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Bonnet C, Dian AL, Espie-Caullet T, Fabbri L, Lagadec L, Pivron T, Dutertre M, Luco R, Navickas A, Vagner S, Verga D, Uguen P. Post-transcriptional gene regulation: From mechanisms to RNA chemistry and therapeutics. Bull Cancer 2024; 111:782-790. [PMID: 38824069 DOI: 10.1016/j.bulcan.2024.04.005] [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] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 06/03/2024]
Abstract
A better understanding of the RNA biology and chemistry is necessary to then develop new RNA therapeutic strategies. This review is the synthesis of a series of conferences that took place during the 6th international course on post-transcriptional gene regulation at Institut Curie. This year, the course made a special focus on RNA chemistry.
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Affiliation(s)
- Clara Bonnet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Ana Luisa Dian
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Tristan Espie-Caullet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucilla Fabbri
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucie Lagadec
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Thibaud Pivron
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Martin Dutertre
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Reini Luco
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Albertas Navickas
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Stephan Vagner
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, Inserm U1196, Chemistry and Modelling for the Biology of Cancer, Institut Curie, université Paris-Saclay, 91405 Orsay, France
| | - Patricia Uguen
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France.
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2
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Rong C, Liang C, Shen J, Zhang Y, Wang Q, Yang F, Chen Y, Luo Y, Gu M, Gao P, Xia Y, Duan S. CLLU1 as an emerging biomarker in chronic lymphoid leukemia. Hum Cell 2024; 37:625-632. [PMID: 38507118 DOI: 10.1007/s13577-024-01051-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
CLLU1, a disease-specific gene associated with chronic lymphoid leukemia (CLL), is located on chromosome 12q22. Previous studies considered CLLU1 to be a non-coding RNA; however, recent research has discovered that its coding sequence region possesses the potential to encode a short peptide similar to interleukin-4. Remarkably, abnormally elevated expression of CLLU1 has only been detected in chronic lymphoid leukemia among all hematological cancers. High CLLU1 expression often indicates more malignant pathological features and an unfavorable prognosis for patients. Importantly, the expression level of CLLU1 remains unaffected by the passage of time or therapeutic interventions, thus rendering it a novel prognostic marker. This article provides a comprehensive summary of relevant research findings on CLLU1 in the context of CLL prognosis and clinical applications, aiming to guide subsequent theoretical and clinical investigations in this field.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Neoplasm Proteins/genetics
- RNA, Long Noncoding/genetics
- Biomarkers, Tumor/genetics
- Genes, Neoplasm
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Affiliation(s)
- Chunmeng Rong
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Chenhao Liang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yuhua Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Fang Yang
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yalu Chen
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yuqing Luo
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Meier Gu
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Panpan Gao
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China
| | - Yongming Xia
- Department of Hematology, Yuyao People's Hospital of Zhejiang Province, Ningbo, Zhejiang, China.
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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3
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Liu X, Xiao C, Xu X, Zhang J, Mo F, Chen JY, Delihas N, Zhang L, An NA, Li CY. Origin of functional de novo genes in humans from "hopeful monsters". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1845. [PMID: 38605485 DOI: 10.1002/wrna.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming, China
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4
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Sandmann CL, Schulz JF, Ruiz-Orera J, Kirchner M, Ziehm M, Adami E, Marczenke M, Christ A, Liebe N, Greiner J, Schoenenberger A, Muecke MB, Liang N, Moritz RL, Sun Z, Deutsch EW, Gotthardt M, Mudge JM, Prensner JR, Willnow TE, Mertins P, van Heesch S, Hubner N. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames. Mol Cell 2023; 83:994-1011.e18. [PMID: 36806354 PMCID: PMC10032668 DOI: 10.1016/j.molcel.2023.01.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/12/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023]
Abstract
All species continuously evolve short open reading frames (sORFs) that can be templated for protein synthesis and may provide raw materials for evolutionary adaptation. We analyzed the evolutionary origins of 7,264 recently cataloged human sORFs and found that most were evolutionarily young and had emerged de novo. We additionally identified 221 previously missed sORFs potentially translated into peptides of up to 15 amino acids-all of which are smaller than the smallest human microprotein annotated to date. To investigate the bioactivity of sORF-encoded small peptides and young microproteins, we subjected 266 candidates to a mass-spectrometry-based interactome screen with motif resolution. Based on these interactomes and additional cellular assays, we can associate several candidates with mRNA splicing, translational regulation, and endocytosis. Our work provides insights into the evolutionary origins and interaction potential of young and small proteins, thereby helping to elucidate this underexplored territory of the human proteome.
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Affiliation(s)
- Clara-L Sandmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany
| | - Jana F Schulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | - Eleonora Adami
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maike Marczenke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Annabel Christ
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nina Liebe
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Johannes Greiner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Aaron Schoenenberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Michael B Muecke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Ning Liang
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | - Zhi Sun
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Michael Gotthardt
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John R Prensner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Thomas E Willnow
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Proteomics, 10117 Berlin, Germany
| | | | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany.
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5
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Sun X, Wang L, Li H, Jin C, Yu Y, Hou L, Liu X, Yu Y, Yan R, Xue F. Identification of microenvironment related potential biomarkers of biochemical recurrence at 3 years after prostatectomy in prostate adenocarcinoma. Aging (Albany NY) 2021; 13:16024-16042. [PMID: 34133324 PMCID: PMC8266350 DOI: 10.18632/aging.203121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/11/2021] [Indexed: 12/15/2022]
Abstract
Prostate adenocarcinoma is one of the leading adult malignancies. Identification of multiple causative biomarkers is necessary and helpful for determining the occurrence and prognosis of prostate adenocarcinoma. We aimed to identify the potential prognostic genes in the prostate adenocarcinoma microenvironment and to estimate the causal effects simultaneously. We obtained the gene expression data of prostate adenocarcinoma from TCGA project and identified the differentially expressed genes based on immune-stromal components. Among these genes, 68 were associated with biochemical recurrence at 3 years after prostatectomy in prostate adenocarcinoma. After adjusting for the minimal sets of confounding covariates, 14 genes (TNFRSF4, ZAP70, ERMN, CXCL5, SPINK6, SLC6A18, CHRM2, TG, CLLU1OS, POSTN, CTSG, NETO1, CEACAM7, and IGLV3-22) related to the microenvironment were identified as prognostic biomarkers using the targeted maximum likelihood estimation. Both the average and individual causal effects were obtained to measure the magnitude of the effect. CIBERSORT and gene set enrichment analyses showed that these prognostic genes were mainly associated with immune responses. POSTN and NETO1 were correlated with androgen receptor expression, a main driver of prostate adenocarcinoma progression. Finally, five genes were validated in another prostate adenocarcinoma cohort (GEO: GSE70770). These findings might lead to the improved prognosis of prostate adenocarcinoma.
