1
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Kashyap MK, Karathia H, Kumar D, Vera Alvarez R, Forero-Forero JV, Moreno E, Lujan JV, Amaya-Chanaga CI, Vidal NM, Yu Z, Ghia EM, Lengerke-Diaz PA, Achinko D, Choi MY, Rassenti LZ, Mariño-Ramírez L, Mount SM, Hannenhalli S, Kipps TJ, Castro JE. Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102202. [PMID: 38846999 PMCID: PMC11154714 DOI: 10.1016/j.omtn.2024.102202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Splicing factor 3b subunit 1 (SF3B1) is the largest subunit and core component of the spliceosome. Inhibition of SF3B1 was associated with an increase in broad intron retention (IR) on most transcripts, suggesting that IR can be used as a marker of spliceosome inhibition in chronic lymphocytic leukemia (CLL) cells. Furthermore, we separately analyzed exonic and intronic mapped reads on annotated RNA-sequencing transcripts obtained from B cells (n = 98 CLL patients) and healthy volunteers (n = 9). We measured intron/exon ratio to use that as a surrogate for alternative RNA splicing (ARS) and found that 66% of CLL-B cell transcripts had significant IR elevation compared with normal B cells (NBCs) and that correlated with mRNA downregulation and low expression levels. Transcripts with the highest IR levels belonged to biological pathways associated with gene expression and RNA splicing. A >2-fold increase of active pSF3B1 was observed in CLL-B cells compared with NBCs. Additionally, when the CLL-B cells were treated with macrolides (pladienolide-B), a significant decrease in pSF3B1, but not total SF3B1 protein, was observed. These findings suggest that IR/ARS is increased in CLL, which is associated with SF3B1 phosphorylation and susceptibility to SF3B1 inhibitors. These data provide additional support to the relevance of ARS in carcinogenesis and evidence of pSF3B1 participation in this process.
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Affiliation(s)
- Manoj Kumar Kashyap
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Gurugram (HR) 122413, India
| | - Hiren Karathia
- Advanced Biomedical Computational Science and National Center for Advancing Translational Sciences, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Greenwood Genetic Center, Greenwood, SC, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Deepak Kumar
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Roberto Vera Alvarez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Eider Moreno
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Juliana Velez Lujan
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | | | - Newton Medeiros Vidal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhe Yu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
| | - Emanuela M. Ghia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Paula A. Lengerke-Diaz
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Daniel Achinko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Y. Choi
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Laura Z. Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Leonardo Mariño-Ramírez
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen M. Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Division of Hematology Oncology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Center for Novel Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093-0820, USA
- Department of Internal Medicine, Division of Hematology-Oncology, Mayo Clinic, Phoenix, AZ 85054, USA
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2
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Tsagiopoulou M, Gut IG. Machine learning and multi-omics data in chronic lymphocytic leukemia: the future of precision medicine? Front Genet 2024; 14:1304661. [PMID: 38283149 PMCID: PMC10811210 DOI: 10.3389/fgene.2023.1304661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
Chronic lymphocytic leukemia is a complex and heterogeneous hematological malignancy. The advance of high-throughput multi-omics technologies has significantly influenced chronic lymphocytic leukemia research and paved the way for precision medicine approaches. In this review, we explore the role of machine learning in the analysis of multi-omics data in this hematological malignancy. We discuss recent literature on different machine learning models applied to single omic studies in chronic lymphocytic leukemia, with a special focus on the potential contributions to precision medicine. Finally, we highlight the recently published machine learning applications in multi-omics data in this area of research as well as their potential and limitations.
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Affiliation(s)
| | - Ivo G. Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
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3
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Morabito F, Adornetto C, Monti P, Amaro A, Reggiani F, Colombo M, Rodriguez-Aldana Y, Tripepi G, D’Arrigo G, Vener C, Torricelli F, Rossi T, Neri A, Ferrarini M, Cutrona G, Gentile M, Greco G. Genes selection using deep learning and explainable artificial intelligence for chronic lymphocytic leukemia predicting the need and time to therapy. Front Oncol 2023; 13:1198992. [PMID: 37719021 PMCID: PMC10501728 DOI: 10.3389/fonc.2023.1198992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/31/2023] [Indexed: 09/19/2023] Open
Abstract
Analyzing gene expression profiles (GEP) through artificial intelligence provides meaningful insight into cancer disease. This study introduces DeepSHAP Autoencoder Filter for Genes Selection (DSAF-GS), a novel deep learning and explainable artificial intelligence-based approach for feature selection in genomics-scale data. DSAF-GS exploits the autoencoder's reconstruction capabilities without changing the original feature space, enhancing the interpretation of the results. Explainable artificial intelligence is then used to select the informative genes for chronic lymphocytic leukemia prognosis of 217 cases from a GEP database comprising roughly 20,000 genes. The model for prognosis prediction achieved an accuracy of 86.4%, a sensitivity of 85.0%, and a specificity of 87.5%. According to the proposed approach, predictions were strongly influenced by CEACAM19 and PIGP, moderately influenced by MKL1 and GNE, and poorly influenced by other genes. The 10 most influential genes were selected for further analysis. Among them, FADD, FIBP, FIBP, GNE, IGF1R, MKL1, PIGP, and SLC39A6 were identified in the Reactome pathway database as involved in signal transduction, transcription, protein metabolism, immune system, cell cycle, and apoptosis. Moreover, according to the network model of the 3D protein-protein interaction (PPI) explored using the NetworkAnalyst tool, FADD, FIBP, IGF1R, QTRT1, GNE, SLC39A6, and MKL1 appear coupled into a complex network. Finally, all 10 selected genes showed a predictive power on time to first treatment (TTFT) in univariate analyses on a basic prognostic model including IGHV mutational status, del(11q) and del(17p), NOTCH1 mutations, β2-microglobulin, Rai stage, and B-lymphocytosis known to predict TTFT in CLL. However, only IGF1R [hazard ratio (HR) 1.41, 95% CI 1.08-1.84, P=0.013), COL28A1 (HR 0.32, 95% CI 0.10-0.97, P=0.045), and QTRT1 (HR 7.73, 95% CI 2.48-24.04, P<0.001) genes were significantly associated with TTFT in multivariable analyses when combined with the prognostic factors of the basic model, ultimately increasing the Harrell's c-index and the explained variation to 78.6% (versus 76.5% of the basic prognostic model) and 52.6% (versus 42.2% of the basic prognostic model), respectively. Also, the goodness of model fit was enhanced (χ2 = 20.1, P=0.002), indicating its improved performance above the basic prognostic model. In conclusion, DSAF-GS identified a group of significant genes for CLL prognosis, suggesting future directions for bio-molecular research.
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Affiliation(s)
| | - Carlo Adornetto
- Department of Mathematics and Computer Science, University of Calabria, Cosenza, Italy
| | - Paola Monti
- Mutagenesis and Cancer Prevention Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Adriana Amaro
- Tumor Epigenetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Francesco Reggiani
- Tumor Epigenetics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Monica Colombo
- Molecular Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Giovanni Tripepi
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica del Consiglio Nazionale delle Ricerche (CNR), Reggio Calabria, Italy
| | - Graziella D’Arrigo
- Consiglio Nazionale delle Ricerche, Istituto di Fisiologia Clinica del Consiglio Nazionale delle Ricerche (CNR), Reggio Calabria, Italy
| | - Claudia Vener
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - Istituto di Ricovero e Cura a Crabtree Scientifico (USL-IRCCS) of Reggio Emilia, Reggio Emilia, Italy
| | - Teresa Rossi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale - Istituto di Ricovero e Cura a Crabtree Scientifico (USL-IRCCS) of Reggio Emilia, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda Unità Sanitaria Locale - Istituto di Ricovero e Cura a Carattere Scientifico (USL-IRCCS) of Reggio Emilia, Reggio Emilia, Italy
| | - Manlio Ferrarini
- Unità Operariva (UO) Molecular Pathology, Ospedale Policlinico San Martino Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Genoa, Italy
| | - Giovanna Cutrona
- Molecular Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale Policlinico San Martino, Genoa, Italy
| | - Massimo Gentile
- Hematology Unit, Department of Onco-Hematology, Azienda Ospedaliera (A.O.) of Cosenza, Cosenza, Italy
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, Cosenza, Italy
| | - Gianluigi Greco
- Department of Mathematics and Computer Science, University of Calabria, Cosenza, Italy
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4
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Wu Y, Jin M, Fernandez M, Hart KL, Liao A, Ge X, Fernandes SM, McDonald T, Chen Z, Röth D, Ghoda LY, Marcucci G, Kalkum M, Pillai RK, Danilov AV, Li JJ, Chen J, Brown JR, Rosen ST, Siddiqi T, Wang L. METTL3-Mediated m6A Modification Controls Splicing Factor Abundance and Contributes to Aggressive CLL. Blood Cancer Discov 2023; 4:228-245. [PMID: 37067905 PMCID: PMC10150290 DOI: 10.1158/2643-3230.bcd-22-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/18/2023] Open
Abstract
RNA splicing dysregulation underlies the onset and progression of cancers. In chronic lymphocytic leukemia (CLL), spliceosome mutations leading to aberrant splicing occur in ∼20% of patients. However, the mechanism for splicing defects in spliceosome-unmutated CLL cases remains elusive. Through an integrative transcriptomic and proteomic analysis, we discover that proteins involved in RNA splicing are posttranscriptionally upregulated in CLL cells, resulting in splicing dysregulation. The abundance of splicing complexes is an independent risk factor for poor prognosis. Moreover, increased splicing factor expression is highly correlated with the abundance of METTL3, an RNA methyltransferase that deposits N6-methyladenosine (m6A) on mRNA. METTL3 is essential for cell growth in vitro and in vivo and controls splicing factor protein expression in a methyltransferase-dependent manner through m6A modification-mediated ribosome recycling and decoding. Our results uncover METTL3-mediated m6A modification as a novel regulatory axis in driving splicing dysregulation and contributing to aggressive CLL. SIGNIFICANCE METTL3 controls widespread splicing factor abundance via translational control of m6A-modified mRNA, contributes to RNA splicing dysregulation and disease progression in CLL, and serves as a potential therapeutic target in aggressive CLL. See related commentary by Janin and Esteller, p. 176. This article is highlighted in the In This Issue feature, p. 171.
