1
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Hanaki S, Habara M, Tomiyasu H, Sato Y, Miki Y, Masaki T, Shibutani S, Shimada M. NFAT activation by FKBP52 promotes cancer cell proliferation by suppressing p53. Life Sci Alliance 2024; 7:e202302426. [PMID: 38803221 PMCID: PMC11109481 DOI: 10.26508/lsa.202302426] [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: 10/09/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
FK506-binding protein 52 (FKBP52) is a member of the FKBP family of proline isomerases. FKBP52 is up-regulated in various cancers and functions as a positive regulator of steroid hormone receptors. Depletion of FKBP52 is known to inhibit cell proliferation; however, the detailed mechanism remains poorly understood. In this study, we found that FKBP52 depletion decreased MDM2 transcription, leading to stabilization of p53, and suppressed cell proliferation. We identified NFATc1 and NFATc3 as transcription factors that regulate MDM2 We also found that FKBP52 associated with NFATc3 and facilitated its nuclear translocation. In addition, calcineurin, a well-known Ca2+ phosphatase essential for activation of NFAT, plays a role in MDM2 transcription. Supporting this notion, MDM2 expression was found to be regulated by intracellular Ca2+ Taken together, these findings reveal a new role of FKBP52 in promoting cell proliferation via the NFAT-MDM2-p53 axis, and indicate that inhibition of FKBP52 could be a new therapeutic tool to activate p53 and inhibit cell proliferation.
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Affiliation(s)
- Shunsuke Hanaki
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
| | - Makoto Habara
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
| | - Haruki Tomiyasu
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
| | - Yuki Sato
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
| | - Yosei Miki
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
| | - Takahiro Masaki
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
| | - Shusaku Shibutani
- https://ror.org/03cxys317 Department of Veterinary Hygiene, Yamaguchi University, Yamaguchi, Japan
| | - Midori Shimada
- https://ror.org/03cxys317 Department of Veterinary Biochemistry, Yamaguchi University, Yamaguchi, Japan
- https://ror.org/04chrp450 Department of Molecular Biology, Nagoya University, Graduate School of Medicine, Nagoya, Japan
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2
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Chatzidavid S, Kontandreopoulou CN, Giannakopoulou N, Diamantopoulos PT, Stafylidis C, Kyrtsonis MC, Dimou M, Panayiotidis P, Viniou NA. The Role of Methylation in Chronic Lymphocytic Leukemia and Its Prognostic and Therapeutic Impacts in the Disease: A Systematic Review. Adv Hematol 2024; 2024:1370364. [PMID: 38435839 PMCID: PMC10907108 DOI: 10.1155/2024/1370364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
Epigenetic regulation has been thoroughly investigated in recent years and has emerged as an important aspect of chronic lymphocytic leukemia (CLL) biology. Characteristic aberrant features such as methylation patterns and global DNA hypomethylation were the early findings of the research during the last decades. The investigation in this field led to the identification of a large number of genes where methylation features correlated with important clinical and laboratory parameters. Gene-specific analyses investigated methylation in the gene body enhancer regions as well as promoter regions. The findings included genes and proteins involved in key pathways that play central roles in the pathophysiology of the disease. Τhe application of these findings beyond the theoretical understanding can not only lead to the creation of prognostic and predictive models and scores but also to the design of novel therapeutic agents. The following is a review focusing on the present knowledge about single gene/gene promoter methylation or mRNA expression in CLL cases as well as records of older data that have been published in past papers.
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Affiliation(s)
- Sevastianos Chatzidavid
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Thalassemia and Sickle Cell Disease Center, Laikon General Hospital, Athens, Greece
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Panagiotis T. Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Stafylidis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Marie-Christine Kyrtsonis
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Maria Dimou
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, School of Medicine, Laikon General Hospital, Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Athens, Greece
- Hematology Department, Iatriko Kentro Palaiou Falirou, Athens, Greece
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3
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Allegra A, Caserta S, Mirabile G, Gangemi S. Aging and Age-Related Epigenetic Drift in the Pathogenesis of Leukemia and Lymphomas: New Therapeutic Targets. Cells 2023; 12:2392. [PMID: 37830606 PMCID: PMC10572300 DOI: 10.3390/cells12192392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
One of the traits of cancer cells is abnormal DNA methylation patterns. The idea that age-related epigenetic changes may partially explain the increased risk of cancer in the elderly is based on the observation that aging is also accompanied by comparable changes in epigenetic patterns. Lineage bias and decreased stem cell function are signs of hematopoietic stem cell compartment aging. Additionally, aging in the hematopoietic system and the stem cell niche have a role in hematopoietic stem cell phenotypes linked with age, such as leukemia and lymphoma. Understanding these changes will open up promising pathways for therapies against age-related disorders because epigenetic mechanisms are reversible. Additionally, the development of high-throughput epigenome mapping technologies will make it possible to identify the "epigenomic identity card" of every hematological disease as well as every patient, opening up the possibility of finding novel molecular biomarkers that can be used for diagnosis, prediction, and prognosis.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
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4
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Wang S, Zha L, Cui X, Yeh Y, Liu R, Jing J, Shi H, Chen W, Hanover J, Yin J, Yu L, Xue B, Shi H. Epigenetic Regulation of Hepatic Lipid Metabolism by DNA Methylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206068. [PMID: 37282749 PMCID: PMC10369300 DOI: 10.1002/advs.202206068] [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: 10/18/2022] [Revised: 04/25/2023] [Indexed: 06/08/2023]
Abstract
While extensive investigations have been devoted to the study of genetic pathways related to fatty liver diseases, much less is known about epigenetic mechanisms underlying these disorders. DNA methylation is an epigenetic link between environmental factors (e.g., diets) and complex diseases (e.g., non-alcoholic fatty liver disease). Here, it is aimed to study the role of DNA methylation in the regulation of hepatic lipid metabolism. A dynamic change in the DNA methylome in the liver of high-fat diet (HFD)-fed mice is discovered, including a marked increase in DNA methylation at the promoter of Beta-klotho (Klb), a co-receptor for the biological functions of fibroblast growth factor (FGF)15/19 and FGF21. DNA methyltransferases (DNMT) 1 and 3A mediate HFD-induced methylation at the Klb promoter. Notably, HFD enhances DNMT1 protein stability via a ubiquitination-mediated mechanism. Liver-specific deletion of Dnmt1 or 3a increases Klb expression and ameliorates HFD-induced hepatic steatosis. Single-nucleus RNA sequencing analysis reveals pathways involved in fatty acid oxidation in Dnmt1-deficient hepatocytes. Targeted demethylation at the Klb promoter increases Klb expression and fatty acid oxidation, resulting in decreased hepatic lipid accumulation. Up-regulation of methyltransferases by HFD may induce hypermethylation of the Klb promoter and subsequent down-regulation of Klb expression, resulting in the development of hepatic steatosis.
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Affiliation(s)
- Shirong Wang
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Lin Zha
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
- The Northern Medical DistrictChinese PLA General HospitalBeijing100094China
| | - Xin Cui
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Yu‐Te Yeh
- Department of Internal MedicineUniversity of Maryland School of MedicineBaltimoreMD21201USA
| | - Ruochuan Liu
- Department of Chemistry and the Center for Diagnosis and TherapeuticsGeorgia State UniversityAtlantaGA30303
| | - Jia Jing
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Huidong Shi
- GRU Cancer Center and Department of Biochemistry and Molecular BiologyMedical College of GeorgiaAugusta UniversityAugustaGA30912USA
| | - Weiping Chen
- Genomic Core Lab of National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20855USA
| | - John Hanover
- Genomic Core Lab of National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20855USA
| | - Jun Yin
- Department of Chemistry and the Center for Diagnosis and TherapeuticsGeorgia State UniversityAtlantaGA30303
| | - Liqing Yu
- Department of Internal MedicineUniversity of Maryland School of MedicineBaltimoreMD21201USA
| | - Bingzhong Xue
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
| | - Hang Shi
- Department of BiologyGeorgia State UniversityAtlantaGA30303USA
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5
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Xiao X, Huo E, Guo C, Zhou X, Hu X, Dong C, Shi H, Dong Z, Wei Q. Hypermethylation suppresses microRNA-219a-2 to activate the ALDH1L2/GSH/PAI-1 pathway for fibronectin degradation in renal fibrosis. RESEARCH SQUARE 2023:rs.3.rs-2986934. [PMID: 37333081 PMCID: PMC10275039 DOI: 10.21203/rs.3.rs-2986934/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Epigenetic regulations, such as DNA methylation and microRNAs, play an important role in renal fibrosis. Here, we report the regulation of microRNA-219a-2 (mir-219a-2) by DNA methylation in fibrotic kidneys, unveiling the crosstalk between these epigenetic mechanisms. Through genome-wide DNA methylation analysis and pyro-sequencing, we detected the hypermethylation of mir-219a-2 in renal fibrosis induced by unilateral ureter obstruction (UUO) or renal ischemia/reperfusion, which was accompanied by a significant decrease in mir-219a-5p expression. Functionally, overexpression of mir-219a-2 enhanced fibronectin induction during hypoxia or TGF-β1 treatment of cultured renal cells. In mice, inhibition of mir-219a-5p suppressed fibronectin accumulation in UUO kidneys. ALDH1L2 was identified to be the direct target gene of mir-219a-5p in renal fibrosis. Mir-219a-5p suppressed ALDH1L2 expression in cultured renal cells, while inhibition of mir-219a-5p prevented the decrease of ALDH1L2 in UUO kidneys. Knockdown of ALDH1L2 enhanced PAI-1 induction during TGF-β1 treatment of renal cells, which was associated with fibronectin expression. In conclusion, the hypermethylation of mir-219a-2 in response to fibrotic stress attenuates mir-219a-5p expression and induces the up-regulation of its target gene ALDH1L2, which may reduce fibronectin deposition by suppressing PAI-1.