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Affiliation(s)
- Xiaoru Sun
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Lu Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Hongkai Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Chuandi Jin
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Yuanyuan Yu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Lei Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Xinhui Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Yifan Yu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Ran Yan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
| | - Fuzhong Xue
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China.,Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan 250012, Shandong, China
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6
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Sevinc M, Karabulut A, Eskazan AE, Catal Tatonyan S, Ozbek U, Soysal T. The Impact and Prognostic Significance of Chronic Lymphocytic Leukemia Upregulated 1 (CLLU1) Gene Expression in Patients with Chronic Lymphocytic Leukemia: A Single Center Experience. Lab Med 2020; 51:259-264. [PMID: 31589746 DOI: 10.1093/labmed/lmz058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To determine CLLU1 gene levels and the relationship of that gene among other prognostic parameters in patients with chronic lymphocytic leukemia. METHODS Bone-marrow infiltration pattern, β2-microglobulin (β 2-M), cluster of differentiation (CD)38, and ZAP-70 status were recorded. CLLU1 levels were assessed by real-time polymerase chain reaction (RT-PCR) and expressed as folds. The relationship between CLLU1 and other known prognostic parameters was evaluated. RESULTS CLLU1 expression was positive in 81 patients and negative in 3 patients. The median (interquartile range [IQR]) CLLU1 level was 6.45 folds (3.75-16.57 folds) in patients with β 2-M normal values and 16.22 folds (3.91-62.00 folds) in patients with increased β 2-M (P = .15). Patients with a higher CD38 value than the median level had 3 times higher CLLU1 levels than the other group (P = .07). The median (IQR) CLLU1 level was 4.25 folds (2.75-13.71 folds) in patients with CLL who tested negative on ZAP-70, whereas it was 49.52 folds (15.06-446.36 folds) in those who tested positive via ZAP-70 (P = .005). CONCLUSIONS CLLU1 is a specific parameter to CLL, and its level corresponds well with the ZAP-70 level.
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Affiliation(s)
- Mustafa Sevinc
- Department of Nephrology, Sisli Etfal Training and Research Hospital, Istanbul, Turkey
| | - Aydın Karabulut
- Vocational School of Health Services, Health Sciences University, Istanbul, Turkey
| | - Ahmet Emre Eskazan
- Division of Hematology, Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | | | - Ugur Ozbek
- Department of Medical Genetics, Medical Faculty, Acibadem University, Istanbul, Turkey
| | - Teoman Soysal
- Division of Hematology, Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
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7
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Yue C, Ren Y, Ge H, Liang C, Xu Y, Li G, Wu J. Comprehensive analysis of potential prognostic genes for the construction of a competing endogenous RNA regulatory network in hepatocellular carcinoma. Onco Targets Ther 2019; 12:561-576. [PMID: 30679912 PMCID: PMC6338110 DOI: 10.2147/ott.s188913] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is an extremely common malignant tumor with worldwide prevalence. The aim of this study was to identify potential prognostic genes and construct a competing endogenous RNA (ceRNA) regulatory network to explore the mechanisms underlying the development of HCC. METHODS Integrated analysis was used to identify potential prognostic genes in HCC with R software based on the GSE14520, GSE17548, GSE19665, GSE29721, GSE60502, and the Cancer Genome Atlas databases. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enrichment analyses were performed to explore the molecular mechanisms of potential prognostic genes. Differentially expressed miRNAs (DEMs) and lncRNAs (DELs) were screened based on the Cancer Genome Atlas database. An lncRNA-miRNA-mRNA ceRNA regulatory network was constructed based on information about interactions derived from the miRcode, TargetScan, miRTarBase, and miRDB databases. RESULTS A total of 152 potential prognostic genes were screened that were differentially expressed in HCC tissue and significantly associated with overall survival of HCC patients. There were 13 key potential prognostic genes in the ceRNA regulatory network: eleven upregulated genes (CCNB1, CEP55, CHEK1, EZH2, KPNA2, LRRC1, PBK, RRM2, SLC7A11, SUCO, and ZWINT) and two downregulated genes (ACSL1 and CDC37L1) whose expression might be regulated by eight DEMs and 61 DELs. Kaplan-Meier curve analysis showed that nine DELs (AL163952.1, AL359878.1, AP002478.1, C2orf48, C10orf91, CLLU1, CLRN1-AS1, ERVMER61-1, and WARS2-IT1) in the ceRNA regulatory network were significantly associated with HCC-patient prognoses. CONCLUSION This study identified potential prognostic genes and constructed an lncRNA- miRNA-mRNA ceRNA regulatory network of HCC, which not only has important clinical significance for early diagnoses but also provides effective targets for HCC treatments and could provide new insights for HCC-interventional strategies.