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Affiliation(s)
- Yiming Wu
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Meiling Jin
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Mike Fernandez
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Kevyn L. Hart
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Aijun Liao
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Xinzhou Ge
- Department of Statistics, University of California, Los Angeles, California
- Department of Computational Medicine, University of California, Los Angeles, California
| | - Stacey M. Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tinisha McDonald
- The Hematopoietic Tissue Biorepository, City of Hope National Comprehensive Cancer Center, Duarte, California
- Department of Hematological Malignancies Translational Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Daniel Röth
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, California
| | - Lucy Y. Ghoda
- The Hematopoietic Tissue Biorepository, City of Hope National Comprehensive Cancer Center, Duarte, California
- Department of Hematological Malignancies Translational Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Guido Marcucci
- The Hematopoietic Tissue Biorepository, City of Hope National Comprehensive Cancer Center, Duarte, California
- Department of Hematological Malignancies Translational Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, California
| | - Raju K. Pillai
- Department of Pathology, City of Hope National Comprehensive Cancer Center, Duarte, California
| | - Alexey V. Danilov
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, California
- Department of Computational Medicine, University of California, Los Angeles, California
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Steven T. Rosen
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Tanya Siddiqi
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope Comprehensive Cancer Center, Duarte, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
- Toni Stephenson Lymphoma Center, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, California
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5
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Xin R, Feng X, Zhang H, Wang Y, Duan M, Xie T, Dong L, Yu Q, Huang L, Zhou F. Seven non-differentially expressed 'dark biomarkers' show transcriptional dysregulation in chronic lymphocytic leukemia. Per Med 2023. [PMID: 36705049 DOI: 10.2217/pme-2022-0123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aim: Transcriptional regulation is actively involved in the onset and progression of various diseases. This study used the feature-engineering approach model-based quantitative transcription regulation to quantitatively measure the correlation between mRNA and transcription factors in a reference dataset of chronic lymphocytic leukemia (CLL) transcriptomes. Methods: A comprehensive investigation of transcriptional regulation changes in CLL was conducted using 973 samples in six independent datasets. Results & conclusion: Seven mRNAs were detected to have significantly differential model-based quantitative transcription regulation values but no differential expression between CLL patients and controls. We called these genes 'dark biomarkers' because their original expression levels did not show differential changes in the CLL patients. The overlapping lncRNAs might have contributed their transcripts to the expression miscalculations of these dark biomarkers.
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Affiliation(s)
- Ruihao Xin
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China.,College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin,132000, China.,Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Hang Zhang
- College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Yueying Wang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Tunyang Xie
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Lin Dong
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Qiong Yu
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Lan Huang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
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6
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Catapano R, Sepe L, Toscano E, Paolella G, Chiurazzi F, Barbato SP, Bruzzese D, Arianna R, Grosso M, Romano S, Romano MF, Costanzo P, Cesaro E. Biological relevance of ZNF224 expression in chronic lymphocytic leukemia and its implication IN NF-kB pathway regulation. Front Mol Biosci 2022; 9:1010984. [PMID: 36425656 PMCID: PMC9681601 DOI: 10.3389/fmolb.2022.1010984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/20/2022] [Indexed: 12/21/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, whose presentation and clinical course are highly variable. Identification of novel prognostic factors may contribute to improving the CLL classification and providing indications for treatment options. The zinc finger protein ZNF224 plays a key role in cell transformation, through the control of apoptotic and survival pathways. In this study, we evaluated the potential application of ZNF224 as a novel marker of CLL progression and therapy responsiveness. To this aim, we analyzed ZNF224 expression levels in B lymphocytes from CLL patients at different stages of the disease and in patients showing different treatment outcomes. The expression of ZNF224 was significantly increased in disease progression and dramatically decreased in patients in complete remission after chemotherapy. Gene expression correlation analysis performed on datasets of CLL patients revealed that ZNF224 expression was well correlated with that of some prognostic and predictive markers. Moreover, bioinformatic analysis coupled ZNF224 to NF-κB pathway, and experimental data demonstrated that RNA interference of ZNF224 reduced the activity of the NF-κB survival pathway in CLL cells. Consistently with a pro-survival role, ZNF224 knockdown raised spontaneous and drug-induced apoptosis and inhibited the proliferation of peripheral blood mononuclear cells from CLL patients. Our findings provide evidence for the involvement of ZNF224 in the survival of CLL cells via NF-κB pathway modulation, and also suggest ZNF224 as a prognostic and predictive molecular marker of CLL disease.
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Affiliation(s)
- Rosa Catapano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Elvira Toscano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Federico Chiurazzi
- Division of Hematology, Department of Clinical and Experimental Medicine, University of Naples Federico II, Naples, Italy
| | - Serafina Patrizia Barbato
- Division of Hematology, Department of Clinical and Experimental Medicine, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rosa Arianna
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Ceinge Advanced Technologies, Naples, Italy
| | - Simona Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Maria Fiammetta Romano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Paola Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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7
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Luo TY, Shi Y, Wang G, Spaner DE. Enhanced IFN Sensing by Aggressive Chronic Lymphocytic Leukemia Cells. THE JOURNAL OF IMMUNOLOGY 2022; 209:1662-1673. [DOI: 10.4049/jimmunol.2200199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/18/2022] [Indexed: 01/04/2023]
Abstract
Abstract
Type I IFN is made by cells in response to stress. Cancer cells exist in a state of stress, but their IFN response is complex and not completely understood. This study investigated the role of autocrine IFN in human chronic lymphocytic leukemia (CLL) cells. CLL cells were found to make low amounts of IFN via TANK-binding kinase 1 pathways, but p-STAT1 and -STAT2 proteins along with IFN-stimulated genes that reflect IFN activation were variably downregulated in cultured CLL cells by the neutralizing IFNAR1 Ab anifrolumab. Patients with CLL were segregated into two groups based on the response of their leukemia cells to anifrolumab. Samples associated with more aggressive clinical behavior indicated by unmutated IGHV genes along with high CD38 and p-Bruton’s tyrosine kinase expression exhibited responses to low amounts of IFN that were blocked by anifrolumab. Samples with more indolent behavior were unaffected by anifrolumab. Hypersensitivity to IFN was associated with higher expression of IFNAR1, MX1, STAT1, and STAT2 proteins and lower activity of negative regulatory tyrosine phosphatases. Autocrine IFN protected responsive CLL cells from stressful tissue culture environments and therapeutic drugs such as ibrutinib and venetoclax in vitro, in part by upregulating Mcl-1 expression. These findings suggest hypersensitivity to IFN may promote aggressive clinical behavior. Specific blockade of IFN signaling may improve outcomes for patients with CLL with higher-risk disease.
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Affiliation(s)
- Tina YuXuan Luo
- *Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
- †Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Yonghong Shi
- *Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Guizhi Wang
- *Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - David E. Spaner
- *Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
- †Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- ‡Biology Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; and
- ¶Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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8
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Liang T, Wang X, Liu Y, Ai H, Wang Q, Wang X, Wei X, Song Y, Yin Q. Decreased TCF1 and BCL11B expression predicts poor prognosis for patients with chronic lymphocytic leukemia. Front Immunol 2022; 13:985280. [PMID: 36211334 PMCID: PMC9539190 DOI: 10.3389/fimmu.2022.985280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
T cell immune dysfunction is a prominent characteristic of chronic lymphocytic leukemia (CLL) and the main cause of failure for immunotherapy and multi-drug resistance. There remains a lack of specific biomarkers for evaluating T cell immune status with outcome for CLL patients. T cell factor 1 (TCF1, encoded by the TCF7 gene) can be used as a critical determinant of successful anti-tumor immunotherapy and a prognostic indicator in some solid tumors; however, the effects of TCF1 in CLL remain unclear. Here, we first analyzed the biological processes and functions of TCF1 and co-expressing genes using the GEO and STRING databases with the online tools Venny, Circos, and Database for Annotation, Visualization, and Integrated Discovery (DAVID). Then the expression and prognostic values of TCF1 and its partner gene B cell leukemia/lymphoma 11B (BCL11B) were explored for 505 CLL patients from 6 datasets and validated with 50 CLL patients from Henan cancer hospital (HNCH). TCF1 was downregulated in CLL patients, particularly in CD8+ T cells, which was significantly correlated with poor time-to-first treatment (TTFT) and overall survival (OS) as well as short restricted mean survival time (RMST). Function and pathway enrichment analysis revealed that TCF1 was positively correlated with BCL11B, which is involved in regulating the activation and differentiation of T cells in CLL patients. Intriguingly, BCL11B was highly consistent with TCF1 in its decreased expression and prediction of poor prognosis. More importantly, the combination of TCF1 and BCL11B could more accurately assess prognosis than either alone. Additionally, decreased TCF1 and BCL11B expression serves as an independent risk factor for rapid disease progression, coinciding with high-risk indicators, including unmutated IGHV, TP53 alteration, and advanced disease. Altogether, this study demonstrates that decreased TCF1 and BCL11B expression is significantly correlated with poor prognosis, which may be due to decreased TCF1+CD8+ T cells, impairing the effector CD8+ T cell differentiation regulated by TCF1/BCL11B.
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Liang X, Meng Y, Li C, Liu L, Wang Y, Pu L, Hu L, Li Q, Zhai Z. Super-Enhancer–Associated nine-gene prognostic score model for prediction of survival in chronic lymphocytic leukemia patients. Front Genet 2022; 13:1001364. [PMID: 36186463 PMCID: PMC9521409 DOI: 10.3389/fgene.2022.1001364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a type of highly heterogeneous mature B-cell malignancy with various disease courses. Although a multitude of prognostic markers in CLL have been reported, insights into the role of super-enhancer (SE)–related risk indicators in the occurrence and development of CLL are still lacking. A super-enhancer (SE) is a cluster of enhancers involved in cell differentiation and tumorigenesis, and is one of the promising therapeutic targets for cancer therapy in recent years. In our study, the CLL-related super-enhancers in the training database were processed by LASSO-penalized Cox regression analysis to screen a nine-gene prognostic model including TCF7, VEGFA, MNT, GMIP, SLAMF1, TNFRSF25, GRWD1, SLC6AC, and LAG3. The SE-related risk score was further constructed and it was found that the predictive performance with overall survival and time-to-treatment (TTT) was satisfactory. Moreover, a high correlation was found between the risk score and already known prognostic markers of CLL. In the meantime, we noticed that the expressions of TCF7, GMIP, SLAMF1, TNFRSF25, and LAG3 in CLL were different from those of healthy donors (p < 0.01). Moreover, the risk score and LAG3 level of matched pairs before and after treatment samples varied significantly. Finally, an interactive nomogram consisting of the nine-gene risk group and four clinical traits was established. The inhibitors of mTOR and cyclin-dependent kinases (CDKs) were considered effective in patients in the high-risk group according to the pRRophetic algorithm. Collectively, the SE-associated nine-gene prognostic model developed here may be used to predict the prognosis and assist in the risk stratification and treatment of CLL patients in the future.