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Affiliation(s)
- Xiao Xiao
- Zhongnan Hospital of Wuhan University
| | | | - Chunyuan Guo
- Shanghai Skin Disease Hospital, Tongji University School of Medicine
| | | | - Xiaoru Hu
- The Second Xiangya Hospital at Central South University
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6
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Nannini DR, Cortese R, Egwom P, Palaniyandi S, Hildebrandt GC. Time to relapse in chronic lymphocytic leukemia and DNA-methylation-based biological age. Clin Epigenetics 2023; 15:81. [PMID: 37165442 PMCID: PMC10170738 DOI: 10.1186/s13148-023-01496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a mature B cell neoplasm with a predilection for older individuals. While previous studies have identified epigenetic signatures associated with CLL, whether age-related DNA methylation changes modulate CLL relapse remains elusive. In this study, we examined the association between epigenetic age acceleration and time to CLL relapse in a publicly available dataset. DNA methylation profiling of 35 CLL patients prior to initiating chemoimmunotherapy was performed using the Infinium HumanMethylation450 BeadChip. Four epigenetic age acceleration metrics (intrinsic epigenetic age acceleration [IEAA], extrinsic epigenetic age acceleration [EEAA], PhenoAge acceleration [PhenoAA], and GrimAge acceleration [GrimAA]) were estimated from blood DNA methylation levels. Linear, quantile, and logistic regression and receiver operating characteristic curve analyses were conducted to assess the association between each epigenetic age metric and time to CLL relapse. EEAA (p = 0.011) and PhenoAA (p = 0.046) were negatively and GrimAA (p = 0.040) was positively associated with time to CLL relapse. Simultaneous assessment of EEAA and GrimAA in male patients distinguished patients who relapsed early from patients who relapsed later (p = 0.039). No associations were observed with IEAA. These findings suggest epigenetic age acceleration prior to chemoimmunotherapy initiation is associated with time to CLL relapse. Our results provide novel insight into the association between age-related DNA methylation changes and CLL relapse and may serve has biomarkers for treatment relapse, and potentially, treatment selection.
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Affiliation(s)
- Drew R Nannini
- Department of Internal Medicine, School of Medicine, University of Missouri at Columbia, MA408 Medical Science Building, Columbia, MO, 65212, USA.
| | - Rene Cortese
- Department of Child Health and Department of Obstetrics, Gynecology, and Women's Health, School of Medicine, University of Missouri at Columbia, Columbia, MO, 65212, USA
- Ellis Fischel Cancer Center, University of Missouri at Columbia, Columbia, MO, 65212, USA
| | - Peter Egwom
- Department of Internal Medicine, School of Medicine, University of Missouri at Columbia, MA408 Medical Science Building, Columbia, MO, 65212, USA
| | - Senthilnathan Palaniyandi
- Ellis Fischel Cancer Center, University of Missouri at Columbia, Columbia, MO, 65212, USA
- Division of Hematology and Medical Oncology, School of Medicine, University of Missouri at Columbia, Columbia, MO, 65212, USA
| | - Gerhard C Hildebrandt
- Ellis Fischel Cancer Center, University of Missouri at Columbia, Columbia, MO, 65212, USA
- Division of Hematology and Medical Oncology, School of Medicine, University of Missouri at Columbia, Columbia, MO, 65212, USA
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7
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Sahinyan K, Lazure F, Blackburn DM, Soleimani VD. Decline of regenerative potential of old muscle stem cells: contribution to muscle aging. FEBS J 2023; 290:1267-1289. [PMID: 35029021 DOI: 10.1111/febs.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Muscle stem cells (MuSCs) are required for life-long muscle regeneration. In general, aging has been linked to a decline in the numbers and the regenerative potential of MuSCs. Muscle regeneration depends on the proper functioning of MuSCs, which is itself dependent on intricate interactions with its niche components. Aging is associated with both cell-intrinsic and niche-mediated changes, which can be the result of transcriptional, posttranscriptional, or posttranslational alterations in MuSCs or in the components of their niche. The interplay between cell intrinsic alterations in MuSCs and changes in the stem cell niche environment during aging and its impact on the number and the function of MuSCs is an important emerging area of research. In this review, we discuss whether the decline in the regenerative potential of MuSCs with age is the cause or the consequence of aging skeletal muscle. Understanding the effect of aging on MuSCs and the individual components of their niche is critical to develop effective therapeutic approaches to diminish or reverse the age-related defects in muscle regeneration.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
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8
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Chatzidavid S, Kontandreopoulou CN, Diamantopoulos PT, Giannakopoulou N, Katsiampoura P, Stafylidis C, Dryllis G, Kyrtsonis MC, Dimou M, Panayiotidis P, Viniou NA. The Clinical and Prognostic Significance of Ribonucleotide Reductase Subunits RRM1 and RRM2 mRNA Levels in Patients with Chronic Lymphocytic Leukemia. Clin Hematol Int 2023:10.1007/s44228-023-00033-x. [PMID: 36811764 DOI: 10.1007/s44228-023-00033-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
Ribonucleotide Reductase (RNR) converts ribonucleotides to deoxyribonucleotides required for DNA replication and repair. RNR consists of subunits M1 and M2. It has been studied as a prognostic factor in several solid tumors and in chronic hematological malignancies, but not in chronic lymphocytic leukemia (CLL). Peripheral blood samples were collected from 135 CLL patients. M1/M2 gene mRNA levels were measured and expressed as a RRM1-2/GAPDH ratio. M1 gene promoter methylation was studied in a patients' subgroup. M1 mRNA expression was higher in patients without anemia (p = 0.026), without lymphadenopathy (p = 0.005) and 17p gene deletion (p = 0.031). Abnormal LDH (p = 0.022) and higher Rai stage (p = 0.019) were associated with lower M1 mRNA levels. Higher M2 mRNA levels were found in patients without lymphadenopathy (p = .048), Rai stage 0 (p = 0.025) and Trisomy 12 (p = 0.025). The correlation between RNR subunits and clinic-biological characteristics in CLL patients demonstrate RNR's potential role as a prognostic factor.
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Affiliation(s)
- Sevastianos Chatzidavid
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece.
| | - Christina-Nefeli Kontandreopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Panagiotis T Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Nefeli Giannakopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Panagiota Katsiampoura
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Christos Stafylidis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Georgios Dryllis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
| | - Marie-Christine Kyrtsonis
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Maria Dimou
- Hematology Section of the First Department of Propaedeutic Internal Medicine, Laikon University Hospital, Athens, Greece
| | - Panayiotis Panayiotidis
- Department of Hematology and Bone Marrow Transplantation Unit, National and Kapodistrian University of Athens, School of Medicine, Laikon General Hospital, Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 17 Agiou Thoma Street, Athens, Greece
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9
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Targeting DNA Methylation in Leukemia, Myelodysplastic Syndrome, and Lymphoma: A Potential Diagnostic, Prognostic, and Therapeutic Tool. Int J Mol Sci 2022; 24:ijms24010633. [PMID: 36614080 PMCID: PMC9820560 DOI: 10.3390/ijms24010633] [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: 12/05/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
DNA methylation represents a crucial mechanism of epigenetic regulation in hematologic malignancies. The methylation process is controlled by specific DNA methyl transferases and other regulators, which are often affected by genetic alterations. Global hypomethylation and hypermethylation of tumor suppressor genes are associated with hematologic cancer development and progression. Several epi-drugs have been successfully implicated in the treatment of hematologic malignancies, including the hypomethylating agents (HMAs) decitabine and azacytidine. However, combinations with other treatment modalities and the discovery of new molecules are still the subject of research to increase sensitivity to anti-cancer therapies and improve patient outcomes. In this review, we summarized the main functions of DNA methylation regulators and genetic events leading to changes in methylation landscapes. We provide current knowledge about target genes with aberrant methylation levels in leukemias, myelodysplastic syndromes, and malignant lymphomas. Moreover, we provide an overview of the clinical trials, focused mainly on the combined therapy of HMAs with other treatments and its impact on adverse events, treatment efficacy, and survival rates among hematologic cancer patients. In the era of precision medicine, a transition from genes to their regulation opens up the possibility of an epigenetic-based approach as a diagnostic, prognostic, and therapeutic tool.
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10
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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11
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Fernández A, Astorga J, Bordagaray MJ, Lira MJ, Gebicke-Haerter PJ, Hernández M. Effect of TLR9 methylation on its transcription in apical inflammation. Int Endod J 2022; 55:784-794. [PMID: 35416307 DOI: 10.1111/iej.13745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/25/2022]
Abstract
AIM to explore the methylation pattern, its role on transcriptional regulation and potential modifiers of methylation of theTLR9 gene in chronic periapical inflammation. METHODOLOGY In this cross-sectional study, apical lesions of endodontic origin (ALEO, n=61) and healthy periodontal ligaments (HPL, n=15) were included. Products from bisulfited and PCR-amplified DNA were analyzed for their methylation profiles in the promoter region and at each CpG island. Additionally, TLR9 mRNA levels were quantified by qPCR and bivariate and multiple modelling were performed to better understand the influence of methylations on gene transcription. RESULTS TLR9 mRNA levels were upregulated in ALEO compared to HPL (p<0.001). TLR9 promoter CpG sites and CpG +2086 in the intragenic island 1 were demethylated in ALEO compared to HPL (p<0.05). Multivariate analysis, adjusted by smoking and gender, revealed that demethylation of TLR9 promoter sites enhanced transcriptional activity, specifically demethylated CpGs at positions -736 and -683, (p=0.02), which are close to CRE binding. Whereas ALEO reduced the global methylation of the gene-promoter and intragenic-island 2 (p<0.05) by -42.5 and -9.5 percentage points, respectively, age reduced the global methylation of intragenic-island 3 within the exon 2. CONCLUSIONS Demethylations of TLR9 promoter CpG sites, along with the intragenic DNA methylation status, were involved in higher transcription in ALEO. Hence, chronic periapical inflammation and aging modify the methylation status both in the gene promoter and in intragenic CpG islands.