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Affiliation(s)
- Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Yaoyao Ren
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Hua Ge
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Chaojie Liang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Yingchen Xu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Guangming Li
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China, ;
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8
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Abur Ü, Oğur G, Akar ÖS, Altundağ E, Aymelek HS, Özatlı D, Turgut M. Impact of Fluorescent In Situ Hybridization Aberrations and CLLU1 Expression on the Prognosis of Chronic Lymphocytic Leukemia: Presentation of 156 Patients from Turkey. Turk J Haematol 2018; 35:61-65. [PMID: 29129824 PMCID: PMC5843776 DOI: 10.4274/tjh.2017.0112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE This study evaluates the impact of CLLU1 expression and fluorescent in situ hybridization (FISH) analysis of a group of Turkish chronic lymphocytic leukemia (CLL) patients. MATERIALS AND METHODS A total of 156 CLL patients were analyzed by FISH method; 47 of them were also evaluated for CLLU1 expression. Results were correlated with clinical parameters. RESULTS FISH aberrations were found in 62% of patients. These aberrations were del13q14 (67%), trisomy 12 (27%), del11q22 (19%), del17p (8%), and 14q32 rearrangements (20%). Overall del11q22 and del17p were associated with the highest mortality rates, shortest overall survival (OS), and highest need for medication. Homozygous del13q14, 14q32 rearrangements, and higher CLLU1 expression correlated with shorter OS. CONCLUSION Cytogenetics/FISH analysis is still indicated for routine evaluation of CLL. Special consideration is needed for the poor prognostic implications of del11q22, del17p, 14q32 rearrangements, and homozygous del13q14. The impact of CLLU1 expression is not yet clear and it requires more data before becoming routine in genetic testing in CLL patients.
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Affiliation(s)
- Ümmet Abur
- Ondokuz Mayıs University Faculty of Medicine, Department of Medical Genetics, Samsun, Turkey
| | - Gönül Oğur
- Ondokuz Mayıs University Faculty of Medicine, Department of Medical Genetics, Samsun, Turkey
| | - Ömer Salih Akar
- Ondokuz Mayıs University Faculty of Medicine, Department of Medical Genetics, Samsun, Turkey
| | - Engin Altundağ
- Ondokuz Mayıs University Faculty of Medicine, Department of Medical Genetics, Samsun, Turkey
| | - Huri Sema Aymelek
- Ondokuz Mayıs University Faculty of Medicine, Department of Medical Genetics, Samsun, Turkey
| | - Düzgün Özatlı
- Ondokuz Mayıs University Faculty of Medicine, Department of Hematology, Samsun, Turkey
| | - Mehmet Turgut
- Ondokuz Mayıs University Faculty of Medicine, Department of Hematology, Samsun, Turkey
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9
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Motzer RJ, Figlin RA, Martini JF, Hariharan S, Agarwal N, Li CX, Williams JA, Hutson TE. Germline Genetic Biomarkers of Sunitinib Efficacy in Advanced Renal Cell Carcinoma: Results From the RENAL EFFECT Trial. Clin Genitourin Cancer 2017; 15:526-533. [DOI: 10.1016/j.clgc.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/10/2017] [Accepted: 02/19/2017] [Indexed: 10/20/2022]
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10
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McLysaght A, Hurst LD. Open questions in the study of de novo genes: what, how and why. Nat Rev Genet 2016; 17:567-78. [PMID: 27452112 DOI: 10.1038/nrg.2016.78] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes.
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Affiliation(s)
- Aoife McLysaght
- The Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK
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11
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Kozlov AP. Expression of evolutionarily novel genes in tumors. Infect Agent Cancer 2016; 11:34. [PMID: 27437030 PMCID: PMC4949931 DOI: 10.1186/s13027-016-0077-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Abstract
The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.
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Affiliation(s)
- A. P. Kozlov
- The Biomedical Center and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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12
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McLysaght A, Guerzoni D. New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140332. [PMID: 26323763 PMCID: PMC4571571 DOI: 10.1098/rstb.2014.0332] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces, Drosophila, Plasmodium, Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.
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Affiliation(s)
- Aoife McLysaght
- Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Republic of Ireland
| | - Daniele Guerzoni
- Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Republic of Ireland
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13
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Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, Decara JM, Gilad Y, Ober C. Integrated analyses of gene expression and genetic association studies in a founder population. Hum Mol Genet 2016; 25:2104-2112. [PMID: 26931462 PMCID: PMC5062579 DOI: 10.1093/hmg/ddw061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 02/21/2016] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWASs) have become a standard tool for dissecting genetic contributions to disease risk. However, these studies typically require extraordinarily large sample sizes to be adequately powered. Strategies that incorporate functional information alongside genetic associations have proved successful in increasing GWAS power. Following this paradigm, we present the results of 20 different genetic association studies for quantitative traits related to complex diseases, conducted in the Hutterites of South Dakota. To boost the power of these association studies, we collected RNA-sequencing data from lymphoblastoid cell lines for 431 Hutterite individuals. We then used Sherlock, a tool that integrates GWAS and expression quantitative trait locus (eQTL) data, to identify weak GWAS signals that are also supported by eQTL data. Using this approach, we found novel associations with quantitative phenotypes related to cardiovascular disease, including carotid intima-media thickness, left atrial volume index, monocyte count and serum YKL-40 levels.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jack A Elias
- Division of Biology and Medicine, Brown University, Providence, RI 02912, USA and
| | - Geoffrey L Chupp
- Pulmonary and Critical Care, Yale School of Medicine, New Haven, CT 06519, USA
| | - Roberto M Lang
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
| | - Sanjiv J Shah
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
| | - Jeanne M Decara
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
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14
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Abstract
The great ape families are the species most closely related to our own, comprising chimpanzees, bonobos, gorillas, and orangutans. They live exclusively in tropical rainforests in Central Africa and the islands of Southeast Asia. Due to their close evolutionary relationship with humans, great apes share many cognitive, physiological, and morphological similarities with humans. The members of the great ape family make obvious models to facilitate the further understanding about humans' biology and history. This review will discuss how the recent addition of genome-wide data from great apes has furthered humans' understanding of these species and humanity, especially in the realm of evolutionary genetics.
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15
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Sevov M, Rosenquist R, Mansouri L. RNA-based markers as prognostic factors in chronic lymphocytic leukemia. Expert Rev Hematol 2014; 5:69-79. [DOI: 10.1586/ehm.11.80] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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16
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CD49d is overexpressed by trisomy 12 chronic lymphocytic leukemia cells: evidence for a methylation-dependent regulation mechanism. Blood 2013; 122:3317-21. [DOI: 10.1182/blood-2013-06-507335] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Key Points
CD49d, a negative prognosticator with a key role for microenvironmental interactions in CLL, is near universally expressed in trisomy 12 CLL. CD49d overexpression in trisomy 12 CLL is regulated by a methylation-dependent mechanism.