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Sha Y, Jiang R, Miao Y, Qin S, Wu W, Xia Y, Wang L, Fan L, Jin H, Xu W, Li J, Zhu H. The pyroptosis-related gene signature predicts prognosis and indicates the immune microenvironment status of chronic lymphocytic leukemia. Front Immunol 2022; 13:939978. [PMID: 36177050 PMCID: PMC9513039 DOI: 10.3389/fimmu.2022.939978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world with great heterogeneity. Pyroptosis has recently been recognized as an inflammatory form of programmed cell death (PCD) and shares a close relationship with apoptosis. Although the role of apoptosis in CLL was comprehensively studied and successfully applied in clinical treatment, the relationship between pyroptosis genes and CLL remained largely unknown. In this study, eight differentially expressed pyroptosis-related genes (PRGs) were identified between CLL and normal B cells. In order to screen out the prognostic value of differentially expressed PRGs, univariate and multivariate Cox regression analyses were conducted and a risk model with three PRG signatures (GSDME, NLRP3, and PLCG1) was constructed. All CLL samples were stratified into high- and low-risk subgroups according to risk scores. The risk model showed high efficacy in predicting both overall survival (OS) and time to first treatment (TTFT). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) showed the dysregulation of immune and inflammatory response in the high-risk group. Single-sample GSEA (ssGSEA) of immune cell infiltration and the activity of immune-related pathways also displayed decreased antitumor immunity in the high-risk group. In conclusion, PRGs are of prognostic value in CLL and may play important roles in tumor immunity, and the underlying relationship between PRGs and CLL needs to be explored further.
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MESH Headings
- Gene Ontology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- NLR Family, Pyrin Domain-Containing 3 Protein
- Prognosis
- Pyroptosis/genetics
- Tumor Microenvironment/genetics
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Affiliation(s)
- Yeqin Sha
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Rui Jiang
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Miao
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Shuchao Qin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Xia
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Lei Fan
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hui Jin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Wei Xu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Wei Xu, ; Jianyong Li, ; Huayuan Zhu,
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Wei Xu, ; Jianyong Li, ; Huayuan Zhu,
| | - Huayuan Zhu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
- Pukou Chronic Lymphocytic Leukemia (CLL) Center, Pukou Division of Jiangsu Province Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Wei Xu, ; Jianyong Li, ; Huayuan Zhu,
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Kotlyar M, Wong SWH, Pastrello C, Jurisica I. Improving Analysis and Annotation of Microarray Data with Protein Interactions. Methods Mol Biol 2022; 2401:51-68. [PMID: 34902122 DOI: 10.1007/978-1-0716-1839-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gene expression microarrays are one of the most widely used high-throughput technologies in molecular biology, with applications such as identification of disease mechanisms and development of diagnostic and prognostic gene signatures. However, the success of these tasks is often limited because microarray analysis does not account for the complex relationships among genes, their products, and overall signaling and regulatory cascades. Incorporating protein-protein interaction data into microarray analysis can help address these challenges. This chapter reviews how protein-protein interactions can help with microarray analysis, leading to benefits such as better explanations of disease mechanisms, more complete gene annotations, improved prioritization of genes for future experiments, and gene signatures that generalize better to new data.
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Affiliation(s)
- Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Serene W H Wong
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada.
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Lu J, Cannizzaro E, Meier-Abt F, Scheinost S, Bruch PM, Giles HAR, Lütge A, Hüllein J, Wagner L, Giacopelli B, Nadeu F, Delgado J, Campo E, Mangolini M, Ringshausen I, Böttcher M, Mougiakakos D, Jacobs A, Bodenmiller B, Dietrich S, Oakes CC, Zenz T, Huber W. Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia. NATURE CANCER 2021; 2:853-864. [PMID: 34423310 PMCID: PMC7611543 DOI: 10.1038/s43018-021-00216-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/10/2021] [Indexed: 11/10/2022]
Abstract
Chronic Lymphocytic Leukemia (CLL) has a complex pattern of driver mutations and much of its clinical diversity remains unexplained. We devised a method for simultaneous subgroup discovery across multiple data types and applied it to genomic, transcriptomic, DNA methylation and ex-vivo drug response data from 217 Chronic Lymphocytic Leukemia (CLL) cases. We uncovered a biological axis of heterogeneity strongly associated with clinical behavior and orthogonal to the known biomarkers. We validated its presence and clinical relevance in four independent cohorts (n=547 patients). We find that this axis captures the proliferative drive (PD) of CLL cells, as it associates with lymphocyte doubling rate, global hypomethylation, accumulation of driver aberrations and response to pro-proliferative stimuli. CLL-PD was linked to the activation of mTOR-MYC-oxidative phosphorylation (OXPHOS) through transcriptomic, proteomic and single cell resolution analysis. CLL-PD is a key determinant of disease outcome in CLL. Our multi-table integration approach may be applicable to other tumors whose inter-individual differences are currently unexplained.
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Affiliation(s)
- Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Ester Cannizzaro
- Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Fabienne Meier-Abt
- Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Sebastian Scheinost
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Peter-Martin Bruch
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
| | - Holly AR Giles
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Almut Lütge
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Jennifer Hüllein
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Lena Wagner
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Brian Giacopelli
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Julio Delgado
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Elías Campo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Maurizio Mangolini
- Wellcome Trust/MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK
| | - Ingo Ringshausen
- Wellcome Trust/MRC Cambridge Stem Cell Institute & Department of Haematology, University of Cambridge, Cambridge CB2 0AH, UK
| | - Martin Böttcher
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Dimitrios Mougiakakos
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Andrea Jacobs
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Sascha Dietrich
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
- Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher C. Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
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Alsagaby SA, Brewis IA, Vijayakumar R, Alhumaydhi FA, Alwashmi AS, Alharbi NK, Al Abdulmonem W, Premanathan M, Pratt G, Fegan C, Pepper C, Brennan P. Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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14
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Guo C, Gao YY, Ju QQ, Zhang CX, Gong M, Li ZL. HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. J Transl Med 2021; 19:42. [PMID: 33485349 PMCID: PMC7825181 DOI: 10.1186/s12967-021-02708-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/16/2021] [Indexed: 11/16/2022] Open
Abstract
Background IGHV mutation status is a crucial prognostic biomarker for CLL. In the present study, we investigated the transcriptomic signatures associating with IGHV mutation status and CLL prognosis. Methods The co-expression modules and hub genes correlating with IGHV status, were identified using the GSE28654, by ‘WGCNA’ package and R software (version 4.0.2). The over-representation analysis was performed to reveal enriched cell pathways for genes of correlating modules. Then 9 external cohorts were used to validate the correlation of hub genes expression with IGHV status or clinical features (treatment response, transformation to Richter syndrome, etc.). Moreover, to elucidate the significance of hub genes on disease course and prognosis of CLL patients, the Kaplan–Meier analysis for the OS and TTFT of were performed between subgroups dichotomized by the median expression value of individual hub genes. Results 2 co-expression modules and 9 hub genes ((FCRL1/FCRL2/HELQ/EGR3LPL/LDOC1/ZNF667/SOWAHC/SEPTIN10) correlating with IGHV status were identified by WGCNA, and validated by external datasets. The modules were found to be enriched in NF-kappaB, HIF-1 and other important pathways, involving cell proliferation and apoptosis. The expression of hub genes was revealed to be significantly different, not only between CLL and normal B cell, but also between various types of lymphoid neoplasms. HELQ expression was found to be related with response of immunochemotherapy treatment significantly (p = 0.0413), while HELQ and ZNF667 were expressed differently between stable CLL and Richter syndrome patients (p < 0.0001 and p = 0.0278, respectively). By survival analysis of subgroups, EGR3 expression was indicated to be significantly associated with TTFT by 2 independent cohorts (GSE39671, p = 0.0311; GSE22762, p = 0.0135). While the expression of HELQ and EGR3 was found to be associated with OS (p = 0.0291 and 0.0114 respectively).The Kras, Hedgehog and IL6-JAK-STAT3 pathways were found to be associating with the expression of hub genes, resulting from GSEA. Conclusions The expression of HELQ and EGR3 were correlated with IGHV mutation status in CLL patients. Additionally, the expression of HELQ/EGR3 were prognostic markers for CLL associating with targetable cell signaling pathways.
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Affiliation(s)
- Chao Guo
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Ya-Yue Gao
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Qian-Qian Ju
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Chun-Xia Zhang
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Ming Gong
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China
| | - Zhen-Ling Li
- Department of Hematology, China-Japan Friendship Hospital, Yinghua East Street, Beijing, 100029, China.
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Lucchetta M, Pellegrini M. Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. Sci Rep 2020; 10:17628. [PMID: 33077837 PMCID: PMC7573595 DOI: 10.1038/s41598-020-74705-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
Genes are organized in functional modules (or pathways), thus their action and their dysregulation in diseases may be better understood by the identification of the modules most affected by the disease (aka disease modules, or active subnetworks). We describe how an algorithm based on the Core&Peel method is used to detect disease modules in co-expression networks of genes. We first validate Core&Peel for the general task of functional module detection by comparison with 42 methods participating in the Disease Module Identification DREAM challenge. Next, we use four specific disease test cases (colorectal cancer, prostate cancer, asthma, and rheumatoid arthritis), four state-of-the-art algorithms (ModuleDiscoverer, Degas, KeyPathwayMiner, and ClustEx), and several pathway databases to validate the proposed algorithm. Core&Peel is the only method able to find significant associations of the predicted disease module with known validated relevant pathways for all four diseases. Moreover, for the two cancer datasets, Core&Peel detects further eight relevant pathways not discovered by the other methods used in the comparative analysis. Finally, we apply Core&Peel and other methods to explore the transcriptional response of human cells to SARS-CoV-2 infection, finding supporting evidence for drug repositioning efforts at a pre-clinical level.
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Affiliation(s)
- Marta Lucchetta
- Institute of Informatics and Telematics (IIT), CNR, Pisa, 56124, Italy
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, 53100, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics (IIT), CNR, Pisa, 56124, Italy.
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16
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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.
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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
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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
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Al-Harazi O, El Allali A, Colak D. Biomolecular Databases and Subnetwork Identification Approaches of Interest to Big Data Community: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:138-151. [PMID: 30883301 DOI: 10.1089/omi.2018.0205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Next-generation sequencing approaches and genome-wide studies have become essential for characterizing the mechanisms of human diseases. Consequently, many researchers have applied these approaches to discover the genetic/genomic causes of common complex and rare human diseases, generating multiomics big data that span the continuum of genomics, proteomics, metabolomics, and many other system science fields. Therefore, there is a significant and unmet need for biological databases and tools that enable and empower the researchers to analyze, integrate, and make sense of big data. There are currently large number of databases that offer different types of biological information. In particular, the integration of gene expression profiles and protein-protein interaction networks provides a deeper understanding of the complex multilayered molecular architecture of human diseases. Therefore, there has been a growing interest in developing methodologies that integrate and contextualize big data from molecular interaction networks to identify biomarkers of human diseases at a subnetwork resolution as well. In this expert review, we provide a comprehensive summary of most popular biomolecular databases for molecular interactions (e.g., Biological General Repository for Interaction Datasets, Kyoto Encyclopedia of Genes and Genomes and Search Tool for The Retrieval of Interacting Genes/Proteins), gene-disease associations (e.g., Online Mendelian Inheritance in Man, Disease-Gene Network, MalaCards), and population-specific databases (e.g., Human Genetic Variation Database), and describe some examples of their usage and potential applications. We also present the most recent subnetwork identification approaches and discuss their main advantages and limitations. As the field of data science continues to emerge, the present analysis offers a deeper and contextualized understanding of the available databases in molecular biomedicine.