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Affiliation(s)
- Alejandra Fernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Faculty of Dentistry, Universidad Andres Bello, Santiago, Chile
| | - Jessica Astorga
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - María José Bordagaray
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - María Jesús Lira
- Department of Orthopaedic Surgery, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter J Gebicke-Haerter
- Institute of Psychopharmacology, Central Institute of Mental Health, Faculty of Medicine, University of Heidelberg, Mannheim, Germany
| | - Marcela Hernández
- Laboratory of Periodontal Biology, Faculty of Dentistry, Universidad de Chile, Santiago, Chile.,Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
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12
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van Dijk AD, Griffen TL, Qiu YH, Hoff FW, Toro E, Ruiz K, Ruvolo PP, Lillard JW, de Bont ESJM, Burger JA, Wierda W, Kornblau SM. RPPA-based proteomics recognizes distinct epigenetic signatures in chronic lymphocytic leukemia with clinical consequences. Leukemia 2022; 36:712-722. [PMID: 34625713 DOI: 10.1038/s41375-021-01438-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/11/2021] [Accepted: 09/21/2021] [Indexed: 11/08/2022]
Abstract
The chronic lymphocytic leukemia (CLL) armamentarium has evolved significantly, with novel therapies that inhibit Bruton Tyrosine Kinase, PI3K delta and/or the BCL2 protein improving outcomes. Still, the clinical course of CLL patients is highly variable and most previously recognized prognostic features lack the capacity to predict response to modern treatments indicating the need for new prognostic markers. In this study, we identified four epigenetically distinct proteomic signatures of a large cohort of CLL and related diseases derived samples (n = 871) using reverse phase protein array technology. These signatures are associated with clinical features including age, cytogenetic abnormalities [trisomy 12, del(13q) and del(17p)], immunoglobulin heavy-chain locus (IGHV) mutational load, ZAP-70 status, Binet and Rai staging as well as with the outcome measures of time to treatment and overall survival. Protein signature membership was identified as predictive marker for overall survival regardless of other clinical features. Among the analyzed epigenetic proteins, EZH2, HDAC6, and loss of H3K27me3 levels were the most independently associated with poor survival. These findings demonstrate that proteomic based epigenetic biomarkers can be used to better classify CLL patients and provide therapeutic guidance.
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Affiliation(s)
- Anneke D van Dijk
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, the Netherlands.
| | - Ti'ara L Griffen
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Yihua H Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fieke W Hoff
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, the Netherlands
| | - Endurance Toro
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Ruiz
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter P Ruvolo
- Department of Molecular Hematology and Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James W Lillard
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, University Medical Center Groningen, Groningen, the Netherlands
| | - Jan A Burger
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Wierda
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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13
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Biran A, Yin S, Kretzmer H, Ten Hacken E, Parvin S, Lucas F, Uduman M, Gutierrez C, Dangle N, Billington L, Regis FF, Rassenti LZ, Mohammad A, Hoffmann GB, Stevenson K, Zheng M, Witten E, Fernandes SM, Tausch E, Sun C, Stilgenbauer S, Brown JR, Kipps TJ, Aster JC, Gnirke A, Neuberg DS, Letai A, Wang L, Carrasco RD, Meissner A, Wu CJ. Activation of Notch and Myc Signaling via B-cell-Restricted Depletion of Dnmt3a Generates a Consistent Murine Model of Chronic Lymphocytic Leukemia. Cancer Res 2021; 81:6117-6130. [PMID: 34686499 PMCID: PMC8678341 DOI: 10.1158/0008-5472.can-21-1273] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/18/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by disordered DNA methylation, suggesting these epigenetic changes might play a critical role in disease onset and progression. The methyltransferase DNMT3A is a key regulator of DNA methylation. Although DNMT3A somatic mutations in CLL are rare, we found that low DNMT3A expression is associated with more aggressive disease. A conditional knockout mouse model showed that homozygous depletion of Dnmt3a from B cells results in the development of CLL with 100% penetrance at a median age of onset of 5.3 months, and heterozygous Dnmt3a depletion yields a disease penetrance of 89% with a median onset at 18.5 months, confirming its role as a haploinsufficient tumor suppressor. B1a cells were confirmed as the cell of origin of disease in this model, and Dnmt3a depletion resulted in focal hypomethylation and activation of Notch and Myc signaling. Amplification of chromosome 15 containing the Myc gene was detected in all CLL mice tested, and infiltration of high-Myc-expressing CLL cells in the spleen was observed. Notably, hyperactivation of Notch and Myc signaling was exclusively observed in the Dnmt3a CLL mice, but not in three other CLL mouse models tested (Sf3b1-Atm, Ikzf3, and MDR), and Dnmt3a-depleted CLL were sensitive to pharmacologic inhibition of Notch signaling in vitro and in vivo. Consistent with these findings, human CLL samples with lower DNMT3A expression were more sensitive to Notch inhibition than those with higher DNMT3A expression. Altogether, these results suggest that Dnmt3a depletion induces CLL that is highly dependent on activation of Notch and Myc signaling. SIGNIFICANCE: Loss of DNMT3A expression is a driving event in CLL and is associated with aggressive disease, activation of Notch and Myc signaling, and enhanced sensitivity to Notch inhibition.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Proliferation
- DNA Methyltransferase 3A/genetics
- DNA Methyltransferase 3A/metabolism
- DNA Methyltransferase 3A/physiology
- Daptomycin/pharmacology
- Disease Models, Animal
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Mice
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Prognosis
- Proto-Oncogene Proteins c-myc/genetics
- Proto-Oncogene Proteins c-myc/metabolism
- RNA-Seq
- Receptors, Notch/antagonists & inhibitors
- Receptors, Notch/genetics
- Receptors, Notch/metabolism
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Anat Biran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Elisa Ten Hacken
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Salma Parvin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mohamed Uduman
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Nathan Dangle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Leah Billington
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Fara Faye Regis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laura Z Rassenti
- Moores Cancer Center, University of California San Diego Health, La Jolla, California
| | - Arman Mohammad
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Kristen Stevenson
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mei Zheng
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Witten
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Thomas J Kipps
- Moores Cancer Center, University of California San Diego Health, La Jolla, California
| | - John C Aster
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andreas Gnirke
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Comprehensive Cancer Center, Monrovia, California
| | - Ruben D Carrasco
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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14
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Cuesta-Mateos C, Terrón F, Herling M. CCR7 in Blood Cancers - Review of Its Pathophysiological Roles and the Potential as a Therapeutic Target. Front Oncol 2021; 11:736758. [PMID: 34778050 PMCID: PMC8589249 DOI: 10.3389/fonc.2021.736758] [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: 07/05/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Abstract
According to the classical paradigm, CCR7 is a homing chemokine receptor that grants normal lymphocytes access to secondary lymphoid tissues such as lymph nodes or spleen. As such, in most lymphoproliferative disorders, CCR7 expression correlates with nodal or spleen involvement. Nonetheless, recent evidence suggests that CCR7 is more than a facilitator of lymphatic spread of tumor cells. Here, we review published data to catalogue CCR7 expression across blood cancers and appraise which classical and novel roles are attributed to this receptor in the pathogenesis of specific hematologic neoplasms. We outline why novel therapeutic strategies targeting CCR7 might provide clinical benefits to patients with CCR7-positive hematopoietic tumors.