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17
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Rosenquist R, Cortese D, Bhoi S, Mansouri L, Gunnarsson R. Prognostic markers and their clinical applicability in chronic lymphocytic leukemia: where do we stand? Leuk Lymphoma 2013; 54:2351-64. [PMID: 23480493 DOI: 10.3109/10428194.2013.783913] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease where the majority of patients have an indolent disease course, while others may experience a far more aggressive disease, treatment failure and poor overall survival. During the last two decades, there has been an intense search to find novel biomarkers that can predict prognosis as well as guide treatment decisions. Two of the most reliable molecular prognostic markers, both of which are offered in routine diagnostics, are the immunoglobulin heavy chain variable (IGHV) gene mutational status and fluorescence in situ hybridization (FISH) detection of prognostically relevant genomic aberrations (e.g. 11q-, 13q-, +12 and 17p-). In addition to these markers, a myriad of additional biomarkers have been postulated as potential prognosticators in CLL, on the protein (e.g. CD38, ZAP70, TCL1), the RNA (e.g. LPL, CLLU1, micro-RNAs) and the genomic (e.g. TP53, NOTCH1, SF3B1 and BIRC3 mutations) level. Efforts are now being made to test these novel markers in larger patient cohorts as well as in prospective trials, with the ultimate goal to combine the "best" markers in a "CLL prognostic index" applicable for the individual patient. Although it is clear that these studies have significantly improved our knowledge regarding both prognostication and the biology of the disease, there is still an immediate need for recognizing biomarkers that can predict therapy response, and efforts should now focus on addressing this pertinent issue. In the present article, we review the extensive literature in the field of prognostic markers in CLL, focus on the most clinically relevant markers and discuss future directions regarding biomarkers in CLL.
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Affiliation(s)
- Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
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18
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Rodríguez-Vicente AE, Díaz MG, Hernández-Rivas JM. Chronic lymphocytic leukemia: a clinical and molecular heterogenous disease. Cancer Genet 2013; 206:49-62. [DOI: 10.1016/j.cancergen.2013.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 12/11/2022]
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19
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Gonzalez D, Else M, Wren D, Usai M, Buhl AM, Parker A, Oscier D, Morgan G, Catovsky D. CLLU1 expression has prognostic value in chronic lymphocytic leukemia after first-line therapy in younger patients and in those with mutated IGHV genes. Haematologica 2013; 98:274-8. [PMID: 22899580 PMCID: PMC3561436 DOI: 10.3324/haematol.2012.070201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 08/10/2012] [Indexed: 11/09/2022] Open
Abstract
CLLU1, located at chromosome 12q22, encodes a transcript specific to chronic lymphocytic leukemia and has potential prognostic value. We assessed the value of CLLU1 expression in the LRF CLL4 randomized trial. Samples from 515 patients with chronic lymphocytic leukemia were collected immediately before the start of treatment. After RNA extraction and cDNA synthesis, CLLU1 expression was assessed by quantitative polymerase chain reaction. In total, 247 and 268 samples were identified as having low and high CLLU1 expression, respectively. The median follow-up was 88 months. High CLLU1 expression was significantly correlated with unmutated IGHV genes, ZAP-70 and CD38 positivity, and absence of 13q deletion (all r>0.2, P<0.0001). At 6 years, patients with high CLLU1 expression had significantly worse progression-free survival (9% versus 17%; P=0.03) and overall survival (42% versus 57%; P=0.0003) than patients with low CLLU1 expression. Among patients with mutated IGHV genes, overall survival at 6 years was 50% in those with high CLLU1 expression and 76% in those with low CLLU1 expression (P=0.005). However, CLLU1 expression was not an independent predictor of overall survival in a multivariate model including TP53 aberrations, beta-2 microglobulin level, age and IGHV mutation status. Nor did it predict response to treatment. CLLU1 expression analysis helps to refine the prognosis of patients with chronic lymphocytic leukemia who have mutated IGHV genes.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Female
- Gene Expression
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Middle Aged
- Mutation
- Neoplasm Proteins/genetics
- Prognosis
- RNA, Long Noncoding
- Treatment Outcome
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Affiliation(s)
- David Gonzalez
- Haemato-Oncology Research Unit, Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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20
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Abstract
Given the unprecedented tools that are now available for rapidly comparing genomes, the identification and study of genetic and genomic changes that are unique to our species have accelerated, and we are entering a golden age of human evolutionary genomics. Here we provide an overview of these efforts, highlighting important recent discoveries, examples of the different types of human-specific genomic and genetic changes identified, and salient trends, such as the localization of evolutionary adaptive changes to complex loci that are highly enriched for disease associations. Finally, we discuss the remaining challenges, such as the incomplete nature of current genome sequence assemblies and difficulties in linking human-specific genomic changes to human-specific phenotypic traits.