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Affiliation(s)
- Olfat Al-Harazi
- 1 Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,2 Computer Science Department, College of Computer and Information Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Achraf El Allali
- 2 Computer Science Department, College of Computer and Information Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Dilek Colak
- 1 Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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18
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B-cell-specific IRF4 deletion accelerates chronic lymphocytic leukemia development by enhanced tumor immune evasion. Blood 2020; 134:1717-1729. [PMID: 31537531 DOI: 10.1182/blood.2019000973] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogenous disease that is highly dependent on a cross talk of CLL cells with the microenvironment, in particular with T cells. T cells derived from CLL patients or murine CLL models are skewed to an antigen-experienced T-cell subset, indicating a certain degree of antitumor recognition, but they are also exhausted, preventing an effective antitumor immune response. Here we describe a novel mechanism of CLL tumor immune evasion that is independent of T-cell exhaustion, using B-cell-specific deletion of the transcription factor IRF4 (interferon regulatory factor 4) in Tcl-1 transgenic mice developing a murine CLL highly similar to the human disease. We show enhanced CLL disease progression in IRF4-deficient Tcl-1 tg mice, associated with a severe downregulation of genes involved in T-cell activation, including genes involved in antigen processing/presentation and T-cell costimulation, which massively reduced T-cell subset skewing and exhaustion. We found a strong analogy in the human disease, with inferior prognosis of CLL patients with low IRF4 expression in independent CLL patient cohorts, failed T-cell skewing to antigen-experienced subsets, decreased costimulation capacity, and downregulation of genes involved in T-cell activation. These results have therapeutic relevance because our findings on molecular mechanisms of immune privilege may be responsible for the failure of immune-therapeutic strategies in CLL and may lead to improved targeting in the future.
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19
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Alsagaby SA. Transcriptomics-based validation of the relatedness of heterogeneous nuclear ribonucleoproteins to chronic lymphocytic leukemia as potential biomarkers of the disease aggressiveness. Saudi Med J 2019; 40:328-338. [PMID: 30957125 PMCID: PMC6506648 DOI: 10.15537/smj.2019.4.23380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES To use independent transcriptomics data sets of cancer patients with prognostic information from public repositories to validate the relevance of our previously described chronic lymphocytic leukemia (CLL)-related proteins at the level of transcription (mRNA) to the prognosis of CLL. Methods: This is a validation study that was conducted at Majmaah University, Kingdom of Saudi Arabia between January-2017 and July-2018. Two independent data sets of CLL transcriptomics from Gene Expression Omnibus (GEO) with time-to-first treatment (TTFT) data (GSE39671; 130 patients) and information about overall survival (OS) (GSE22762; 107 patients) were used for the validation analyses. To further investigate the relatedness of a transcript of interest to other neoplasms, 6 independent data sets of cancer transcriptomics with prognostic information (1865 patients) from the cancer genomics atlas (TCGA) were used. Pathway-enrichment analyses were conducted using Reactome; and correlation analyses of gene expression were performed using Pearson score. Results: Nine of the CLL-related proteins exhibited transcript expression that predicted TTFT and 7 of the CLL-related proteins showed mRNA levels that predicted OS in CLL patients (p≤0.05). Of these transcripts, 8 were different types of heterogeneous nuclear ribonucleoproteins (HNRNPs); and 2 (HNRNPUL2 and HIST1C1H) retained prognostic significance in the 2 independent data sets. Furthermore, genes that enriched CLL-related pathways (p≤0.05; false discovery rate [FDR] ≤0.05) were found to correlate with the expression of HNRNPUL2 (Pearson score: ≥0.50; p lessthan 0.00001). Finally, increased expression of HNRNPUL2 was indicative of poor prognosis of various types of cancer other than CLL (p less than 0.05). Conclusion: The cognate transcripts of 14 of our CLL-related proteins significantly predicted CLL prognosis.
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, Kingdom of Saudi Arabia. E-mail.
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20
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Schubert M, Hackl H, Gassner FJ, Greil R, Geisberger R. Investigating epigenetic effects of activation-induced deaminase in chronic lymphocytic leukemia. PLoS One 2018; 13:e0208753. [PMID: 30571766 PMCID: PMC6301619 DOI: 10.1371/journal.pone.0208753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/21/2018] [Indexed: 11/19/2022] Open
Abstract
Activation induced deaminase (AID) has two distinct and well defined roles, both relying on its deoxycytidine (dC) deaminating function: one as a DNA mutator and another in DNA demethylation. In chronic lymphocytic leukemia (CLL), AID was previously shown to be an independent negative prognostic factor. While there is substantial impact on DNA mutations, effects of AID on gene expression by promoter demethylation of disease related target genes in leukemia has not been addressed. To shed light on this question, we aimed at determining genome wide methylation changes as well as gene expression changes in response to AID expression in CLL. Although we found minor differences in individual methylation variable positions following AID expression, we could not find recurrent methylation changes of specific target sites or changes in global methylation.
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MESH Headings
- Computational Biology
- DNA Methylation/physiology
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/enzymology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukocytes, Mononuclear/enzymology
- Porphyria, Acute Intermittent/metabolism
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Affiliation(s)
- Maria Schubert
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, Salzburg, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Franz Josef Gassner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, Salzburg, Austria
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, Salzburg, Austria
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute—Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, Salzburg, Austria, Cancer Cluster Salzburg, Salzburg, Austria
- * E-mail:
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21
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Inhibition of maternal embryonic leucine zipper kinase with OTSSP167 displays potent anti-leukemic effects in chronic lymphocytic leukemia. Oncogene 2018; 37:5520-5533. [PMID: 29895969 DOI: 10.1038/s41388-018-0333-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 11/08/2022]
Abstract
TP53 pathway defects contributed to therapy resistance and adverse clinical outcome in chronic lymphocytic leukemia (CLL), which represents an unmet clinical need with few therapeutic options. Maternal embryonic leucine zipper kinase (MELK) is a novel oncogene, which plays crucial roles in mitotic progression and stem cell maintenance. OTSSP167, an orally administrated inhibitor targeting MELK, is currently in a phase I/II clinical trial in patients with advanced breast cancer and acute myeloid leukemia. Yet, no investigation has been elucidated to date regarding the oncogenic role of MELK and effects of OTSSP167 in chronic lymphocytic leukemia (CLL). Previous studies confirmed MELK inhibition abrogated cancer cell survival via p53 signaling pathway. Thus, we aimed to determine the biological function of MELK and therapeutic potential of OTSSP167 in CLL. Herein, MELK over-expression was observed in CLL cells, and correlated with higher WBC count, advanced stage, elevated LDH, increased β2-MG level, unmutated IGHV, positive ZAP-70, deletion of 17p13 and inferior prognosis of CLL patients. In accordance with functional enrichment analyses in gene expression profiling, CLL cells with depletion or inhibition of MELK exhibited impaired cell proliferation, enhanced fast-onset apoptosis, induced G2/M arrest, attenuated cell chemotaxis and promoted sensitivity to fludarabine and ibrutinib. However, gain-of-function assay showed increased cell proliferation and cell chemotaxis. In addition, OTSSP167 treatment reduced phosphorylation of AKT and ERK1/2. It decreased FoxM1 phosphorylation, expression of FoxM1, cyclin B1 and CDK1, while up-regulating p53 and p21 expression. Taken together, MELK served as a candidate of therapeutic target in CLL. OTSSP167 exhibits potent anti-tumor activities in CLL cells, highlighting a novel molecule-based strategy for leukemic interventions.
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22
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Nørgaard CH, Jakobsen LH, Gentles AJ, Dybkær K, El-Galaly TC, Bødker JS, Schmitz A, Johansen P, Herold T, Spiekermann K, Brown JR, Klitgaard JL, Johnsen HE, Bøgsted M. Subtype assignment of CLL based on B-cell subset associated gene signatures from normal bone marrow - A proof of concept study. PLoS One 2018; 13:e0193249. [PMID: 29513759 PMCID: PMC5841735 DOI: 10.1371/journal.pone.0193249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/07/2018] [Indexed: 11/26/2022] Open
Abstract
Diagnostic and prognostic evaluation of chronic lymphocytic leukemia (CLL) involves blood cell counts, immunophenotyping, IgVH mutation status, and cytogenetic analyses. We generated B-cell associated gene-signatures (BAGS) based on six naturally occurring B-cell subsets within normal bone marrow. Our hypothesis is that by segregating CLL according to BAGS, we can identify subtypes with prognostic implications in support of pathogenetic value of BAGS. Microarray-based gene-expression samples from eight independent CLL cohorts (1,024 untreated patients) were BAGS-stratified into pre-BI, pre-BII, immature, naïve, memory, or plasma cell subtypes; the majority falling within the memory (24.5-45.8%) or naïve (14.5-32.3%) categories. For a subset of CLL patients (n = 296), time to treatment (TTT) was shorter amongst early differentiation subtypes (pre-BI/pre-BII/immature) compared to late subtypes (memory/plasma cell, HR: 0.53 [0.35-0.78]). Particularly, pre-BII subtype patients had the shortest TTT among all subtypes. Correlates derived for BAGS subtype and IgVH mutation (n = 405) revealed an elevated mutation frequency in late vs. early subtypes (71% vs. 45%, P < .001). Predictions for BAGS subtype resistance towards rituximab and cyclophosphamide varied for rituximab, whereas all subtypes were sensitive to cyclophosphamide. This study supports our hypothesis that BAGS-subtyping may be of tangible prognostic and pathogenetic value for CLL patients.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents, Alkylating/therapeutic use
- Antineoplastic Agents, Immunological/therapeutic use
- B-Lymphocyte Subsets/metabolism
- Bone Marrow/metabolism
- Cyclophosphamide/therapeutic use
- Drug Resistance, Neoplasm/physiology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Microarray Analysis
- Middle Aged
- Prognosis
- Proof of Concept Study
- Retrospective Studies
- Rituximab/therapeutic use
- Survival Analysis
- Time-to-Treatment
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Affiliation(s)
| | - Lasse Hjort Jakobsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Andrew J. Gentles
- Departments of Medicine and Biomedical Data Science, Stanford, California, United States of America
| | - Karen Dybkær
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Tarec Christoffer El-Galaly
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Julie Støve Bødker
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Alexander Schmitz
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Preben Johansen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Tobias Herold
- Department of Internal Medicine 3, University of Munich, Munich, Germany
| | | | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Josephine L. Klitgaard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Hans Erik Johnsen
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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23
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Bagacean C, Tempescul A, Le Dantec C, Bordron A, Mohr A, Saad H, Olivier V, Zdrenghea M, Cristea V, Cartron PF, Douet-Guilbert N, Berthou C, Renaudineau Y. Alterations in DNA methylation/demethylation intermediates predict clinical outcome in chronic lymphocytic leukemia. Oncotarget 2017; 8:65699-65716. [PMID: 29029465 PMCID: PMC5630365 DOI: 10.18632/oncotarget.20081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/26/2017] [Indexed: 12/12/2022] Open
Abstract
Cytosine derivative dysregulations represent important epigenetic modifications whose impact on the clinical outcome in chronic lymphocytic leukemia (CLL) is incompletely understood. Hence, global levels of 5-methylcytosine (5-mCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-CaCyt) and 5-hydroxymethyluracil were tested in purified B cells from CLL patients (n = 55) and controls (n = 17). The DNA methylation 'writers' (DNA methyltransferases [DNMT1/3A/3B]), 'readers' (methyl-CpG-binding domain [MBD2/4]), 'editors' (ten-eleven translocation [TET1/2/3]) and 'modulators' (SAT1) were also evaluated. Accordingly, patients were stratified into three subgroups. First, a subgroup with a global deficit in cytosine derivatives characterized by hyperlymphocytosis, reduced median progression free survival (PFS = 52 months) and shorter treatment free survival (TFS = 112 months) was identified. In this subgroup, major epigenetic modifications were highlighted including a reduction of 5-mCyt, 5-hmCyt, 5-CaCyt associated with DNMT3A, MBD2/4 and TET1/2 downregulation. Second, the cytosine derivative analysis revealed a subgroup with a partial deficit (PFS = 84, TFS = 120 months), mainly affecting DNA demethylation (5-hmCyt reduction, SAT1 induction). Third, a subgroup epigenetically similar to controls was identified (PFS and TFS > 120 months). The prognostic impact of stratifying CLL patients within three epigenetic subgroups was confirmed in a validation cohort. In conclusion, our results suggest that dysregulations of cytosine derivative regulators represent major events acquired during CLL progression and are independent from IGHV mutational status.