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Affiliation(s)
- Carlos Cuesta-Mateos
- Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria- Instituto la Princesa (IIS-IP), Madrid, Spain.,Immunological and Medicinal Products (IMMED S.L.), Madrid, Spain.,Catapult Therapeutics BV, Lelystad, Netherlands
| | - Fernando Terrón
- Immunological and Medicinal Products (IMMED S.L.), Madrid, Spain.,Catapult Therapeutics BV, Lelystad, Netherlands
| | - Marco Herling
- Clinic of Hematology and Cellular Therapy, University of Leipzig, Leipzig, Germany
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15
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Duan B, Fu D, Zhang C, Ding P, Dong X, Xia B. Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains. J Am Chem Soc 2021; 143:7688-7697. [PMID: 33983734 DOI: 10.1021/jacs.1c00599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Methylation of DNA at CpG sites is a major mark for epigenetic regulation, but how transcription factors are influenced by CpG methylation is not well understood. Here, we report the molecular mechanisms of how the TCF (T-cell factor) and GEF (glucose transporter 4 enhancer factor) families of proteins selectively target unmethylated DNA sequences with a C-clamp type zinc finger domain. The structure of the C-clamp domain from human GEF family protein HDBP1 (C-clampHDBP1) in complex with DNA was determined using NMR spectroscopy, which adopts a unique zinc finger fold and selectively binds RCCGG (R = A/G) DNA sequences with an "Arg···Trp-Lys-Lys" DNA recognition motif inserted in the major groove. The CpG base pairs are central to the binding due to multiple hydrogen bonds formed with the backbone carbonyl groups of Trp378 and Lys379, as well as the side chain ε-amino groups of Lys379 and Lys380 from C-clampHDBP1. Consequently, methylation of the CpG dinucleotide almost abolishes the binding. Homology modeling reveals that the C-clamp domain from human TCF1E (C-clampTCF1E) binds DNA through essentially the same mechanism, with a similar "Arg···Arg-Lys-Lys" DNA recognition motif. The substitution of tryptophan by arginine makes C-clampHDBP1 prefer RCCGC DNA sequences. The two signature DNA recognition motifs are invariant in the GEF and TCF families of proteins, respectively, from fly to human. The recognition of the CpG dinucleotide through two consecutive backbone carbonyl groups is the same as that of the CXXC type unmethylated CpG DNA binding domains, suggesting a common mechanism shared by unmethylated CpG binding proteins.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dihong Fu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoqun Zhang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianzhi Dong
- Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
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16
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Sana I, Mantione ME, Angelillo P, Muzio M. Role of NFAT in Chronic Lymphocytic Leukemia and Other B-Cell Malignancies. Front Oncol 2021; 11:651057. [PMID: 33869054 PMCID: PMC8047411 DOI: 10.3389/fonc.2021.651057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 12/20/2022] Open
Abstract
In recent years significant progress has been made in the clinical management of chronic lymphocytic leukemia (CLL) as well as other B-cell malignancies; targeting proximal B-cell receptor signaling molecules such as Bruton Tyrosine Kinase (BTK) and Phosphoinositide 3-kinase (PI3Kδ) has emerged as a successful treatment strategy. Unfortunately, a proportion of patients are still not cured with available therapeutic options, thus efforts devoted to studying and identifying new potential druggable targets are warranted. B-cell receptor stimulation triggers a complex cascade of signaling events that eventually drives the activation of downstream transcription factors including Nuclear Factor of Activated T cells (NFAT). In this review, we summarize the literature on the expression and function of NFAT family members in CLL where NFAT is not only overexpressed but also constitutively activated; NFAT controls B-cell anergy and targeting this molecule using specific inhibitors impacts on CLL cell viability. Next, we extend our analysis on other mature B-cell lymphomas where a distinct pattern of expression and activation of NFAT is reported. We discuss the therapeutic potential of strategies aimed at targeting NFAT in B-cell malignancies not overlooking the fact that NFAT may play additional roles regulating the inflammatory microenvironment.
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Affiliation(s)
- Ilenia Sana
- Division of Experimental Oncology, San Raffaele Hospital IRCCS, Milano, Italy
| | | | - Piera Angelillo
- Division of Experimental Oncology, San Raffaele Hospital IRCCS, Milano, Italy.,Lymphoma Unit, Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marta Muzio
- Division of Experimental Oncology, San Raffaele Hospital IRCCS, Milano, Italy
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17
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Cuesta-Mateos C, Brown JR, Terrón F, Muñoz-Calleja C. Of Lymph Nodes and CLL Cells: Deciphering the Role of CCR7 in the Pathogenesis of CLL and Understanding Its Potential as Therapeutic Target. Front Immunol 2021; 12:662866. [PMID: 33841445 PMCID: PMC8024566 DOI: 10.3389/fimmu.2021.662866] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/09/2021] [Indexed: 01/13/2023] Open
Abstract
The lymph node (LN) is an essential tissue for achieving effective immune responses but it is also critical in the pathogenesis of chronic lymphocytic leukemia (CLL). Within the multitude of signaling pathways aberrantly regulated in CLL the homeostatic axis composed by the chemokine receptor CCR7 and its ligands is the main driver for directing immune cells to home into the LN. In this literature review, we address the roles of CCR7 in the pathophysiology of CLL, and how this chemokine receptor is of critical importance to develop more rational and effective therapies for this malignancy.
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Affiliation(s)
- Carlos Cuesta-Mateos
- Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria- Instituto de La Princesa (IIS-IP), Madrid, Spain.,IMMED S.L., Immunological and Medicinal Products, Madrid, Spain.,Catapult Therapeutics BV, Lelystad, Netherlands
| | - Jennifer R Brown
- Chronic Lymphocytic Leukemia (CLL) Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Fernando Terrón
- IMMED S.L., Immunological and Medicinal Products, Madrid, Spain.,Catapult Therapeutics BV, Lelystad, Netherlands
| | - Cecilia Muñoz-Calleja
- Immunology Department, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria- Instituto de La Princesa (IIS-IP), Madrid, Spain.,School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
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18
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Domingo-Relloso A, Huan T, Haack K, Riffo-Campos AL, Levy D, Fallin MD, Terry MB, Zhang Y, Rhoades DA, Herreros-Martinez M, Garcia-Esquinas E, Cole SA, Tellez-Plaza M, Navas-Acien A. DNA methylation and cancer incidence: lymphatic-hematopoietic versus solid cancers in the Strong Heart Study. Clin Epigenetics 2021; 13:43. [PMID: 33632303 PMCID: PMC7908806 DOI: 10.1186/s13148-021-01030-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/14/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Epigenetic alterations may contribute to early detection of cancer. We evaluated the association of blood DNA methylation with lymphatic-hematopoietic cancers and, for comparison, with solid cancers. We also evaluated the predictive ability of DNA methylation for lymphatic-hematopoietic cancers. METHODS Blood DNA methylation was measured using the Illumina Infinium methylationEPIC array in 2324 Strong Heart Study participants (41.4% men, mean age 56 years). 788,368 CpG sites were available for differential DNA methylation analysis for lymphatic-hematopoietic, solid and overall cancers using elastic-net and Cox regression models. We conducted replication in an independent population: the Framingham Heart Study. We also analyzed differential variability and conducted bioinformatic analyses to assess for potential biological mechanisms. RESULTS Over a follow-up of up to 28 years (mean 15), we identified 41 lymphatic-hematopoietic and 394 solid cancer cases. A total of 126 CpGs for lymphatic-hematopoietic cancers, 396 for solid cancers, and 414 for overall cancers were selected as predictors by the elastic-net model. For lymphatic-hematopoietic cancers, the predictive ability (C index) increased from 0.58 to 0.87 when adding these 126 CpGs to the risk factor model in the discovery set. The association was replicated with hazard ratios in the same direction in 28 CpGs in the Framingham Heart Study. When considering the association of variability, rather than mean differences, we found 432 differentially variable regions for lymphatic-hematopoietic cancers. CONCLUSIONS This study suggests that differential methylation and differential variability in blood DNA methylation are associated with lymphatic-hematopoietic cancer risk. DNA methylation data may contribute to early detection of lymphatic-hematopoietic cancers.
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Affiliation(s)
- Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA.
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Melchor Fernandez Almagro Street, 5, Madrid, Spain.
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain.
| | - Tianxiao Huan
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - M Daniele Fallin
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Ying Zhang
- Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma, USA
| | - Dorothy A Rhoades
- Department of Medicine, Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK, USA
| | | | - Esther Garcia-Esquinas
- Universidad Autonoma de Madrid, Madrid, Spain
- CIBERESP (CIBER of Epidemiology and Public Health), Madrid, Spain
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Melchor Fernandez Almagro Street, 5, Madrid, Spain
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA.
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19
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Frenquelli M, Tonon G. WNT Signaling in Hematological Malignancies. Front Oncol 2020; 10:615190. [PMID: 33409156 PMCID: PMC7779757 DOI: 10.3389/fonc.2020.615190] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022] Open
Abstract
The role of the WNT signaling pathway in key cellular processes, such as cell proliferation, differentiation and migration is well documented. WNT signaling cascade is initiated by the interaction of WNT ligands with receptors belonging to the Frizzled family, and/or the ROR1/ROR2 and RYK families. The downstream signaling cascade results in the activation of the canonical β-catenin dependent pathway, ultimately leading to transcriptional control of cell proliferation, or the non-canonical pathway, mainly acting on cell migration and cell polarity. The high level of expression of both WNT ligands and WNT receptors in cancer cells and in the surrounding microenvironment suggests that WNT may represent a central conduit of interactions between tumor cells and microenviroment. In this review we will focus on WNT pathways deregulation in hematological cancers, both at the ligand and receptor levels. We will review available literature regarding both the classical β-catenin dependent pathway as well as the non-canonical pathway, with particular emphasis on the possible exploitation of WNT aberrant activation as a therapeutic target, a notion supported by preclinical data.
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Affiliation(s)
- Michela Frenquelli
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
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20
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Epigenome-wide analysis reveals functional modulators of drug sensitivity and post-treatment survival in chronic lymphocytic leukaemia. Br J Cancer 2020; 124:474-483. [PMID: 33082556 PMCID: PMC7852668 DOI: 10.1038/s41416-020-01117-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/16/2020] [Accepted: 09/25/2020] [Indexed: 11/25/2022] Open
Abstract
Background Chronic lymphocytic leukaemia (CLL) patients display a highly variable clinical course, with progressive acquisition of drug resistance. We sought to identify aberrant epigenetic traits that are enriched following exposure to treatment that could impact patient response to therapy. Methods Epigenome-wide analysis of DNA methylation was performed for 20 patients at two timepoints during treatment. The prognostic significance of differentially methylated regions (DMRs) was assessed in independent cohorts of 139 and 163 patients. Their functional role in drug sensitivity was assessed in vitro. Results We identified 490 DMRs following exposure to therapy, of which 31 were CLL-specific and independent of changes occurring in normal B-cell development. Seventeen DMR-associated genes were identified as differentially expressed following treatment in an independent cohort. Methylation of the HOXA4, MAFB and SLCO3A1 DMRs was associated with post-treatment patient survival, with HOXA4 displaying the strongest association. Re-expression of HOXA4 in cell lines and primary CLL cells significantly increased apoptosis in response to treatment with fludarabine, ibrutinib and idelalisib. Conclusion Our study demonstrates enrichment for multiple CLL-specific epigenetic traits in response to chemotherapy that predict patient outcomes, and particularly implicate epigenetic silencing of HOXA4 in reducing the sensitivity of CLL cells to therapy.