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21
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CLLU1 expression distinguishes chronic lymphocytic leukemia from other mature B-cell neoplasms. Leuk Res 2012; 36:1204-7. [DOI: 10.1016/j.leukres.2012.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/19/2022]
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22
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Kaderi MA, Kanduri M, Buhl AM, Sevov M, Cahill N, Gunnarsson R, Jansson M, Smedby KE, Hjalgrim H, Jurlander J, Juliusson G, Mansouri L, Rosenquist R. LPL is the strongest prognostic factor in a comparative analysis of RNA-based markers in early chronic lymphocytic leukemia. Haematologica 2011; 96:1153-60. [PMID: 21508119 PMCID: PMC3148909 DOI: 10.3324/haematol.2010.039396] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/25/2011] [Accepted: 04/20/2011] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The expression levels of LPL, ZAP70, TCL1A, CLLU1 and MCL1 have recently been proposed as prognostic factors in chronic lymphocytic leukemia. However, few studies have systematically compared these different RNA-based markers. DESIGN AND METHODS Using real-time quantitative PCR, we measured the mRNA expression levels of these genes in unsorted samples from 252 newly diagnosed chronic lymphocytic leukemia patients and correlated our data with established prognostic markers (for example Binet stage, CD38, IGHV gene mutational status and genomic aberrations) and clinical outcome. RESULTS High expression levels of all RNA-based markers, except MCL1, predicted shorter overall survival and time to treatment, with LPL being the most significant. In multivariate analysis including the RNA-based markers, LPL expression was the only independent prognostic marker for overall survival and time to treatment. When studying LPL expression and the established markers, LPL expression retained its independent prognostic strength for overall survival. All of the RNA-based markers, albeit with varying ability, added prognostic information to established markers, with LPL expression giving the most significant results. Notably, high LPL expression predicted a worse outcome in good-prognosis subgroups, such as patients with mutated IGHV genes, Binet stage A, CD38 negativity or favorable cytogenetics. In particular, the combination of LPL expression and CD38 could further stratify Binet stage A patients. CONCLUSIONS LPL expression is the strongest RNA-based prognostic marker in chronic lymphocytic leukemia that could potentially be applied to predict outcome in the clinical setting, particularly in the large group of patients with favorable prognosis.
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MESH Headings
- Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Female
- Humans
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lipoprotein Lipase/genetics
- Lipoprotein Lipase/metabolism
- Male
- Middle Aged
- Multivariate Analysis
- Mutation/genetics
- Prognosis
- RNA, Messenger/metabolism
- Survival Analysis
- Treatment Outcome
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Affiliation(s)
- Mohd Arifin Kaderi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Basic Health Sciences, KAHS IIUM Kuantan Campus, Pahang, Malaysia
| | - Meena Kanduri
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anne Mette Buhl
- Department of Hematology, Leukemia Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Marie Sevov
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Nicola Cahill
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rebeqa Gunnarsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Laboratory Medicine, Stem Cell Center, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Mattias Jansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Karin Ekström Smedby
- Department of Medicine, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Jurlander
- Department of Hematology, Leukemia Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Gunnar Juliusson
- Department of Laboratory Medicine, Stem Cell Center, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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de Oliveira FM, de Figueiredo Pontes LL, Bassi SC, Dalmazzo LFF, Falcão RP. Co-existence of t(6;13)(p21;q14.1) and trisomy 12 in chronic lymphocytic leukemia. Med Oncol 2011; 29:1227-30. [PMID: 21528409 DOI: 10.1007/s12032-011-9957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 04/12/2011] [Indexed: 11/26/2022]
Abstract
We report a case of a 57-year-old man diagnosed with chronic lymphocytic leukemia (CLL) and presence of a rare t(6;13)(p21;q14.1) in association with an extra copy of chromosome 12. Classical cytogenetic analysis using the immunostimulatory combination of DSP30 and IL-2 showed the karyotype 47,XY,t(6;13)(p21;q14.1), +12 in 75% of the metaphase cells. Spectral karyotype analysis (SKY) confirmed the abnormality previously seen by G-banding. Additionally, interphase fluorescence in situ hybridization using an LSI CEP 12 probe performed on peripheral blood cells without any stimulant agent showed trisomy of chromosome 12 in 67% of analyzed cells (134/200). To the best of our knowledge, the association of t(6;13)(p21;q14.1) and +12 in CLL has never been described. The prognostic significance of these new findings in CLL remains to be elucidated. However, the patient has been followed up since 2009 without any therapeutic intervention and has so far remained stable.
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MESH Headings
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 6/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Karyotyping
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Male
- Middle Aged
- Translocation, Genetic/genetics
- Trisomy/genetics
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Affiliation(s)
- Fábio Morato de Oliveira
- Department of Internal Medicine, Division of Hematology, School of Medicine of Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP 14049-900, Brazil.
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24
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Cavazzini F, Ciccone M, Negrini M, Rigolin GM, Cuneo A. Clinicobiologic importance of cytogenetic lesions in chronic lymphocytic leukemia. Expert Rev Hematol 2011; 2:305-14. [PMID: 21082972 DOI: 10.1586/ehm.09.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular cytogenetic lesions play a major role in the pathogenesis of chronic lymphocytic leukemia (CLL) and represent important prognostic markers. Besides FISH, conventional banding analysis using effective mitogens is important for an accurate assessment of the cytogenetic profile of CLL. The most frequent aberrations are represented by 13q-, 11q-, +12, 6q- and 14q32/IGH translocations and 17p-. Chromosome translocations and complex karyotype may occur in up to 30 and 16% of the cases, respectively. The frequency of 17p- and 11q- is higher in patients requiring treatment and in relapsed/refractory patients, reflecting the association of these rearrangements with unfavorable prognosis. Mutations of the TP53 gene may also confer an inferior outcome, as is the case with 14q32 translocations and unbalanced translocations. Evidence was provided that distinct treatment approaches may be effective in specific cytogenetic entities of CLL, making molecular cytogenetic investigations a necessary tool for a modern diagnostic work-up in CLL.
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Affiliation(s)
- Francesco Cavazzini
- Section of Hematology, Department of Biomedical Sciences and Advanced Therapies, University of Ferrara, Via Savonarola 9, Ferrara, Italy
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25
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Buhl AM, James DF, Neuberg D, Jain S, Rassenti LZ, Kipps TJ. Analysis of CLLU1 expression levels before and after therapy in patients with chronic lymphocytic leukemia. Eur J Haematol 2011; 86:405-411. [PMID: 21323738 DOI: 10.1111/j.1600-0609.2011.01588.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Chronic lymphocytic leukemia (CLL) is incurable, but therapy leading to eradication of minimal residual disease (MRD) in CLL is associated with improved clinical outcomes. CLL upregulated gene 1 (CLLU1) is solely upregulated in CLL patient samples. We hypothesized that CLLU1 could be used to monitor for residual disease in CLL patient samples after therapy. METHODS We examined whether the CLLU1 real-time quantitative PCR (RQ-PCR) could detect small numbers of CLL cells in mixtures of normal peripheral blood mononuclear (PBMC) cells. We then performed a retrospective analysis on time-matched cryo-preserved specimens from patients who achieved MRD-negative remissions that underwent serial marrow biopsies for evaluation of residual disease by 4-color flow cytometry. RNA from PBMC samples collected at the time of the marrow assessments was analyzed for CLLU1. Nine patients underwent a total of 46 paired blood and marrow evaluations (median 5 assessments per patient). RESULTS CLLU1 RQ-PCR on PBMCs of healthy donors reconstituted with varying amounts of CLL cells demonstrated leukemia cells could be reliably detected with high sensitivities depending on the CLLU1 expression level. Analysis of time-matched samples assessed for CLLU1 levels in the blood by RQ-PCR and residual disease of the marrow determined by 4-color flow cytometry revealed a correlation coefficient of 0.96 (P < 0.0001). CONCLUSION The CLLU1 RQ-PCR is a sensitive and specific assay for detecting residual CLL cells after therapy. Assessment of blood CLLU1 levels can be used as a reliable marker of tumor burden and has the potential to complement currently used techniques for MRD monitoring in patients with CLL.