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Affiliation(s)
- Cristina Bagacean
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Adrian Tempescul
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Christelle Le Dantec
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Anne Bordron
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Audrey Mohr
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
| | - Hussam Saad
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Valerie Olivier
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
| | - Mihnea Zdrenghea
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, ‘Ion Chiricuta’ Oncology Institute, Cluj-Napoca, Romania
| | - Victor Cristea
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | | | - Christian Berthou
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Department of Hematology, Brest University Medical School Hospital, Brest, France
| | - Yves Renaudineau
- U1227 B Lymphocytes and Autoimmunity, University of Brest, INSERM, IBSAM, Labex IGO, Networks IC-CGO and REpiCGO from Cancéropôle Grand Ouest, Brest, France
- Laboratory of Immunology and Immunotherapy, Brest University Medical School Hospital, Brest, France
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24
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Barisione G, Fabbi M, Cutrona G, De Cecco L, Zupo S, Leitinger B, Gentile M, Manzoni M, Neri A, Morabito F, Ferrarini M, Ferrini S. Heterogeneous expression of the collagen receptor DDR1 in chronic lymphocytic leukaemia and correlation with progression. Blood Cancer J 2017; 6:e513. [PMID: 28060374 PMCID: PMC5301030 DOI: 10.1038/bcj.2016.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- G Barisione
- IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - M Fabbi
- IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - G Cutrona
- IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - L De Cecco
- Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - S Zupo
- IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - B Leitinger
- Section of Molecular Medicine, National Heart and Lung Institute, Imperial College London, UK
| | - M Gentile
- Hematology Unit Azienda Ospedaliera of Cosenza, Cosenza, Italy
| | - M Manzoni
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - A Neri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy.,Hematology Unit, Fondazione Cà Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - F Morabito
- Hematology Unit Azienda Ospedaliera of Cosenza, Cosenza, Italy.,Biotechnology Research Unit, Aprigliano, ASP of Cosenza, Cosenza, Italy
| | - M Ferrarini
- IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - S Ferrini
- IRCCS AOU San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
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25
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High-level ROR1 associates with accelerated disease progression in chronic lymphocytic leukemia. Blood 2016; 128:2931-2940. [PMID: 27815263 DOI: 10.1182/blood-2016-04-712562] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/22/2016] [Indexed: 11/20/2022] Open
Abstract
ROR1 is an oncoembryonic orphan receptor found on chronic lymphocytic leukemia (CLL) B cells, but not on normal postpartum tissues. ROR1 is a receptor for Wnt5a that may complex with TCL1, a coactivator of AKT that is able to promote development of CLL. We found the CLL cells of a few patients expressed negligible ROR1 (ROR1Neg), but expressed TCL1A at levels comparable to those of samples that expressed ROR1 (ROR1Pos). Transcriptome analyses revealed that ROR1Neg cases generally could be distinguished from those that were ROR1Pos in unsupervised gene-expression clustering analysis. Gene-set enrichment analyses demonstrated that ROR1Neg CLL had lower expression and activation of AKT signaling pathways relative to ROR1Pos CLL, similar to what was noted for leukemia that respectively developed in TCL1 vs ROR1xTCL1 transgenic mice. In contrast to its effect on ROR1Pos CLL, Wnt5a did not enhance the proliferation, chemotaxis, or survival of ROR1Neg CLL. We examined the CLL cells from 1568 patients, which we randomly assigned to a training or validation set of 797 or 771 cases, respectively. Using recursive partitioning, we defined a threshold for ROR1 surface expression that could segregate samples of the training set into ROR1-Hi vs ROR1-Lo subgroups that differed significantly in their median treatment-free survival (TFS). Using this threshold, we found that ROR1-Hi cases had a significantly shorter median TFS and overall survival than ROR1-Lo cases in the validation set. These data demonstrate that expression of ROR1 may promote leukemia-cell activation and survival and enhance disease progression in patients with CLL.
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Ma J, Shojaie A, Michailidis G. Network-based pathway enrichment analysis with incomplete network information. Bioinformatics 2016; 32:3165-3174. [PMID: 27357170 DOI: 10.1093/bioinformatics/btw410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/22/2016] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of changes in cellular activity in response to treatments and/or in disease states. Methods that use existing pathway network information have been shown to outperform simpler methods that only take into account pathway membership. However, despite significant progress in understanding the association amongst members of biological pathways, and expansion of data bases containing information about interactions of biomolecules, the existing network information may be incomplete or inaccurate and is not cell-type or disease condition-specific. RESULTS We propose a constrained network estimation framework that combines network estimation based on cell- and condition-specific high-dimensional Omics data with interaction information from existing data bases. The resulting pathway topology information is subsequently used to provide a framework for simultaneous testing of differences in expression levels of pathway members, as well as their interactions. We study the asymptotic properties of the proposed network estimator and the test for pathway enrichment, and investigate its small sample performance in simulated and real data settings. AVAILABILITY AND IMPLEMENTATION The proposed method has been implemented in the R-package netgsa available on CRAN. CONTACT jinma@upenn.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jing Ma
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, PA 19104, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, WA 98915, USA
| | - George Michailidis
- Department of Statistics, University of Florida, Gainesville, FL 32611, USA
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27
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Haas M, Stephenson D, Romero K, Gordon MF, Zach N, Geerts H. Big data to smart data in Alzheimer's disease: Real-world examples of advanced modeling and simulation. Alzheimers Dement 2016; 12:1022-1030. [PMID: 27327540 DOI: 10.1016/j.jalz.2016.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 04/08/2016] [Accepted: 05/22/2016] [Indexed: 12/25/2022]
Abstract
Many disease-modifying clinical development programs in Alzheimer's disease (AD) have failed to date, and development of new and advanced preclinical models that generate actionable knowledge is desperately needed. This review reports on computer-based modeling and simulation approach as a powerful tool in AD research. Statistical data-analysis techniques can identify associations between certain data and phenotypes, such as diagnosis or disease progression. Other approaches integrate domain expertise in a formalized mathematical way to understand how specific components of pathology integrate into complex brain networks. Private-public partnerships focused on data sharing, causal inference and pathway-based analysis, crowdsourcing, and mechanism-based quantitative systems modeling represent successful real-world modeling examples with substantial impact on CNS diseases. Similar to other disease indications, successful real-world examples of advanced simulation can generate actionable support of drug discovery and development in AD, illustrating the value that can be generated for different stakeholders.
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Affiliation(s)
- Magali Haas
- Orion Bionetworks, Inc., Cambridge, MA, USA.
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28
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Liu ZP. Identifying network-based biomarkers of complex diseases from high-throughput data. Biomark Med 2016; 10:633-50. [DOI: 10.2217/bmm-2015-0035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this work, we review the main available computational methods of identifying biomarkers of complex diseases from high-throughput data. The emerging omics techniques provide powerful alternatives to measure thousands of molecules in cells in parallel manners. The generated genomic, transcriptomic, proteomic, metabolomic and phenomic data provide comprehensive molecular and cellular information for detecting critical signals served as biomarkers by classifying disease phenotypic states. Networks are often employed to organize these profiles in the identification of biomarkers to deal with complex diseases in diagnosis, prognosis and therapy as well as mechanism deciphering from systematic perspectives. Here, we summarize some representative network-based bioinformatics methods in order to highlight the importance of computational strategies in biomarker discovery.
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Affiliation(s)
- Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science & Engineering, Shandong University, Jinan, Shandong 250061, China
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29
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Feng L, Tong R, Liu X, Zhang K, Wang G, Zhang L, An N, Cheng S. A network-based method for identifying prognostic gene modules in lung squamous carcinoma. Oncotarget 2016; 7:18006-20. [PMID: 26919109 PMCID: PMC4951267 DOI: 10.18632/oncotarget.7632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/13/2016] [Indexed: 12/23/2022] Open
Abstract
Similarities in gene expression between both developing embryonic and precancerous tissues and cancer tissues may help identify much-needed biomarkers and therapeutic targets in lung squamous carcinoma. In this study, human lung samples representing ten successive time points, from embryonic development to carcinogenesis, were used to construct global gene expression profiles. Differentially expressed genes with similar expression in precancerous and cancer samples were identified. Using a network-based greedy searching algorithm to analyze the training cohort (n = 69) and three independent testing cohorts, we successfully identified a significant 22-gene module in which expression levels were correlated with overall survival in lung squamous carcinoma patients.
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Affiliation(s)
- Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
| | - Run Tong
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohong Liu
- Department of Gynecology and Obstetrics, Maternal and Child Health Care Hospital of Haidian, Beijing, China
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
| | - Guiqi Wang
- Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Zhang
- Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ning An
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
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30
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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: 54] [Impact Index Per Article: 6.8] [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.
