analyses, variables associated with inferior PFS and OS respectively were age (p = 0.002, p < 0.001), Rai stage (p = 0.006, p = 0.02) and sex (p = 0.03, PFS only). Del(17)(p13.1) predicted shorter PFS and OS (p < 0.0001 for each), as did del(11q)(22.3) (p < 0.0001, p = 0.005, respectively), trisomy 12 with mutated Notch1 (p = 0.003, p = 0.03, respectively) and unmutated IGHV (p = 0.009, p = 0.002, respectively), all relative to patients without these features. These data confirm results from shorter follow-up and further justify targeted therapies for CLL.
Collapse
Affiliation(s)
- David M Lucas
- a Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | - Amy S Ruppert
- a Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | - Gerard Lozanski
- a Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | | | - Arletta Lozanski
- a Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | - Rainer Claus
- c University of Freiburg Medical Center , Freiburg , Germany.,d German Cancer Research Center , Heidelberg , Germany
| | | | - Ian W Flinn
- e Sarah Cannon Research Institute and Tennessee Oncology , Nashville , TN , USA
| | | | | | | | | | - John G Gribben
- i Barts Cancer Institute, Queen Mary University of London , London , UK
| | | | | | | | | | | | - John C Byrd
- a Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| | - Michael R Grever
- a Ohio State University Comprehensive Cancer Center , Columbus , OH , USA
| |
Collapse
|
46
|
Zelenetz AD, Gordon LI, Wierda WG, Abramson JS, Advani RH, Andreadis CB, Bartlett N, Byrd JC, Czuczman MS, Fayad LE, Fisher RI, Glenn MJ, Habermann TM, Harris NL, Hoppe RT, Horwitz SM, Kelsey CR, Kim YH, Krivacic S, LaCasce AS, Nademanee A, Porcu P, Press O, Rabinovitch R, Reddy N, Reid E, Saad AA, Sokol L, Swinnen LJ, Tsien C, Vose JM, Wilson L, Yahalom J, Zafar N, Dwyer M, Sundar H. Chronic lymphocytic leukemia/small lymphocytic lymphoma, version 1.2015. J Natl Compr Canc Netw 2015; 13:326-62. [PMID: 25736010 PMCID: PMC4841457 DOI: 10.6004/jnccn.2015.0045] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chronic lymphocytic leukemia (CLL) and small lymphocytic lymphoma (SLL) are different manifestations of the same disease, which are managed in the same way. The advent of novel monoclonal antibodies (ofatumumab and obinutuzumab) led to the development of effective chemoimmunotherapy regimens. The recently approved small molecule kinase inhibitors (ibrutinib and idelalisib) are effective treatment options for CLL in elderly patients with decreased tolerance for aggressive regimens and in patients with poor prognostic features who do not benefit from conventional chemoimmunotherapy regimens. This portion of the NCCN Guidelines for Non-Hodgkin's Lymphomas describes the recent specific to the incorporation of recently approved targeted therapies for the management of patients with newly diagnosed and relapsed or refractory CLL/SLL.
Collapse
MESH Headings
- Algorithms
- Comorbidity
- Disease Management
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/epidemiology
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Neoplasm Staging
- Prognosis
Collapse
|
47
|
TCL1 targeting miR-3676 is codeleted with tumor protein p53 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 2015; 112:2169-74. [PMID: 25646413 DOI: 10.1073/pnas.1500010112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
B-cell chronic lymphocytic leukemia (CLL) is the most common human leukemia and dysregulation of the T-cell leukemia/lymphoma 1 (TCL1) oncogene is a contributing event in the pathogenesis of the aggressive form of this disease based on transgenic mouse studies. To determine a role of microRNAs on the pathogenesis of the aggressive form of CLL we studied regulation of TCL1 expression in CLL by microRNAs. We identified miR-3676 as a regulator of TCL1 expression. We demonstrated that miR-3676 targets three consecutive 28-bp repeats within 3'UTR of TCL1 and showed that miR-3676 is a powerful inhibitor of TCL1. We further showed that miR-3676 expression is significantly down-regulated in four groups of CLL carrying the 11q deletions, 13q deletions, 17p deletions, or a normal karyotype compared with normal CD19(+) cord blood and peripheral blood B cells. In addition, the sequencing of 539 CLL samples revealed five germ-line mutations in six samples (1%) in miR-3676. Two of these mutations were loss-of-function mutations. Because miR-3676 is located at 17p13, only 500-kb centromeric of tumor protein p53 (Tp53), and is codeleted with Tp53, we propose that loss of miR-3676 causes high levels of TCL1 expression contributing to CLL progression.
Collapse
|
48
|
Rodríguez D, Bretones G, Arango JR, Valdespino V, Campo E, Quesada V, López-Otín C. Molecular pathogenesis of CLL and its evolution. Int J Hematol 2015; 101:219-28. [PMID: 25630433 DOI: 10.1007/s12185-015-1733-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
In spite of being the most prevalent adult leukemia in Western countries, the molecular mechanisms driving the establishment and progression of chronic lymphocytic leukemia (CLL) remain largely unknown. In recent years, the use of next-generation sequencing techniques has uncovered new and, in some cases, unexpected driver genes with prognostic and therapeutic value. The mutational landscape of CLL is characterized by high-genetic and epigenetic heterogeneity, low mutation recurrence and a long tail of cases with undefined driver genes. On the other hand, the use of deep sequencing has also revealed high intra-tumor heterogeneity and provided a detailed picture of clonal evolution processes. This phenomenon, in which aberrant DNA methylation can also participate, appears to be tightly associated to poor outcomes and chemo-refractoriness, thus providing a new subject for therapeutic intervention. Hence, and having in mind the limitations derived from the CLL complexity thus described, the application of massively parallel sequencing studies has unveiled a wealth of information that is expected to substantially improve patient staging schemes and CLL clinical management.
Collapse
Affiliation(s)
- David Rodríguez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología-IUOPA, Universidad de Oviedo, 33006, Oviedo, Spain
| | | | | | | | | | | | | |
Collapse
|
49
|
Prognosis and therapy of chronic lymphocytic leukemia and small lymphocytic lymphoma. Cancer Treat Res 2015; 165:147-75. [PMID: 25655609 DOI: 10.1007/978-3-319-13150-4_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course that has guided treatment principles in as much as anti-leukemic therapy is reserved for patients with active disease. This heterogeneity is somewhat dissected by prognostic markers, many of which represent pathogenic mechanisms. Recently, the introduction of highly active targeted agents and maturing data on predictive markers may lead to more individualized therapeutic approaches. In this chapter, we review key prognostic markers, current and emerging therapy, and will attempt to outline a future "where the two may connect".
Collapse
|