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Affiliation(s)
- Anne Mette Buhl
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark.,Division of Hematology/Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA
| | - Danelle F James
- Division of Hematology/Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA.,The CLL Research Consortium, Dana-Farber Cancer Institute, Boston, MA
| | - Donna Neuberg
- The CLL Research Consortium, Dana-Farber Cancer Institute, Boston, MA.,Department of Biostatics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Sonia Jain
- Division of Biostatistics and Bioinformatics, UCSD, La Jolla, CA, USA
| | - Laura Z Rassenti
- Division of Hematology/Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA.,The CLL Research Consortium, Dana-Farber Cancer Institute, Boston, MA
| | - Thomas J Kipps
- Division of Hematology/Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA.,The CLL Research Consortium, Dana-Farber Cancer Institute, Boston, MA
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26
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Affiliation(s)
- Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA.
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27
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Kienle D, Benner A, Läufle C, Winkler D, Schneider C, Bühler A, Zenz T, Habermann A, Jäger U, Lichter P, Dalla-Favera R, Döhner H, Stilgenbauer S. Gene expression factors as predictors of genetic risk and survival in chronic lymphocytic leukemia. Haematologica 2009; 95:102-9. [PMID: 19951976 DOI: 10.3324/haematol.2009.010298] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND A variety of surrogate markers for genetic features and outcome have been described in chronic lymphocytic leukemia based on gene expression analyses. Previous studies mostly focused on individual markers and selected disease characteristics, which makes it difficult to estimate the relative value of the novel markers. Therefore, in the present study a comprehensive approach was chosen investigating 18 promising, partly novel expression markers in a well characterized cohort of patients with long clinical follow-up and full genetic information (IGHV status, genomic abnormalities). DESIGN AND METHODS Expression markers were evaluated using real-time quantitative reverse transcriptase polymerase chain reaction in CD19(+)-purified samples from 151 patients. Multivariate analyses were performed to test the markers' ability to identify patients at genetic risk and as prognostic markers in the context of established prognostic factors. RESULTS For individual markers, ZAP70 expression provided the highest rate (81%) of correct assignment of patients at genetic risk (IGHV unmutated, V3-21 usage, 11q- or 17p-), followed by LPL and TCF7 (76% both). The assignment rate was improved to 88% by information from a four-gene combination (ZAP70, TCF7, DMD, ATM). In multivariate analysis of treatment-free survival, IGHV mutation status and expression of ADAM29 were of independent prognostic value besides disease stage. With regards to overall survival, expression of ATM, ADAM29, TCL1, and SEPT10 provided prognostic information in addition to that derived from clinical and genetic factors. CONCLUSIONS Gene expression markers are suitable for screening but not as surrogates for the information from genetic risk factors. While many individual markers may be associated with outcome, only a few are of independent prognostic significance. With regard to prognosis estimation, the genetic prognostic factors cannot be replaced by the expression markers.
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Affiliation(s)
- Dirk Kienle
- Department of Internal Medicine III, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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28
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Abstract
The origin of new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or recombination. The origin of new genes from noncoding DNA is extremely rare, and very few eukaryotic examples are known. We present evidence for the de novo origin of at least three human protein-coding genes since the divergence with chimp. Each of these genes has no protein-coding homologs in any other genome, but is supported by evidence from expression and, importantly, proteomics data. The absence of these genes in chimp and macaque cannot be explained by sequencing gaps or annotation error. High-quality sequence data indicate that these loci are noncoding DNA in other primates. Furthermore, chimp, gorilla, gibbon, and macaque share the same disabling sequence difference, supporting the inference that the ancestral sequence was noncoding over the alternative possibility of parallel gene inactivation in multiple primate lineages. The genes are not well characterized, but interestingly, one of them was first identified as an up-regulated gene in chronic lymphocytic leukemia. This is the first evidence for entirely novel human-specific protein-coding genes originating from ancestrally noncoding sequences. We estimate that 0.075% of human genes may have originated through this mechanism leading to a total expectation of 18 such cases in a genome of 24,000 protein-coding genes.
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Dal-Bo M, Bertoni F, Forconi F, Zucchetto A, Bomben R, Marasca R, Deaglio S, Laurenti L, Efremov DG, Gaidano G, Del Poeta G, Gattei V. Intrinsic and extrinsic factors influencing the clinical course of B-cell chronic lymphocytic leukemia: prognostic markers with pathogenetic relevance. J Transl Med 2009; 7:76. [PMID: 19715592 PMCID: PMC2747913 DOI: 10.1186/1479-5876-7-76] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 08/28/2009] [Indexed: 11/13/2022] Open
Abstract
B-cell chronic lymphocytic leukemia (CLL), the most frequent leukemia in the Western world, is characterized by extremely variable clinical courses with survivals ranging from 1 to more than 15 years. The pathogenetic factors playing a key role in defining the biological features of CLL cells, hence eventually influencing the clinical aggressiveness of the disease, are here divided into "intrinsic factors", mainly genomic alterations of CLL cells, and "extrinsic factors", responsible for direct microenvironmental interactions of CLL cells; the latter group includes interactions of CLL cells occurring via the surface B cell receptor (BCR) and dependent to specific molecular features of the BCR itself and/or to the presence of the BCR-associated molecule ZAP-70, or via other non-BCR-dependent interactions, e.g. specific receptor/ligand interactions, such as CD38/CD31 or CD49d/VCAM-1. A putative final model, discussing the pathogenesis and the clinicobiological features of CLL in relationship of these factors, is also provided.