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21
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Hashemi M, Mohammadipour M, Rostami S, Soltanpour MS. Promoter DNA Methylation Frequency and Clinicopathological Role o f miR-129-2 Gene in Patients with Chronic Lymphocytic Leukemia. Oman Med J 2020; 35:e151. [PMID: 32724662 PMCID: PMC7383833 DOI: 10.5001/omj.2020.71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/30/2019] [Indexed: 01/14/2023] Open
Abstract
Objectives Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of apparently mature B-type lymphocytes in the lymphohematopoietic organs. Methylation in promoters of tumor suppressor genes is one of the mechanisms that causes blood malignancy. In this study, we evaluated the promoter DNA methylation status of miR-129-2 tumor suppressor gene and its association with clinical and laboratory parameters of patients with CLL. Methods We studied the promoter DNA methylation frequency of the miR-129-2 gene in 50 patients with CLL and 50 healthy controls using methylation-specific polymerase chain reaction methods. Statistical analysis was performed using SPSS-18 software, and a p-value < 0.050 was considered statistically significant. Results The frequency of promoter DNA methylation of the miR-129-2 gene was significantly higher in the CLL group compared with control group (38.0% vs. 0.0%, p < 0.001; χ2 = 23.457). The promoter DNA methylation frequency of miR-129-2 gene was not significantly different between the two sexes (p = 0.236). A significant but weak correlation was seen between the methylated state of the miR-129-2 gene and organomegaly (p = 0.019, r = 0.330) as well as hemoglobin levels (p = 0.020, r = -0.233). However, binary logistic regression analysis indicated organomegaly as the only clinical biomarker with a statistically significant association with the hypermethylated miR-129-2 gene state (p = 0.046). Conclusions The high frequency of promoter DNA methylation of the miR-129-2 gene in the CLL group compared to the control group, as well as its significant association with organomegaly, suggests the importance of this epigenetic biomarker in the pathogenesis and prognosis of CLL disease.
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Affiliation(s)
- Morteza Hashemi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mahshid Mohammadipour
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Shahrbano Rostami
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Soleiman Soltanpour
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
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22
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Joshi SR, Kitagawa A, Jacob C, Hashimoto R, Dhagia V, Ramesh A, Zheng C, Zhang H, Jordan A, Waddell I, Leopold J, Hu CJ, McMurtry IF, D'Alessandro A, Stenmark KR, Gupte SA. Hypoxic activation of glucose-6-phosphate dehydrogenase controls the expression of genes involved in the pathogenesis of pulmonary hypertension through the regulation of DNA methylation. Am J Physiol Lung Cell Mol Physiol 2020; 318:L773-L786. [PMID: 32159369 PMCID: PMC7191486 DOI: 10.1152/ajplung.00001.2020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is considered important in the pathogenesis of the occlusive vasculopathy observed in pulmonary hypertension (PH). However, the mechanisms that link reprogrammed metabolism to aberrant expression of genes, which modulate functional phenotypes of cells in PH, remain enigmatic. Herein, we demonstrate that, in mice, hypoxia-induced PH was prevented by glucose-6-phosphate dehydrogenase deficiency (G6PDDef), and further show that established severe PH in Cyp2c44-/- mice was attenuated by knockdown with G6PD shRNA or by G6PD inhibition with an inhibitor (N-ethyl-N'-[(3β,5α)-17-oxoandrostan-3-yl]urea, NEOU). Mechanistically, G6PDDef, knockdown and inhibition in lungs: 1) reduced hypoxia-induced changes in cytoplasmic and mitochondrial metabolism, 2) increased expression of Tet methylcytosine dioxygenase 2 (Tet2) gene, and 3) upregulated expression of the coding genes and long noncoding (lnc) RNA Pint, which inhibits cell growth, by hypomethylating the promoter flanking region downstream of the transcription start site. These results suggest functional TET2 is required for G6PD inhibition to increase gene expression and to reverse hypoxia-induced PH in mice. Furthermore, the inhibitor of G6PD activity (NEOU) decreased metabolic reprogramming, upregulated TET2 and lncPINT, and inhibited growth of control and diseased smooth muscle cells isolated from pulmonary arteries of normal individuals and idiopathic-PAH patients, respectively. Collectively, these findings demonstrate a previously unrecognized function for G6PD as a regulator of DNA methylation. These findings further suggest that G6PD acts as a link between reprogrammed metabolism and aberrant gene regulation and plays a crucial role in regulating the phenotype of cells implicated in the pathogenesis of PH, a debilitating disorder with a high mortality rate.
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Affiliation(s)
| | - Atsushi Kitagawa
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Christina Jacob
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Ryota Hashimoto
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Vidhi Dhagia
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Amrit Ramesh
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Connie Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Hui Zhang
- Division of Pediatric Critical Care Medicine, Cardiovascular Pulmonary Research and Developmental Lung Biology Laboratories, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Allan Jordan
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Ian Waddell
- Drug Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Jane Leopold
- Department of Medicine, Division of Cardiology, Brigham Women and Children's Hospital, Harvard School of Medicine, Boston, Massachusetts
| | - Cheng-Jun Hu
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Ivan F McMurtry
- Departments of Pharmacology and Internal Medicine and Center for Lung Biology, University of South Alabama, Mobile, Alabama
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kurt R Stenmark
- Division of Pediatric Critical Care Medicine, Cardiovascular Pulmonary Research and Developmental Lung Biology Laboratories, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sachin A Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York
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23
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Novel genes exhibiting DNA methylation alterations in Korean patients with chronic lymphocytic leukaemia: a methyl-CpG-binding domain sequencing study. Sci Rep 2020; 10:1085. [PMID: 31974418 PMCID: PMC6978354 DOI: 10.1038/s41598-020-57919-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023] Open
Abstract
Chronic lymphocytic leukaemia (CLL) exhibits differences between Asians and Caucasians in terms of incidence rate, age at onset, immunophenotype, and genetic profile. We performed genome-wide methylation profiling of CLL in an Asian cohort for the first time. Eight Korean patients without somatic immunoglobulin heavy chain gene hypermutations underwent methyl-CpG-binding domain sequencing (MBD-seq), as did five control subjects. Gene Ontology, pathway analysis, and network-based prioritization of differentially methylated genes were also performed. More regions were hypomethylated (2,062 windows) than were hypermethylated (777 windows). Promoters contained the highest proportion of differentially methylated regions (0.08%), while distal intergenic and intron regions contained the largest number of differentially methylated regions. Protein-coding genes were the most abundant, followed by long noncoding and short noncoding genes. The most significantly over-represented signalling pathways in the differentially methylated gene list included immune/cancer-related pathways and B-cell receptor signalling. Among the top 10 hub genes identified via network-based prioritization, four (UBC, GRB2, CREBBP, and GAB2) had no known relevance to CLL, while the other six (STAT3, PTPN6, SYK, STAT5B, XPO1, and ABL1) have previously been linked to CLL in Caucasians. As such, our analysis identified four novel candidate genes of potential significance to Asian patients with CLL.
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24
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Tsagiopoulou M, Papakonstantinou N, Moysiadis T, Mansouri L, Ljungström V, Duran-Ferrer M, Malousi A, Queirós AC, Plevova K, Bhoi S, Kollia P, Oscier D, Anagnostopoulos A, Trentin L, Ritgen M, Pospisilova S, Stavroyianni N, Ghia P, Martin-Subero JI, Pott C, Rosenquist R, Stamatopoulos K. DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy. Clin Epigenetics 2019; 11:177. [PMID: 31791414 PMCID: PMC6889736 DOI: 10.1186/s13148-019-0783-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/19/2019] [Indexed: 01/01/2023] Open
Abstract
Background In order to gain insight into the contribution of DNA methylation to disease progression of chronic lymphocytic leukemia (CLL), using 450K Illumina arrays, we determined the DNA methylation profiles in paired pre-treatment/relapse samples from 34 CLL patients treated with chemoimmunotherapy, mostly (n = 31) with the fludarabine-cyclophosphamide-rituximab (FCR) regimen. Results The extent of identified changes in CLL cells versus memory B cells from healthy donors was termed “epigenetic burden” (EB) whereas the number of changes between the pre-treatment versus the relapse sample was termed “relapse changes” (RC). Significant (p < 0.05) associations were identified between (i) high EB and short time-to-first-treatment (TTFT); and, (ii) few RCs and short time-to-relapse. Both the EB and the RC clustered in specific genomic regions and chromatin states, including regulatory regions containing binding sites of transcription factors implicated in B cell and CLL biology. Conclusions Overall, we show that DNA methylation in CLL follows different dynamics in response to chemoimmunotherapy. These epigenetic alterations were linked with specific clinical and biological features.