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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
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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
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Wagner A, Cohen N, Kelder T, Amit U, Liebman E, Steinberg DM, Radonjic M, Ruppin E. Drugs that reverse disease transcriptomic signatures are more effective in a mouse model of dyslipidemia. Mol Syst Biol 2016; 11:791. [PMID: 26148350 PMCID: PMC4380926 DOI: 10.15252/msb.20145486] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
High-throughput omics have proven invaluable in studying human disease, and yet day-to-day clinical practice still relies on physiological, non-omic markers. The metabolic syndrome, for example, is diagnosed and monitored by blood and urine indices such as blood cholesterol levels. Nevertheless, the association between the molecular and the physiological manifestations of the disease, especially in response to treatment, has not been investigated in a systematic manner. To this end, we studied a mouse model of diet-induced dyslipidemia and atherosclerosis that was subject to various drug treatments relevant to the disease in question. Both physiological data and gene expression data (from the liver and white adipose) were analyzed and compared. We find that treatments that restore gene expression patterns to their norm are associated with the successful restoration of physiological markers to their baselines. This holds in a tissue-specific manner—treatments that reverse the transcriptomic signatures of the disease in a particular tissue are associated with positive physiological effects in that tissue. Further, treatments that introduce large non-restorative gene expression alterations are associated with unfavorable physiological outcomes. These results provide a sound basis to in silico methods that rely on omic metrics for drug repurposing and drug discovery by searching for compounds that reverse a disease's omic signatures. Moreover, they highlight the need to develop drugs that restore the global cellular state to its healthy norm rather than rectify particular disease phenotypes.
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Affiliation(s)
- Allon Wagner
- The Blavatnik School of Computer Science, Tel Aviv UniversityTel Aviv, Israel
- Department of Electrical Engineering and Computer Science, University of CaliforniaBerkeley, CA, USA
- * Corresponding author. Tel. +972 3 640 5378; E-mail:
| | - Noa Cohen
- The Blavatnik School of Computer Science, Tel Aviv UniversityTel Aviv, Israel
| | - Thomas Kelder
- Microbiology and Systems Biology, TNOZeist, the Netherlands
| | - Uri Amit
- Neufeld Cardiac Research Institute, Tel Aviv UniversityTel Aviv, Israel
- Regenerative Medicine Stem Cells and Tissue Engineering Center, Sheba Medical CenterTel Hashomer, Israel
| | - Elad Liebman
- Department of Computer Science, University of Texas at AustinAustin, TX, USA
| | - David M Steinberg
- Department of Statistics and Operations Research, Tel Aviv UniversityTel Aviv, Israel
| | | | - Eytan Ruppin
- The Blavatnik School of Computer Science, Tel Aviv UniversityTel Aviv, Israel
- The Sackler School of Medicine, Tel Aviv UniversityTel Aviv, Israel
- Department of Computer Science, Institute of Advanced Computer Sciences (UMIACS) & the Center for Bioinformatics and Computational Biology, University of MarylandCollege Park, MD, USA
- ** Corresponding author. Tel. +972 3 640 6528; E-mail:
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32
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Trends in survival of chronic lymphocytic leukemia patients in Germany and the USA in the first decade of the twenty-first century. J Hematol Oncol 2016; 9:28. [PMID: 27000264 PMCID: PMC4802710 DOI: 10.1186/s13045-016-0257-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/11/2016] [Indexed: 01/26/2023] Open
Abstract
Background Recent population-based studies in the United States of America (USA) and other countries have shown improvements in survival for patients with chronic lymphocytic leukemia (CLL) diagnosed in the early twenty-first century. Here, we examine the survival for patients diagnosed with CLL in Germany in 1997–2011. Methods Data were extracted from 12 cancer registries in Germany and compared to the data from the USA. Period analysis was used to estimate 5- and 10-year relative survival (RS). Results Five- and 10-year RS estimates in 2009–2011 of 80.2 and 59.5 %, respectively, in Germany and 82.4 and 64.7 %, respectively, in the USA were observed. Overall, 5-year RS increased significantly in Germany and the difference compared to the survival in the USA which slightly decreased between 2003–2005 and 2009–2011. However, age-specific analyses showed persistently higher survival for all ages except for 15–44 in the USA. In general, survival decreased with age, but the age-related disparity was small for patients younger than 75. In both countries, 5-year RS was >80 % for patients less than 75 years of age but <70 % for those age 75+. Conclusions Overall, 5-year survival for patients with CLL is good, but 10-year survival is significantly lower, and survival was much lower for those age 75+. Major differences in survival between countries were not observed. Further research into ways to increase survival for older CLL patients are needed to reduce the persistent large age-related survival disparity.
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Al-Harazi O, Al Insaif S, Al-Ajlan MA, Kaya N, Dzimiri N, Colak D. Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network. J Genet Genomics 2015; 43:349-67. [PMID: 27318646 DOI: 10.1016/j.jgg.2015.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/22/2015] [Accepted: 11/20/2015] [Indexed: 12/16/2022]
Abstract
A disease phenotype generally reflects various pathobiological processes that interact in a complex network. The highly interconnected nature of the human protein interaction network (interactome) indicates that, at the molecular level, it is difficult to consider diseases as being independent of one another. Recently, genome-wide molecular measurements, data mining and bioinformatics approaches have provided the means to explore human diseases from a molecular basis. The exploration of diseases and a system of disease relationships based on the integration of genome-wide molecular data with the human interactome could offer a powerful perspective for understanding the molecular architecture of diseases. Recently, subnetwork markers have proven to be more robust and reliable than individual biomarker genes selected based on gene expression profiles alone, and achieve higher accuracy in disease classification. We have applied one of these methodologies to idiopathic dilated cardiomyopathy (IDCM) data that we have generated using a microarray and identified significant subnetworks associated with the disease. In this paper, we review the recent endeavours in this direction, and summarize the existing methodologies and computational tools for network-based analysis of complex diseases and molecular relationships among apparently different disorders and human disease network. We also discuss the future research trends and topics of this promising field.
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Affiliation(s)
- Olfat Al-Harazi
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Sadiq Al Insaif
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Monirah A Al-Ajlan
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia; College of Computer and Information Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Nduna Dzimiri
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia.
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Yepes S, Torres MM, López-Kleine L. Regulatory network reconstruction reveals genes with prognostic value for chronic lymphocytic leukemia. BMC Genomics 2015; 16:1002. [PMID: 26606983 PMCID: PMC4659237 DOI: 10.1186/s12864-015-2189-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
Background The clinical course of chronic lymphocytic leukemia (CLL) is highly variable; some patients follow an indolent course, but others progress to a more advanced stage. The mutational status of rearranged immunoglobulin heavy chain variable (IGVH) genes in CLL is a feature that is widely recognized for dividing patients into groups that are related to their prognoses. However, the regulatory programs associated with the IGVH statuses are poorly understood, and markers that can precisely predict survival outcomes have yet to be identified. Methods In this study, (i) we reconstructed gene regulatory networks in CLL by applying an information-theoretic approach to the expression profiles of 5 cohorts. (ii) We applied master regulator analysis (MRA) to these networks to identify transcription factors (TFs) that regulate an IGVH mutational status signature. The IGVH mutational status signature was developed by searching for differentially expressed genes between the IGVH mutational statuses in numerous CLL cohorts. (iii) To evaluate the biological implication of the inferred regulators, prognostic values were determined using time to treatment (TTT) and overall survival (OS) in two different cohorts. Results A robust IGVH expression signature was obtained, and various TFs emerged as regulators of the signature in most of the reconstructed networks. The TF targets expression profiles exhibited significant differences with respect to survival, which allowed the definition of a reduced profile with a high value for OS. TCF7 and its targets stood out for their roles in progression. Conclusion TFs and their targets, which were obtained merely from inferred regulatory associations, have prognostic implications and reflect a regulatory context for prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2189-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sally Yepes
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Maria Mercedes Torres
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia.
| | - Liliana López-Kleine
- Departamento de Estadística, Universidad Nacional de Colombia, Bogotá D.C., Colombia.
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35
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Graph-based unsupervised feature selection and multiview clustering for microarray data. J Biosci 2015; 40:755-67. [DOI: 10.1007/s12038-015-9559-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Yepes S, Torres MM, Andrade RE. Clustering of Expression Data in Chronic Lymphocytic Leukemia Reveals New Molecular Subdivisions. PLoS One 2015; 10:e0137132. [PMID: 26355846 PMCID: PMC4565688 DOI: 10.1371/journal.pone.0137132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 08/12/2015] [Indexed: 12/18/2022] Open
Abstract
Although the identification of inherent structure in chronic lymphocytic leukemia (CLL) gene expression data using class discovery approaches has not been extensively explored, the natural clustering of patient samples can reveal molecular subdivisions that have biological and clinical implications. To explore this, we preprocessed raw gene expression data from two published studies, combined the data to increase the statistical power, and performed unsupervised clustering analysis. The clustering analysis was replicated in 4 independent cohorts. To assess the biological significance of the resultant clusters, we evaluated their prognostic value and identified cluster-specific markers. The clustering analysis revealed two robust and stable subgroups of CLL patients in the pooled dataset. The subgroups were confirmed by different methodological approaches (non-negative matrix factorization NMF clustering and hierarchical clustering) and validated in different cohorts. The subdivisions were related with differential clinical outcomes and markers associated with the microenvironment and the MAPK and BCR signaling pathways. It was also found that the cluster markers were independent of the immunoglobulin heavy chain variable (IGVH) genes mutational status. These findings suggest that the microenvironment can influence the clinical behavior of CLL, contributing to prognostic differences. The workflow followed here provides a new perspective on differences in prognosis and highlights new markers that should be explored in this context.