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Affiliation(s)
- Michele Dal-Bo
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano (PN), Italy.
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30
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Chen L, Li J, Zheng W, Zhang Y, Wu Y, Li L, Qian S, Xu W. The prognostic evaluation of CLLU1 expression levels in 50 Chinese patients with chronic lymphocytic leukemia. Leuk Lymphoma 2009; 48:1785-92. [PMID: 17786715 DOI: 10.1080/10428190701534416] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by the relentless accumulation of monoclonal B cells with the appearance of small mature lymphocytes and a characteristic CD5 and CD19 co-expression immunophenotype. The incidence of CLL is lower in Asian countries than in Western countries, where CLL is the most common leukemia. To investigate CLLU1 expression in CLL and explore the relationship between CLLU1 expression and alternative prognostic markers, we measured CLLU1 expression levels by semiquantitative RT-PCR in a cohort of 50 Chinese patients with CLL. Analyses of IgVH somatic mutational status, ZAP-70 expression, CD38 expression, and chromosomal aberrations were also performed. The expression of CLLU1 mRNA was determined in 26 of the 50 cases (52%), among which 7 at Binet A (7/21, 33.33%) and 19 at Binet B + C (19/29, 65.52%). The expression levels of CLLU1 were significantly increased in B + C CLL patients at Binet stage compared with those at Binet stage A (P = 0.005). Data for the IgVH somatic mutational status were available for 20 patients with known CLLU1 expression. Five (25%) patients, all expressed CLLU1 mRNA, displayed unmutated IgVH gene usage. While in 15 patients (15/20, 75%) with mutated IgVH gene, only 6 were CLLU1 positive. Patients with unmutated IgVH genes expressed higher levels of CLLU1 than did those with IgVH mutations (P < 0.05). Among 24 CD38(+)-CLL cases, 17 (70.83%) were CLLU1 positive, whereas only 9 (34.62%) positive cases were identified in 26 CD38(-)-CLL patients. Thus, the expression of CLLU1 in CD38(+)-CLL was significantly higher than that in CD38(-)-CLL. However, no significant difference of CLLU1 expression was found between ZAP-70(+) (14/22, 63.64%) and ZAP-70(-) (12/28, 42.86%) patients (P > 0.05). We conclude that CLLU1 expression was significantly associated with clinical stages, IgVH somatic mutational status and CD38 expression, and might be an important prognostic factor in CLL patients.
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Affiliation(s)
- Lijuan Chen
- Department of Hematology, First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
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31
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Galligan L, Catherwood MA, Matthews C, ‘Curly' Morris TCM, Dennis Alexander H. Mutated IgHV1-69 gene usage represents a distinct subgroup associated with indolent disease in chronic lymphocytic leukemia. Leuk Lymphoma 2009; 49:763-8. [DOI: 10.1080/10428190801911696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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32
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Codony C, Crespo M, Abrisqueta P, Montserrat E, Bosch F. Gene expression profiling in chronic lymphocytic leukaemia. Best Pract Res Clin Haematol 2009; 22:211-22. [DOI: 10.1016/j.beha.2009.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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The CLLU1 expression level is a stable and inherent feature of the chronic lymphocytic leukemia clone. Leukemia 2009; 23:1182-6. [PMID: 19212335 DOI: 10.1038/leu.2009.16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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34
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Van Bockstaele F, Verhasselt B, Philippé J. Prognostic markers in chronic lymphocytic leukemia: A comprehensive review. Blood Rev 2009; 23:25-47. [DOI: 10.1016/j.blre.2008.05.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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35
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36
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Abstract
Chronic lymphocytic leukaemia is the commonest form of leukaemia in Europe and North America, and mainly, though not exclusively, affects older individuals. It has a very variable course, with survival ranging from months to decades. Major progress has been made in identification of molecular and cellular markers that could predict disease progression in patients with chronic lymphocytic leukaemia. In particular, the mutational profile of immunoglobulin genes and some cytogenetic abnormalities are important predictors of prognosis. However, these advances have raised new questions about the biology, prognosis, and management of chronic lymphocytic leukaemia, some of which are addressed here. In particular, we discuss how better understanding of the function of the B-cell receptor, the nature of genetic lesions, and the balance between proliferation and apoptosis have affected our ability to assess prognosis and to manage chronic lymphocytic leukaemia. Available treatments generally induce remission, although nearly all patients relapse, and chronic lymphocytic leukaemia remains an incurable disease. Advances in molecular biology have enhanced our understanding of the pathophysiology of the disease and, together with development of new therapeutic agents, have made management of chronic lymphocytic leukaemia more rational and more effective than previously. Unfortunately, we know of no way that chronic lymphocytic leukaemia can be prevented. Early detection is practised widely, but seemingly makes no difference to the patient's eventual outcome.