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Affiliation(s)
- Maria Tsagiopoulou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece.,Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Andigoni Malousi
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ana C Queirós
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain
| | - Karla Plevova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sujata Bhoi
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Panagoula Kollia
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padua, Italy
| | - Matthias Ritgen
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Medical Faculty of Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Jose I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, 6th km Charilaou-Thermi Rd, 57001, Thermi, Thessaloniki, GR, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
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25
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Jeong SJ, Lee KH, Nam AR, Cho JY. Genome-Wide Methylation Profiling in Canine Mammary Tumor Reveals miRNA Candidates Associated with Human Breast Cancer. Cancers (Basel) 2019; 11:E1466. [PMID: 31569550 PMCID: PMC6827104 DOI: 10.3390/cancers11101466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/27/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-wide methylation profiling is used in breast cancer (BC) studies, because DNA methylation is a crucial epigenetic regulator of gene expression, involved in many diseases including BC. We investigated genome-wide methylation profiles in both canine mammary tumor (CMT) tissues and peripheral blood mononuclear cells (PBMCs) using reduced representation bisulfite sequencing (RRBS) and found unique CMT-enriched methylation signatures. A total of 2.2-4.2 million cytosine-phosphate-guanine (CpG) sites were analyzed in both CMT tissues and PBMCs, which included 40,000 and 28,000 differentially methylated regions (DMRs) associated with 341 and 247 promoters of differentially methylated genes (DMGs) in CMT tissues and PBMCs, respectively. Genes related to apoptosis and ion transmembrane transport were hypermethylated, but cell proliferation and oncogene were hypomethylated in tumor tissues. Gene ontology analysis using DMGs in PBMCs revealed significant methylation changes in the subset of immune cells and host defense system-related genes, especially chemokine signaling pathway-related genes. Moreover, a number of CMT tissue-enriched DMRs were identified from the promoter regions of various microRNAs (miRNAs), including cfa-mir-96 and cfa-mir-149, which were reported as cancer-associated miRNAs in humans. We also identified novel miRNAs associated with CMT which can be candidates for new miRNAs associated with human BC. This study may provide new insight for a better understanding of aberrant methylation associated with both human BC and CMT, as well as possible targets for methylation-based BC diagnostic markers.
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Affiliation(s)
- Su-Jin Jeong
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
| | - A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.
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26
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Dunbar F, Xu H, Ryu D, Ghosh S, Shi H, George V. Detection of Differentially Methylated Regions Using Bayes Factor for Ordinal Group Responses. Genes (Basel) 2019; 10:genes10090721. [PMID: 31533352 PMCID: PMC6770971 DOI: 10.3390/genes10090721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 11/16/2022] Open
Abstract
Researchers in genomics are increasingly interested in epigenetic factors such as DNA methylation, because they play an important role in regulating gene expression without changes in the DNA sequence. There have been significant advances in developing statistical methods to detect differentially methylated regions (DMRs) associated with binary disease status. Most of these methods are being developed for detecting differential methylation rates between cases and controls. We consider multiple severity levels of disease, and develop a Bayesian statistical method to detect the region with increasing (or decreasing) methylation rates as the disease severity increases. Patients are classified into more than two groups, based on the disease severity (e.g., stages of cancer), and DMRs are detected by using moving windows along the genome. Within each window, the Bayes factor is calculated to test the hypothesis of monotonic increase in methylation rates corresponding to severity of the disease versus no difference. A mixed-effect model is used to incorporate the correlation of methylation rates of nearby CpG sites in the region. Results from extensive simulation indicate that our proposed method is statistically valid and reasonably powerful. We demonstrate our approach on a bisulfite sequencing dataset from a chronic lymphocytic leukemia (CLL) study.
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Affiliation(s)
- Fengjiao Dunbar
- Genomics Research Center, AbbVie, North Chicago, IL 60064, USA.
| | - Hongyan Xu
- Department of Population Health Sciences, Augusta University, Augusta, GA 30912, USA.
| | - Duchwan Ryu
- Department of Statistics and Actuarial Science, Northern Illinois University, DeKalb, IL 60178, USA.
| | - Santu Ghosh
- Department of Population Health Sciences, Augusta University, Augusta, GA 30912, USA.
| | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA.
| | - Varghese George
- Department of Population Health Sciences, Augusta University, Augusta, GA 30912, USA.
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27
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Computational Methods for Detection of Differentially Methylated Regions Using Kernel Distance and Scan Statistics. Genes (Basel) 2019; 10:genes10040298. [PMID: 31013791 PMCID: PMC6523914 DOI: 10.3390/genes10040298] [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] [Received: 02/28/2019] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 01/14/2023] Open
Abstract
MOTIVATION Researchers in genomics are increasingly interested in epigenetic factors such as DNA methylation because they play an important role in regulating gene expression without changes in the sequence of DNA. Abnormal DNA methylation is associated with many human diseases. RESULTS We propose two different approaches to test for differentially methylated regions (DMRs) associated with complex traits, while accounting for correlations among CpG sites in the DMRs. The first approach is a nonparametric method using a kernel distance statistic and the second one is a likelihood-based method using a binomial spatial scan statistic. The kernel distance method uses the kernel function, while the binomial scan statistic approach uses a mixed-effects model to incorporate correlations among CpG sites. Extensive simulations show that both approaches have excellent control of type I error, and both have reasonable statistical power. The binomial scan statistic approach appears to have higher power, while the kernel distance method is computationally faster. The proposed methods are demonstrated using data from a chronic lymphocytic leukemia (CLL) study.
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28
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Lin S, Liu Y, Goldin LR, Lyu C, Kong X, Zhang Y, Caporaso NE, Xiang S, Gao Y. Sex-related DNA methylation differences in B cell chronic lymphocytic leukemia. Biol Sex Differ 2019; 10:2. [PMID: 30616686 PMCID: PMC6322323 DOI: 10.1186/s13293-018-0213-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/04/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Men are at higher risk of developing chronic lymphocytic leukemia (CLL) than women. DNA methylation has been shown to play important roles in a number of cancers. There are differences in the DNA methylation pattern between men and women. In this study, we investigated whether this contributes to the sex-related difference of B cell CLL risk. METHODS Using the HumanMethylation450 BeadChip, we profiled the genome-wide DNA methylation pattern of CD19+ B cells from 48 CLL patients (29 female patients and 19 male patients) and 28 healthy people (19 women and 9 men). RESULTS We identified 1043 sex-related differentially methylated positions (DMPs) related to CLL, 56 of which are located on autosomes and 987 on the X chromosome. Using published B cell RNA-sequencing data, we found 18 genes covered by the DMPs also have different expression levels in male and female CLL patients. Among them, TRIB1, an autosome gene, has been shown to promote tumor growth by suppressing apoptosis. CONCLUSIONS Our study represents the first epigenome-wide association study (EWAS) that investigates the sex-related differences in cancer, and indicated that DNA methylation differences might contribute to the sex-related difference in CLL risk.
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Affiliation(s)
- Shuchun Lin
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yun Liu
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lynn R Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health-Bloomington, Indiana University, Bloomington, IN, USA
| | - Xiangyin Kong
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong Province, China
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Song Xiang
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying Gao
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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29
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Liu G, Liu B, Zheng S, Dong K, Dong R. Aberrant RASSF5 gene transcribed region hypermethylation in pediatric hepatoblastomas. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:3612-3617. [PMID: 31949741 PMCID: PMC6962826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/18/2018] [Indexed: 06/10/2023]
Abstract
BACKGROUND Aberrant DNA methylation plays an important role in cancer and has been recognized to contribute to the activity of oncogenes and inactivity of tumor suppressor genes. RAS association domain family (RASSF) members have been shown to be epigenetically silenced by promoter methylation in cancers, including hepatoblastoma. METHODS We assessed the methylation patterns in the gene of RASSF5 from hepatoblastoma tissue samples harvested from patients using high-throughput mass spectrometry on a matrix-assisted laser desorption/ionization time-of-flight mass array. RESULTS Hypermethylation was found in the RASSF5 gene transcribed regionand was correlated with downregulation of RASSF5 RNA expression levels in the hepatoblastoma samples. CONCLUSIONS The results indicate that aberrant methylation of RASSF5 may contribute to its downregulated mRNA expression in hepatoblastoma.
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Affiliation(s)
- Gongbao Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, Key Laboratory of Neonatal Disease, Ministry of Health 399 Wan Yuan Road, Shanghai 201102, China
| | - Baihui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, Key Laboratory of Neonatal Disease, Ministry of Health 399 Wan Yuan Road, Shanghai 201102, China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, Key Laboratory of Neonatal Disease, Ministry of Health 399 Wan Yuan Road, Shanghai 201102, China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, Key Laboratory of Neonatal Disease, Ministry of Health 399 Wan Yuan Road, Shanghai 201102, China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, Key Laboratory of Neonatal Disease, Ministry of Health 399 Wan Yuan Road, Shanghai 201102, China
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30
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Nair SS, Luu PL, Qu W, Maddugoda M, Huschtscha L, Reddel R, Chenevix-Trench G, Toso M, Kench JG, Horvath LG, Hayes VM, Stricker PD, Hughes TP, White DL, Rasko JEJ, Wong JJL, Clark SJ. Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten. Epigenetics Chromatin 2018; 11:24. [PMID: 29807544 PMCID: PMC5971424 DOI: 10.1186/s13072-018-0194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 12/24/2022] Open
Abstract
Background Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. Results In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16–20× genome-wide coverage per single lane of HiSeq X Ten, HCS 3.3.76. To process and analyse the data, we developed a WGBS pipeline (METH10X) that is fast and can call SNPs. We performed WGBS on both high-quality intact DNA and degraded DNA from formalin-fixed paraffin-embedded tissue. First, we compared different library preparation methods on the HiSeq 2500 platform to identify the best method for sequencing on the HiSeq X Ten. Second, we optimised the PhiX and genome spike-ins to achieve higher quality and coverage of WGBS data on the HiSeq X Ten. Third, we performed integrated whole genome sequencing (WGS) and WGBS of the same DNA sample in a single lane of HiSeq X Ten to improve data output. Finally, we compared methylation data from the HiSeq 2500 and HiSeq X Ten and found high concordance (Pearson r > 0.9×). Conclusions Together we provide a systematic, efficient and complete approach to perform and analyse WGBS on the HiSeq X Ten. Our protocol allows for large-scale WGBS studies at reasonable processing time and cost on the HiSeq X Ten platform. Electronic supplementary material The online version of this article (10.1186/s13072-018-0194-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shalima S Nair
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Phuc-Loi Luu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Wenjia Qu
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Madhavi Maddugoda
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia
| | - Lily Huschtscha
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Roger Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | | | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Lisa G Horvath
- Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia.,Clinical Prostate Cancer Research, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Chris O'Brien Lifehouse, Camperdown, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia.,Central Clinical School, Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
| | - Phillip D Stricker
- Department of Urology, St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia.,Department of Haematology, SA Pathology, Adelaide, SA, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia.,Australian Leukaemia and Lymphoma Group, Melbourne, Australia.,Faculty of Health Science and Faculty of Science, University of Adelaide, Adelaide, SA, Australia.,Australian Genomic Health Alliance, Melbourne, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - Justin J-L Wong
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, UNSW, Sydney, NSW, 2010, Australia. .,Epigenetics Research Program, The Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, NSW, 2010, Australia.