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MESH Headings
- Biomarkers, Tumor/metabolism
- Cluster Analysis
- Cohort Studies
- Gene Expression Regulation, Leukemic
- Genes, Neoplasm
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/classification
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Survival Analysis
- Transcription, Genetic
- Treatment Outcome
- Tumor Microenvironment/genetics
- Up-Regulation/genetics
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Affiliation(s)
- Sally Yepes
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia
- * E-mail:
| | - Maria Mercedes Torres
- Facultad de Ciencias, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá D.C., Colombia
| | - Rafael E. Andrade
- Facultad de Medicina, Universidad de los Andes, Departamento de Patología, Hospital Universitario, Fundación Santa Fe de Bogotá, Bogotá D.C., Colombia
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Au R, Piers RJ, Lancashire L. Back to the future: Alzheimer's disease heterogeneity revisited. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2015; 1:368-370. [PMID: 27077132 PMCID: PMC4827150 DOI: 10.1016/j.dadm.2015.05.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Rhoda Au
- Department of Neurology and Framingham Heart Study, Boston University School of Medicine, Boston, MA, USA
| | - Ryan J. Piers
- Department of Neurology and Framingham Heart Study, Boston University School of Medicine, Boston, MA, USA
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38
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Shi M, Wu M, Pan P, Zhao R. Network-based sub-network signatures unveil the potential for acute myeloid leukemia therapy. MOLECULAR BIOSYSTEMS 2015; 10:3290-7. [PMID: 25313005 DOI: 10.1039/c4mb00440j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although gene expression profiling studies of acute myeloid leukemia (AML) patients have provided key insights into potential diagnostic and prognostic markers and therapeutic targets, it is not clear that the patterns of molecular heterogeneity affect the tumor biology and respond to the treatment. We hypothesized that network-based gene expression signatures of AML represent the mechanistically important genes and may improve the predicted performance of prognosis and clinical outcome. We provided the random walk with restart (RWR) analysis to discover the sub-network of genomic alterations. The RWR approach integrates the signature genes derived from the random forest (RF) analysis as "seeds" to identify genes critical to the AML recurrence phenotype. To test whether the 81-gene biomarkers could predict AML recurrence, we developed Survival Support Vector Machine (SSVM) models using a gene expression dataset and test on an independent dataset. The random forest classifier was built based on 81-gene biomarkers to separate the AML patients into "recurrence" and "non-recurrence" groups. The 81-gene biomarkers showed significant enrichment related to cancer pathophysiology and provided good coverage of sub-network biomarkers and AML-related signaling pathways. The SSVM-based score was significantly associated with overall survival (hazard ratio [HR], 2.16; 95% confidence interval [CI], 1.18-3.97; p = 0.01). Similar results were obtained with reversed training and testing datasets (hazard ratio [HR], 1.6; 95% confidence interval [CI], 1.08-2.37; p = 0.02). The 81-gene biomarker based RF classifier improved classification performance. Overall, 81-gene biomarkers might be useful prognostic and predictive molecular markers to predict the clinical outcome of AML patients.
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Affiliation(s)
- Mingguang Shi
- School of Electric Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China.
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Systems biology approach to studying proliferation-dependent prognostic subnetworks in breast cancer. Sci Rep 2015; 5:12981. [PMID: 26257336 PMCID: PMC4530341 DOI: 10.1038/srep12981] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 06/25/2015] [Indexed: 12/19/2022] Open
Abstract
Tumor proliferative capacity is a major biological correlate of breast tumor metastatic potential. In this paper, we developed a systems approach to investigate associations among gene expression patterns, representative protein-protein interactions, and the potential for clinical metastases, to uncover novel survival-related subnetwork signatures as a function of tumor proliferative potential. Based on the statistical associations between gene expression patterns and patient outcomes, we identified three groups of survival prognostic subnetwork signatures (SPNs) corresponding to three proliferation levels. We discovered 8 SPNs in the high proliferation group, 8 SPNs in the intermediate proliferation group, and 6 SPNs in the low proliferation group. We observed little overlap of SPNs between the three proliferation groups. The enrichment analysis revealed that most SPNs were enriched in distinct signaling pathways and biological processes. The SPNs were validated on other cohorts of patients, and delivered high accuracy in the classification of metastatic vs non-metastatic breast tumors. Our findings indicate that certain biological networks underlying breast cancer metastasis differ in a proliferation-dependent manner. These networks, in combination, may form the basis of highly accurate prognostic classification models and may have clinical utility in guiding therapeutic options for patients.
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Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell 2015; 58:690-8. [PMID: 26000852 PMCID: PMC5359018 DOI: 10.1016/j.molcel.2015.05.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Progress in DNA sequencing has revealed the startling complexity of cancer genomes, which typically carry thousands of somatic mutations. However, it remains unclear which are the key driver mutations or dependencies in a given cancer and how these influence pathogenesis and response to therapy. Although tumors of similar types and clinical outcomes can have patterns of mutations that are strikingly different, it is becoming apparent that these mutations recurrently hijack the same hallmark molecular pathways and networks. For this reason, it is likely that successful interpretation of cancer genomes will require comprehensive knowledge of the molecular networks under selective pressure in oncogenesis. Here we announce the creation of a new effort, The Cancer Cell Map Initiative (CCMI), aimed at systematically detailing these complex interactions among cancer genes and how they differ between diseased and healthy states. We discuss recent progress that enables creation of these cancer cell maps across a range of tumor types and how they can be used to target networks disrupted in individual patients, significantly accelerating the development of precision medicine.
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Affiliation(s)
- Nevan J Krogan
- California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; J. David Gladstone Institutes, San Francisco, CA 94143, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Scott Lippman
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - David A Agard
- California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 92093, USA
| | - Alan Ashworth
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 92093, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA; Moores Cancer Center, University of California, San Diego, San Diego, CA 92093, USA.
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Álvarez-Silva MC, Yepes S, Torres MM, Barrios AFG. Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. Theor Biol Med Model 2015; 12:12. [PMID: 26088082 PMCID: PMC4479082 DOI: 10.1186/s12976-015-0008-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/08/2015] [Indexed: 12/30/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B-lymphocytes, characterized as being a heterogeneous disease with variable clinical manifestation and survival. Mutational statuses of rearranged immunoglobulin heavy chain variable (IGVH) genes has been consider one of the most important prognostic factors in CLL, but despite of its proven value to predict the course of the disease, the regulatory programs and biological mechanisms responsible for the differences in clinical behavior are poorly understood. Methods In this study, (i) we performed differential gene expression analysis between the IGVH statuses using multiple and independent CLL cohorts in microarrays platforms, based on this information, (ii) we constructed a simplified protein-protein interaction (PPI) network and (iii) investigated its structure and critical genes. This provided the basis to (iv) develop a Boolean model, (v) infer biological regulatory mechanism and (vi) performed perturbation simulations in order to analyze the network in dynamic state. Results The result of topological analysis and the Boolean model showed that the transcriptional relationships of IGVH mutational status were determined by specific regulatory proteins (PTEN, FOS, EGR1, TNF, TGFBR3, IFGR2 and LPL). The dynamics of the network was controlled by attractors whose genes were involved in multiple and diverse signaling pathways, which may suggest a variety of mechanisms related with progression occurring over time in the disease. The overexpression of FOS and TNF fixed the fate of the system as they can activate important genes implicated in the regulation of process of adhesion, apoptosis, immune response, cell proliferation and other signaling pathways related with cancer. Conclusion The differences in prognosis prediction of the IGVH mutational status are related with several regulatory hubs that determine the dynamic of the system. Electronic supplementary material The online version of this article (doi:10.1186/s12976-015-0008-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Camila Álvarez-Silva
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, DC, Colombia.
| | - Sally Yepes
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, DC, Colombia.
| | - Maria Mercedes Torres
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, DC, Colombia.
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, DC, Colombia.
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Weiler S, Ademokun JA, Norton JD. ID helix-loop-helix proteins as determinants of cell survival in B-cell chronic lymphocytic leukemia cells in vitro. Mol Cancer 2015; 14:30. [PMID: 25644253 PMCID: PMC4320821 DOI: 10.1186/s12943-014-0286-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/30/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Members of the inhibitor of DNA-binding (ID) family of helix-loop-helix proteins have been causally implicated in the pathogenesis of several types of B-cell lineage malignancy, either on the basis of mutation or by altered expression. B-cell chronic lymphocytic leukemia encompasses a heterogeneous group of disorders and is the commonest leukaemia type in the Western world. In this study, we have investigated the pathobiological functions of the ID2 and ID3 proteins in this disease with an emphasis on their role in regulating leukemic cell death/survival. METHODS Bioinformatics analysis of microarray gene expression data was used to investigate expression of ID2/ID3 in leukemic versus normal B cells, their association with clinical course of disease and molecular sub-type and to reconstruct a gene regulatory network using the 'maximum information coefficient' (MIC) for target gene inference. In vitro cultured primary leukemia cells, either in isolation or co-cultured with accessory vascular endothelial cells, were used to investigate ID2/ID3 protein expression by western blotting and to assess the cytotoxic response of different drugs (fludarabine, chlorambucil, ethacrynic acid) by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. ID2/ID3 protein levels in primary leukemia cells and in MEC1 cells were manipulated by transduction with siRNA reagents. RESULTS Datamining showed that the expression profiles of ID2 and ID3 are associated with distinct pathobiological features of disease and implicated both genes in regulating cell death/survival by targeting multiple non-overlapping sets of apoptosis effecter genes. Consistent with microarray data, the overall pattern of ID2/ID3 protein expression in relation to cell death/survival responses of primary leukemia cells was suggestive of a pro-survival function for both ID proteins. This was confirmed by siRNA knock-down experiments in MEC1 cells and in primary leukemia cells, but with variability in the dependence of leukemic cells from different patients on ID protein expression for cell survival. Vascular endothelial cells rescued leukemia cells from spontaneous and cytotoxic drug-induced cell death at least in part, via an ID protein-coupled redox-dependent mechanism. CONCLUSIONS Our study provides evidence for a pro-survival function of the ID2/ID3 proteins in chronic lymphocytic leukemia cells and also highlights these proteins as potential determinants of the pathobiology of this disorder.
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Affiliation(s)
- Sarah Weiler
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK.
| | - Jolaolu A Ademokun
- Department of Haematology, Ipswich Hospital NHS Trust, Heath Road, Ipswich, Suffolk, IP4 5PD, UK.
| | - John D Norton
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK.
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Yang L, Ainali C, Kittas A, Nestle FO, Papageorgiou LG, Tsoka S. Pathway-level disease data mining through hyper-box principles. Math Biosci 2015; 260:25-34. [DOI: 10.1016/j.mbs.2014.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/11/2014] [Accepted: 09/13/2014] [Indexed: 01/16/2023]
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Yang L, Ainali C, Tsoka S, Papageorgiou LG. Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework. BMC Bioinformatics 2014; 15:390. [PMID: 25475756 PMCID: PMC4269079 DOI: 10.1186/s12859-014-0390-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Applying machine learning methods on microarray gene expression profiles for disease classification problems is a popular method to derive biomarkers, i.e. sets of genes that can predict disease state or outcome. Traditional approaches where expression of genes were treated independently suffer from low prediction accuracy and difficulty of biological interpretation. Current research efforts focus on integrating information on protein interactions through biochemical pathway datasets with expression profiles to propose pathway-based classifiers that can enhance disease diagnosis and prognosis. As most of the pathway activity inference methods in literature are either unsupervised or applied on two-class datasets, there is good scope to address such limitations by proposing novel methodologies. RESULTS A supervised multiclass pathway activity inference method using optimisation techniques is reported. For each pathway expression dataset, patterns of its constituent genes are summarised into one composite feature, termed pathway activity, and a novel mathematical programming model is proposed to infer this feature as a weighted linear summation of expression of its constituent genes. Gene weights are determined by the optimisation model, in a way that the resulting pathway activity has the optimal discriminative power with regards to disease phenotypes. Classification is then performed on the resulting low-dimensional pathway activity profile. CONCLUSIONS The model was evaluated through a variety of published gene expression profiles that cover different types of disease. We show that not only does it improve classification accuracy, but it can also perform well in multiclass disease datasets, a limitation of other approaches from the literature. Desirable features of the model include the ability to control the maximum number of genes that may participate in determining pathway activity, which may be pre-specified by the user. Overall, this work highlights the potential of building pathway-based multi-phenotype classifiers for accurate disease diagnosis and prognosis problems.