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MESH Headings
- Antibodies, Monoclonal/therapeutic use
- Antineoplastic Agents/adverse effects
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/genetics
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/physiopathology
- Male
- Prognosis
- Randomized Controlled Trials as Topic
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Affiliation(s)
- G Dighiero
- Institut Pasteur de Montevideo, Montevideo, Uruguay
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37
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Cotter FE, Auer RL. Genetic alteration associated with chronic lymphocytic leukemia. Cytogenet Genome Res 2007; 118:310-9. [PMID: 18000385 DOI: 10.1159/000108315] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2007] [Accepted: 03/14/2007] [Indexed: 12/19/2022] Open
Abstract
The genetics of B-cell chronic lymphocytic leukemia (B-CLL) differ considerably from most other forms of hematologic malignancy which are usually characterized by chromosome translocations. B-CLL typically contains chromosomal deletions and chromosomes 13q14 and 11q22-->q23 are the most common. These two regions appear to share a common ancestral origin (Auer et al., 2007b). Overall, chromosomal abnormalities can be found in the majority of patients with B-CLL when using sensitive techniques (Dohneret al., 2000) and possibly reflects an underlying predisposition, with a small but significant number of familial cases. Although single and consistent abnormalities are most common, multiple rearrangements can occur, often with disease progression (Feganetal., 1995; Dohner et al., 2000). Regions of recurrent deletion suggest the presence of tumor suppressor genes if following Knudson's theoretical 2-hit model. However, despite extensive sequencing analysis over the last decade and lack of pathogenic mutations identified, there has been a move away from this suggested hypothesis and alternative mechanisms of gene inactivation involving epigenetic silencing or haploinsufficiency may be considered as more likely in this disease. This review focuses on the common genetic abnormalities in B-CLL and relates them to some of the more recent hypotheses on inactivation of genes within these regions of deletion.
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Affiliation(s)
- F E Cotter
- Centre for Haematology, Institute of Cell and Molecular Sciences, Barts and the London Queen Mary School of Medicine, London, UK.
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38
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Abstract
Chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL) is a clonal lymphoproliferative disorder characterized by proliferation of morphologically and immunophenotypically mature lymphocytes. CLL/SLL may proceed through different phases: an early phase in which tumor cells are predominantly small in size, with a low proliferation rate and prolonged cell survival, and a transformation phase with the frequent occurrence of extramedullary proliferation and an increase in large, immature cells. Although some patients with CLL have an indolent disease course and die after many years of unrelated causes, others have very rapidly disease progression and die of the disease within a few years of the diagnosis. In the past few years, considerable progress has been made in our ability to diagnose and classify CLL accurately. Through cytogenetics and molecular biology, it has been shown that CLL and variants are associated with a unique genotypic profile and that these genetic lesions often have a direct bearing on the pathogenesis and prognosis of the disease. Similarly, the development of antibodies to new biologic markers has allowed the identification of a unique immunophenotypic profile for CLL and variants. Moreover, accumulating evidence suggests that CLL cells respond to selected microenvironmental signals and that this confers a growth advantage and an extended survival to CLL cells. In this article, we will review the progress in the pathobiology of CLL and give an update on prognostic markers and tools in current pathology practice for risk stratification of CLL.
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MESH Headings
- Bone Marrow/pathology
- Chromosome Aberrations
- Diagnosis, Differential
- Female
- Humans
- Immunophenotyping
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymph Nodes/pathology
- Male
- Prognosis
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Affiliation(s)
- Kedar V Inamdar
- Department of Hematopathology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
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39
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Rosenwald A. CLLU1 expression: the latest risk predictor in chronic lymphocytic leukemia. Leuk Lymphoma 2007; 48:1665-6. [PMID: 17786698 DOI: 10.1080/10428190701559165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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40
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Takahashi T, Watanabe M, Minato M, Yoshimoto M, Tsujisaki M. A novel t(12;15)(q22;q13) in a patient with acute monoblastic leukemia. ACTA ACUST UNITED AC 2007; 177:164-5. [PMID: 17854677 DOI: 10.1016/j.cancergencyto.2007.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 05/29/2007] [Indexed: 10/22/2022]
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41
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Josefsson P, Geisler CH, Leffers H, Petersen JH, Andersen MK, Jurlander J, Buhl AM. CLLU1 expression analysis adds prognostic information to risk prediction in chronic lymphocytic leukemia. Blood 2007; 109:4973-9. [PMID: 17284524 DOI: 10.1182/blood-2006-11-054916] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractWe recently identified a disease-specific gene CLLU1 in chronic lymphocytic leukemia (CLL) and also demonstrated that high CLLU1 expression levels predict poor clinical outcome. To validate this finding, we measured CLLU1 mRNA expression levels by real-time reverse transcriptase–polymerase chain reaction (RT-PCR) in 175 patients with CLL. Analyses of IgVH mutational status, ZAP-70 expression, CD38 expression, and chromosomal aberrations were also performed. High levels of CLLU1 expression were associated with shorter overall survival (P < .001), with a 7% increase in risk of early death by each doubling of the CLLU1 expression level. Stratification for age at diagnosis demonstrated a strong prognostic significance of CLLU1 expression in patients younger than 70 years (P < .001), but not in patients aged 70 or older (P = .61). The prognostic significance of IgVH mutational status and ZAP-70 expression had a similar age-dependent variation. Multivariate analysis in the younger age group showed that CLLU1 expression analysis added further prognostic information within all prognostic subgroups, with the exception of patients with unmutated IgVH CLL. Only CLLU1 expression and IgVH mutational status had independent predictive power. Thus, analysis of CLLU1 expression is highly applicable in risk prediction in CLL for patients of an age eligible for risk stratification.
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Affiliation(s)
- Pär Josefsson
- The Leukemia Laboratory, Department of Hematology, Rigshospitalet and University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark.
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42
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Microarray expression technology in clinical research of non-Hodgkin lymphoma. ARCHIVE OF ONCOLOGY 2007. [DOI: 10.2298/aoo0702028b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nowadays, in genomocentric era accelerated research of the human genome coupled with advances is enabling the comprehensive molecular profiling of human tissue. Particularly, DNA microarrays are powerful tools for obtaining global view of human non-Hodgkin lymphomas gene expression. Complex information from lymphomas "expression profiling" studies can, in turn, be used to create molecular markers that have diagnostic or prognostic implications. The gene "expression profiling" is not of routine clinical oncology practice, but is used in genomic classification of clinically relevant subgroups of non-Hodgkin lymphoma. The genomics biomarkers have been incorporated into current prognostic models which are based on IPI, R-IPI, and FLIPI. Molecular or pharmacogenomic profiling can be used as new therapeutic targets for patients who are refractory to current therapy. We discus the utility of DNA microarray-based lymphoma profiling in clinical oncology research, and identify future of research in lymphoma evolving fields.
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43
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Current Awareness in Hematological Oncology. Hematol Oncol 2006. [DOI: 10.1002/hon.755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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