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Yassi M, Shams Davodly E, Mojtabanezhad Shariatpanahi A, Heidari M, Dayyani M, Heravi-Moussavi A, Moattar MH, Kerachian MA. DMRFusion: A differentially methylated region detection tool based on the ranked fusion method. Genomics 2018; 110:366-374. [PMID: 29309841 DOI: 10.1016/j.ygeno.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/05/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
Abstract
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylation analysis of DMRs on methylation sequencing data. This tool is designed base on the integration of several ranking methods; Information gain, Between versus within Class scatter ratio, Fisher ratio, Z-score and Welch's t-test. In this study, DMRFusion on reduced representation bisulfite sequencing (RRBS) data in chronic lymphocytic leukemia cancer displayed 30 nominated regions and CpG sites with a maximum methylation difference detected in the hypermethylation DMRs. We realized that DMRFusion is able to process methylation sequencing data in an efficient and accurate manner and to provide annotation and visualization for DMRs with high fold difference score (p-value and FDR<0.05 and type I error: 0.04).
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Affiliation(s)
- Maryam Yassi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Ehsan Shams Davodly
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | | | - Mehdi Heidari
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Mahdieh Dayyani
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Mohammad Amin Kerachian
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran; Cancer Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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32
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Janovská P, Bryja V. Wnt signalling pathways in chronic lymphocytic leukaemia and B-cell lymphomas. Br J Pharmacol 2017; 174:4701-4715. [PMID: 28703283 PMCID: PMC5727250 DOI: 10.1111/bph.13949] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
In this review, we discuss the intricate roles of the Wnt signalling network in the development and progression of mature B-cell-derived haematological malignancies, with a focus on chronic lymphocytic leukaemia (CLL) and related B-cell lymphomas. We review the current literature and highlight the differences between the β-catenin-dependent and -independent branches of Wnt signalling. Special attention is paid to the role of the non-canonical Wnt/planar cell polarity (PCP) pathway, mediated by the Wnt-5-receptor tyrosine kinase-like orphan receptor (ROR1)-Dishevelled signalling axis in CLL. This is mainly because the Wnt/PCP co-receptor ROR1 was found to be overexpressed in CLL and the Wnt/PCP pathway contributes to numerous aspects of CLL pathogenesis. We also discuss the possibilities of therapeutically targeting the Wnt signalling pathways as an approach to disrupt the crucial interaction between malignant cells and their micro-environment. We also advocate the need for research in this direction for other lymphomas, namely, diffuse large B-cell lymphoma, Hodgkin lymphoma, mantle cell lymphoma, Burkitt lymphoma and follicular lymphoma where the Wnt signalling pathway probably plays a similar role. LINKED ARTICLES This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
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Affiliation(s)
- Pavlína Janovská
- Institute of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Vítězslav Bryja
- Institute of Experimental Biology, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
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33
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Wolf C, Garding A, Filarsky K, Bahlo J, Robrecht S, Becker N, Zucknick M, Rouhi A, Weigel A, Claus R, Weichenhan D, Eichhorst B, Fischer K, Hallek M, Kuchenbauer F, Plass C, Döhner H, Stilgenbauer S, Lichter P, Mertens D. NFATC1 activation by DNA hypomethylation in chronic lymphocytic leukemia correlates with clinical staging and can be inhibited by ibrutinib. Int J Cancer 2017; 142:322-333. [PMID: 28921505 DOI: 10.1002/ijc.31057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/31/2017] [Indexed: 12/22/2022]
Abstract
B cell receptor (BCR) signaling is a key for survival of chronic lymphocytic leukemia (CLL) cells, and BCR signaling inhibitors are clinically active. However, relapse and resistance to treatment require novel treatment options. To detect novel candidate therapeutic targets, we performed a genome-wide DNA methylation screen with custom arrays and identified aberrant promoter DNA methylation in 2,192 genes. The transcription factor NFATC1 that is a downstream effector of BCR signaling was among the top hypomethylated genes and was concomitantly transcriptionally upregulated in CLL. Intriguingly, NFATC1 promoter DNA hypomethylation levels were significantly variant in clinical trial cohorts from different disease progression stages and furthermore correlated with Binet disease staging and thymidine kinase levels, strongly suggesting a central role of NFATC1 in CLL development. Functionally, DNA hypomethylation at NFATC1 promoter inversely correlated with RNA levels of NFATC1 and dysregulation correlated with expression of target genes BCL-2, CCND1 and CCR7. The inhibition of the NFAT regulator calcineurin with tacrolimus and cyclosporin A and the BCR signaling inhibitor ibrutinib significantly reduced NFAT activity in leukemic cell lines, and NFAT inhibition resulted in increased apoptosis of primary CLL cells. In summary, our results indicate that the aberrant activation of NFATC1 by DNA hypomethylation and BCR signaling plays a major role in the pathomechanism of CLL.
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Affiliation(s)
- Christine Wolf
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Garding
- Signaling to Chromatin Laboratory, Institute of Molecular Biology, Mainz, Germany
| | - Katharina Filarsky
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jasmin Bahlo
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Sandra Robrecht
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Natalia Becker
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Zucknick
- Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Arefeh Rouhi
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Anja Weigel
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | - Rainer Claus
- Department Medical Clinic II, Klinikum Augsburg, Augsburg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Eichhorst
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Kirsten Fischer
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | - Michael Hallek
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Köln, Germany
| | | | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Mertens
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, University of Ulm, Ulm, Germany
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34
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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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35
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Guo C, Pei L, Xiao X, Wei Q, Chen JK, Ding HF, Huang S, Fan G, Shi H, Dong Z. DNA methylation protects against cisplatin-induced kidney injury by regulating specific genes, including interferon regulatory factor 8. Kidney Int 2017; 92:1194-1205. [PMID: 28709638 DOI: 10.1016/j.kint.2017.03.038] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/23/2017] [Accepted: 03/30/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is an epigenetic mechanism that regulates gene transcription without changing primary nucleotide sequences. In mammals, DNA methylation involves the covalent addition of a methyl group to the 5-carbon position of cytosine by DNA methyltransferases (DNMTs). The change of DNA methylation and its pathological role in acute kidney injury (AKI) remain largely unknown. Here, we analyzed genome-wide DNA methylation during cisplatin-induced AKI by reduced representation bisulfite sequencing. This technique identified 215 differentially methylated regions between the kidneys of control and cisplatin-treated animals. While most of the differentially methylated regions were in the intergenic, intronic, and coding DNA sequences, some were located in the promoter or promoter-regulatory regions of 15 protein-coding genes. To determine the pathological role of DNA methylation, we initially examined the effects of the DNA methylation inhibitor 5-aza-2'-deoxycytidine and showed it increased cisplatin-induced apoptosis in a rat kidney proximal tubular cell line. We further established a kidney proximal tubule-specific DNMT1 (PT-DNMT1) knockout mouse model, which showed more severe AKI during cisplatin treatment than wild-type mice. Finally, interferon regulatory factor 8 (Irf8), a pro-apoptotic factor, was identified as a hypomethylated gene in cisplatin-induced AKI, and this hypomethylation was associated with a marked induction of Irf8. In the rat kidney proximal tubular cells, the knockdown of Irf8 suppressed cisplatin-induced apoptosis, supporting a pro-death role of Irf8 in renal tubular cells. Thus, DNA methylation plays a protective role in cisplatin-induced AKI by regulating specific genes, such as Irf8.
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Affiliation(s)
- Chunyuan Guo
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia 30912, USA
| | - Lirong Pei
- Georgia Cancer Center, Augusta University, Augusta, Georgia 30912, USA
| | - Xiao Xiao
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia 30912, USA
| | - Qingqing Wei
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia 30912, USA
| | - Jian-Kang Chen
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia 30912, USA
| | - Han-Fei Ding
- Georgia Cancer Center, Augusta University, Augusta, Georgia 30912, USA
| | - Shuang Huang
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida 32611, USA
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, California 90095
| | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, Georgia 30912, USA
| | - Zheng Dong
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University and Charlie Norwood VA Medical Center, Augusta, Georgia 30912, USA.