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Affiliation(s)
- Lingjian Yang
- Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, London, WC1E 7JE, UK.
| | - Chrysanthi Ainali
- Department of Informatics, School of Natural and Mathematical Sciences, King's College London, London, WC2R 2LS, UK.
| | - Sophia Tsoka
- Department of Informatics, School of Natural and Mathematical Sciences, King's College London, London, WC2R 2LS, UK.
| | - Lazaros G Papageorgiou
- Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, London, WC1E 7JE, UK.
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Identification of a 20-gene expression-based risk score as a predictor of clinical outcome in chronic lymphocytic leukemia patients. BIOMED RESEARCH INTERNATIONAL 2014; 2014:423174. [PMID: 24883311 PMCID: PMC4026849 DOI: 10.1155/2014/423174] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 12/11/2022]
Abstract
Despite the improvement in treatment options, chronic lymphocytic leukemia (CLL) remains an incurable disease and patients show a heterogeneous clinical course requiring therapy for many of them. In the current work, we have built a 20-gene expression (GE)-based risk score predictive for patients overall survival and improving risk classification using microarray gene expression data. GE-based risk score allowed identifying a high-risk group associated with a significant shorter overall survival (OS) and time to treatment (TTT) (P ≤ .01), comprising 19.6% and 13.6% of the patients in two independent cohorts. GE-based risk score, and NRIP1 and TCF7 gene expression remained independent prognostic factors using multivariate Cox analyses and combination of GE-based risk score together with NRIP1 and TCF7 gene expression enabled the identification of three clinically distinct groups of CLL patients. Therefore, this GE-based risk score represents a powerful tool for risk stratification and outcome prediction of CLL patients and could thus be used to guide clinical and therapeutic decisions prospectively.
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miR-150 influences B-cell receptor signaling in chronic lymphocytic leukemia by regulating expression of GAB1 and FOXP1. Blood 2014; 124:84-95. [PMID: 24787006 DOI: 10.1182/blood-2013-09-527234] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We examined the microRNAs (miRNAs) expressed in chronic lymphocytic leukemia (CLL) and identified miR-150 as the most abundant, but with leukemia cell expression levels that varied among patients. CLL cells that expressed ζ-chain-associated protein of 70 kDa (ZAP-70) or that used unmutated immunoglobulin heavy chain variable (IGHV) genes, each had a median expression level of miR-150 that was significantly lower than that of ZAP-70-negative CLL cells or those that used mutated IGHV genes. In samples stratified for expression of miR-150, CLL cells with low-level miR-150 expressed relatively higher levels of forkhead box P1 (FOXP1) and GRB2-associated binding protein 1 (GAB1), genes with 3' untranslated regions having evolutionary-conserved binding sites for miR-150. High-level expression of miR-150 could repress expression of these genes, which encode proteins that enhance B-cell receptor signaling, a putative CLL-growth/survival signal. Also, high-level expression of miR-150 was a significant independent predictor of longer treatment-free survival or overall survival, whereas an inverse association was observed for high-level expression of GAB1 or FOXP1 for overall survival. This study demonstrates that expression of miR-150 can influence the relative expression of GAB1 and FOXP1 and the signaling potential of the B-cell receptor, thereby possibly accounting for the noted association of expression of miR-150 and disease outcome.
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Kristensen VN, Lingjærde OC, Russnes HG, Vollan HKM, Frigessi A, Børresen-Dale AL. Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer 2014; 14:299-313. [PMID: 24759209 DOI: 10.1038/nrc3721] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Combined analyses of molecular data, such as DNA copy-number alteration, mRNA and protein expression, point to biological functions and molecular pathways being deregulated in multiple cancers. Genomic, metabolomic and clinical data from various solid cancers and model systems are emerging and can be used to identify novel patient subgroups for tailored therapy and monitoring. The integrative genomics methodologies that are used to interpret these data require expertise in different disciplines, such as biology, medicine, mathematics, statistics and bioinformatics, and they can seem daunting. The objectives, methods and computational tools of integrative genomics that are available to date are reviewed here, as is their implementation in cancer research.
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Affiliation(s)
- Vessela N Kristensen
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, 1478 Ahus, Norway
| | - Ole Christian Lingjærde
- 1] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [2] Division for Biomedical Informatics, Department of Computer Science, University of Oslo, 0316 Oslo, Norway
| | - Hege G Russnes
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Pathology, Oslo University Hospital, 0450 Oslo, Norway
| | - Hans Kristian M Vollan
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway. [3] Department of Oncology, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, 0450 Oslo, Norway
| | - Arnoldo Frigessi
- 1] Statistics for Innovation, Norwegian Computing Center, 0314 Oslo, Norway. [2] Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, PO Box 1122 Blindern, 0317 Oslo, Norway
| | - Anne-Lise Børresen-Dale
- 1] Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway. [2] K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0313 Oslo, Norway
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Lindfors E, Jouhten P, Oja M, Rintala E, Orešič M, Penttilä M. Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2014; 8:16. [PMID: 24528924 PMCID: PMC3930817 DOI: 10.1186/1752-0509-8-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 02/07/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Saccharomyces cerevisiae is able to adapt to a wide range of external oxygen conditions. Previously, oxygen-dependent phenotypes have been studied individually at the transcriptional, metabolite, and flux level. However, the regulation of cell phenotype occurs across the different levels of cell function. Integrative analysis of data from multiple levels of cell function in the context of a network of several known biochemical interaction types could enable identification of active regulatory paths not limited to a single level of cell function. RESULTS The graph theoretical method called Enriched Molecular Path detection (EMPath) was extended to enable integrative utilization of transcription and flux data. The utility of the method was demonstrated by detecting paths associated with phenotype differences of S. cerevisiae under three different conditions of oxygen provision: 20.9%, 2.8% and 0.5%. The detection of molecular paths was performed in an integrated genome-scale metabolic and protein-protein interaction network. CONCLUSIONS The molecular paths associated with the phenotype differences of S. cerevisiae under conditions of different oxygen provisions revealed paths of molecular interactions that could potentially mediate information transfer between processes that respond to the particular oxygen availabilities.
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Affiliation(s)
- Erno Lindfors
- VTT Technical Research Centre of Finland, Espoo, Finland
- Currently at: LifeGlimmer GmbH, Markelstrasse 38, D–12136 Berlin, Germany
- Currently at: Chemistry Building, Building 316, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Paula Jouhten
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Eija Rintala
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Matej Orešič
- VTT Technical Research Centre of Finland, Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
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Albrekt AS, Johansson H, Börje A, Borrebaeck C, Lindstedt M. Skin sensitizers differentially regulate signaling pathways in MUTZ-3 cells in relation to their individual potency. BMC Pharmacol Toxicol 2014; 15:5. [PMID: 24517095 PMCID: PMC3932014 DOI: 10.1186/2050-6511-15-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 01/27/2014] [Indexed: 01/10/2023] Open
Abstract
Background Due to the recent European legislations posing a ban of animal tests for safety assessment within the cosmetic industry, development of in vitro alternatives for assessment of skin sensitization is highly prioritized. To date, proposed in vitro assays are mainly based on single biomarkers, which so far have not been able to classify and stratify chemicals into subgroups, related to risk or potency. Methods Recently, we presented the Genomic Allergen Rapid Detection (GARD) assay for assessment of chemical sensitizers. In this paper, we show how the genome wide readout of GARD can be expanded and used to identify differentially regulated pathways relating to individual chemical sensitizers. In this study, we investigated the mechanisms of action of a range of skin sensitizers through pathway identification, pathway classification and transcription factor analysis and related this to the reactive mechanisms and potency of the sensitizing agents. Results By transcriptional profiling of chemically stimulated MUTZ-3 cells, 33 canonical pathways intimately involved in sensitization to chemical substances were identified. The results showed that metabolic processes, cell cycling and oxidative stress responses are the key events activated during skin sensitization, and that these functions are engaged differently depending on the reactivity mechanisms of the sensitizing agent. Furthermore, the results indicate that the chemical reactivity groups seem to gradually engage more pathways and more molecules in each pathway with increasing sensitizing potency of the chemical used for stimulation. Also, a switch in gene regulation from up to down regulation, with increasing potency, was seen both in genes involved in metabolic functions and cell cycling. These observed pathway patterns were clearly reflected in the regulatory elements identified to drive these processes, where 33 regulatory elements have been proposed for further analysis. Conclusions This study demonstrates that functional analysis of biomarkers identified from our genomics study of human MUTZ-3 cells can be used to assess sensitizing potency of chemicals in vitro, by the identification of key cellular events, such as metabolic and cell cycling pathways.
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Affiliation(s)
- Ann-Sofie Albrekt
- Department of Immunotechnology, Lund University, Medicon Village building 406, 223 81 Lund, Sweden.
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Gbormittah FO, Haab BB, Partyka K, Garcia-Ott C, Hancapie M, Hancock WS. Characterization of glycoproteins in pancreatic cyst fluid using a high-performance multiple lectin affinity chromatography platform. J Proteome Res 2013; 13:289-99. [PMID: 24303806 DOI: 10.1021/pr400813u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Currently, pancreatic cancer is the fourth cause of cancer death. In 2013, it is estimated that ∼38 460 people will die of pancreatic cancer. Early detection of malignant cyst (pancreatic cancer precursor) is necessary to help prevent late diagnosis of the tumor. In this study, we characterized glycoproteins and nonglycoproteins on pooled mucinous (n = 10) and nonmucinous (n = 10) pancreatic cyst fluid to identify "proteins of interest" to differentiate between mucinous cyst from nonmucinous cyst and investigate these proteins as potential biomarker targets. An automated multilectin affinity chromatography (M-LAC) platform was utilized for glycoprotein enrichment followed by nano-LC-MS/MS analysis. Spectral count quantitation allowed for the identification of proteins with significant differential levels in mucinous cysts from nonmucinous cysts of which one protein (periostin) was confirmed via immunoblotting. To exhaustively evaluate differentially expressed proteins, we used a number of proteomic tools including gene ontology classification, pathway and network analysis, Novoseek data mining, and chromosome gene mapping. Utilization of complementary proteomic tools revealed that several of the proteins such as mucin 6 (MUC6), bile salt-activated lipase (CEL), and pyruvate kinase lysozyme M1/M2 with significant differential expression have strong association with pancreatic cancer. Furthermore, chromosome gene mapping demonstrated coexpressions and colocalization of some proteins of interest including 14-3-3 protein epsilon (YWHAE), pigment epithelium derived factor (SERPINF1), and oncogene p53.
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Affiliation(s)
- Francisca Owusu Gbormittah
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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