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Rani L, Mathur N, Gupta R, Gogia A, Kaur G, Dhanjal JK, Sundar D, Kumar L, Sharma A. Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia. Clin Epigenetics 2017; 9:57. [PMID: 28572861 PMCID: PMC5450117 DOI: 10.1186/s13148-017-0356-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 05/18/2017] [Indexed: 12/22/2022] Open
Abstract
Background In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers relevant for implementation of personalized medicine. In this study, an attempt has been made to examine and integrate the global DNA methylation changes with gene expression profile and their impact on clinical outcome in early stage CLL patients. Results The integration of DNA methylation profile (n = 14) with the gene expression profile (n = 21) revealed 142 genes as hypermethylated-downregulated and; 62 genes as hypomethylated-upregulated in early stage CLL patients compared to CD19+ B-cells from healthy individuals. The mRNA expression levels of 17 genes identified to be differentially methylated and/or differentially expressed was further examined in early stage CLL patients (n = 93) by quantitative real time PCR (RQ-PCR). Significant differences were observed in the mRNA expression of MEIS1, PMEPA1, SOX7, SPRY1, CDK6, TBX2, and SPRY2 genes in CLL cells as compared to B-cells from healthy individuals. The analysis in the IGHV mutation based categories (Unmutated = 39, Mutated = 54) revealed significantly higher mRNA expression of CRY1 and PAX9 genes in the IGHV unmutated subgroup (p < 0.001). The relative risk of treatment initiation was significantly higher among patients with high expression of CRY1 (RR = 1.91, p = 0.005) or PAX9 (RR = 1.87, p = 0.001). High expression of CRY1 (HR: 3.53, p < 0.001) or PAX9 (HR: 3.14, p < 0.001) gene was significantly associated with shorter time to first treatment. The high expression of PAX9 gene (HR: 3.29, 95% CI 1.172–9.272, p = 0.016) was also predictive of shorter overall survival in CLL. Conclusions The DNA methylation changes associated with mRNA expression of CRY1 and PAX9 genes allow risk stratification of early stage CLL patients. This comprehensive analysis supports the concept that the epigenetic changes along with the altered expression of genes have the potential to predict clinical outcome in early stage CLL patients. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0356-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lata Rani
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Nitin Mathur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Ajay Gogia
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Gurvinder Kaur
- Laboratory Oncology Unit, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Jaspreet Kaur Dhanjal
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory of Advanced Biomedicine (DAILAB), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016 India
| | - Lalit Kumar
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
| | - Atul Sharma
- Department of Medical Oncology, Dr. B.R.A.IRCH, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, 110029 India
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37
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Purroy N, Wu CJ. Coevolution of Leukemia and Host Immune Cells in Chronic Lymphocytic Leukemia. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026740. [PMID: 28096240 DOI: 10.1101/cshperspect.a026740] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cumulative studies on the dissection of changes in driver genetic lesions in cancer across the course of the disease have provided powerful insights into the adaptive mechanisms of tumors in response to the selective pressures of therapy and environmental changes. In particular, the advent of next-generation-sequencing (NGS)-based technologies and its implementation for the large-scale comprehensive analyses of cancers have greatly advanced our understanding of cancer as a complex dynamic system wherein genetically distinct subclones interact and compete during tumor evolution. Aside from genetic evolution arising from interactions intrinsic to the cell subpopulations within tumors, it is increasingly appreciated that reciprocal interactions between the tumor cell and cellular constituents of the microenvironment further exert selective pressures on specific clones that can impact the balance between tumor immunity and immunologic evasion and escape. Herein, we review the evidence supporting these concepts, with a particular focus on chronic lymphocytic leukemia (CLL), a disease that has been highly amenable to genomic interrogation and studies of clonal heterogeneity and evolution. Better knowledge of the basis for immune escape has an important clinical impact on prognostic stratification and on the pursuit of new therapeutic opportunities.
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Affiliation(s)
- Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.,Harvard Medical School, Boston, Massachusetts 02115
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.,Harvard Medical School, Boston, Massachusetts 02115.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115
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38
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Huang D, Ovcharenko I. Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia. BMC Genomics 2017; 18:236. [PMID: 28302063 PMCID: PMC5353786 DOI: 10.1186/s12864-017-3617-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND To understand the changes of gene regulation in carcinogenesis, we explored signals of DNA methylation - a stable epigenetic mark of gene regulatory elements - and designed a computational model to profile loss and gain of regulatory elements (REs) during carcinogenesis. We also utilized sequencing data to analyze the allele frequency of single nucleotide polymorphisms (SNPs) and detected the cancer-associated SNPs, i.e., the SNPs displaying the significant allele frequency difference between cancer and normal samples. RESULTS After applying this model to chronic lymphocytic leukemia (CLL) data, we identified REs differentially activated (dREs) between normal and CLL cells, consisting of 6,802 dREs gained and 4,606 dREs lost in CLL. The identified regulatory perturbations coincide with changes in the expression of target genes. In particular, the genes encoding DNA methyltransferases harbor multiple lost-in-cancer dREs and zero gained-in-cancer dREs, indicating that the damaged regulation of these genes might be one of the key causes of tumor formation. dREs display a significantly elevated density of the genome-wide association study (GWAS) SNPs associated with CLL and CLL-related traits. We observed that most of dRE GWAS SNPs associated with CLL and CLL-related traits (83%) display a significant haplotype association among the identified cancer-associated alleles and the risk alleles that have been reported in GWAS. Also dREs are enriched for the binding sites of the well-established B-cell and CLL transcription factors (TFs) NF-kB, AP2, P53, E2F1, PAX5, and SP1. We also identified CLL-associated SNPs and demonstrated that the mutations at these SNPs change the binding sites of key TFs much more frequently than expected. CONCLUSIONS Through exploring sequencing data measuring DNA methylation, we identified the epigenetic alterations (more specifically, DNA methylation) and genetic mutations along non-coding genomic regions CLL, and demonstrated that these changes play a critical role in carcinogenesis through damaging the regulation of key genes and alternating the binding of key TFs in B and CLL cells.
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Affiliation(s)
- Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
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Noonepalle SK, Gu F, Lee EJ, Choi JH, Han Q, Kim J, Ouzounova M, Shull AY, Pei L, Hsu PY, Kolhe R, Shi F, Choi J, Chiou K, Huang THM, Korkaya H, Deng L, Xin HB, Huang S, Thangaraju M, Sreekumar A, Ambs S, Tang SC, Munn DH, Shi H. Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers. Cancer Immunol Res 2017; 5:330-344. [PMID: 28264810 DOI: 10.1158/2326-6066.cir-16-0182] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/12/2016] [Accepted: 02/28/2017] [Indexed: 12/21/2022]
Abstract
Triple-negative breast cancer (TNBC) cells are modulated in reaction to tumor-infiltrating lymphocytes. However, their specific responses to this immune pressure are unknown. In order to address this question, we first used mRNA sequencing to compare the immunophenotype of the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were cocultured with activated human T cells. Despite similarities in the cytokine-induced immune signatures of the two cell lines, MDA-MD-231 cells were able to transcribe more IDO1 than MCF7 cells. The two cell lines had similar upstream JAK/STAT1 signaling and IDO1 mRNA stability. However, using a series of breast cancer cell lines, IFNγ stimulated IDO1 protein expression and enzymatic activity only in ER-, not ER+, cell lines. Treatment with 5-aza-deoxycytidine reversed the suppression of IDO1 expression in MCF7 cells, suggesting that DNA methylation was potentially involved in IDO1 induction. By analyzing several breast cancer datasets, we discovered subtype-specific mRNA and promoter methylation differences in IDO1, with TNBC/basal subtypes exhibiting lower methylation/higher expression and ER+/luminal subtypes exhibiting higher methylation/lower expression. We confirmed this trend of IDO1 methylation by bisulfite pyrosequencing breast cancer cell lines and an independent cohort of primary breast tumors. Taken together, these findings suggest that IDO1 promoter methylation regulates anti-immune responses in breast cancer subtypes and could be used as a predictive biomarker for IDO1 inhibitor-based immunotherapy. Cancer Immunol Res; 5(4); 330-44. ©2017 AACR.
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Affiliation(s)
- Satish K Noonepalle
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Franklin Gu
- Verna and Marrs Mclean Department of Biochemistry, Baylor College of Medicine, Houston, Texas
| | - Eun-Joon Lee
- Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Jeong-Hyeon Choi
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Biostatistics and Epidemiology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Qimei Han
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Jaejik Kim
- Department of Statistics, Sungkyunkwan University, Seoul, South Korea
| | | | - Austin Y Shull
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lirong Pei
- Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Pei-Yin Hsu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Ravindra Kolhe
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Fang Shi
- Department of Biostatistics and Epidemiology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Jiseok Choi
- Department of Biostatistics and Epidemiology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Katie Chiou
- Department of Biostatistics and Epidemiology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Tim H M Huang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Hasan Korkaya
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Libin Deng
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Hong-Bo Xin
- Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Shuang Huang
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Arun Sreekumar
- Department of Molecular and Cell Biology and Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Dan L. Duncan Cancer Center and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, Texas
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Shou-Ching Tang
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Tianjing Medical University Cancer Institute and Hospital, Ministry of Education, Tianjin, China
| | - David H Munn
- Georgia Cancer Center, Augusta University, Augusta, Georgia.,Department of Pediatrics, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Huidong Shi
- Georgia Cancer Center, Augusta University, Augusta, Georgia. .,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
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Differential NFATc1 Expression in Primary Cutaneous CD4+ Small/Medium-Sized Pleomorphic T-Cell Lymphoma and Other Forms of Cutaneous T-Cell Lymphoma and Pseudolymphoma. Am J Dermatopathol 2017; 39:95-103. [DOI: 10.1097/dad.0000000000000597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Kipps TJ, Stevenson FK, Wu CJ, Croce CM, Packham G, Wierda WG, O'Brien S, Gribben J, Rai K. Chronic lymphocytic leukaemia. Nat Rev Dis Primers 2017; 3:16096. [PMID: 28102226 PMCID: PMC5336551 DOI: 10.1038/nrdp.2016.96] [Citation(s) in RCA: 293] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) is a malignancy of CD5+ B cells that is characterized by the accumulation of small, mature-appearing lymphocytes in the blood, marrow and lymphoid tissues. Signalling via surface immunoglobulin, which constitutes the major part of the B cell receptor, and several genetic alterations play a part in CLL pathogenesis, in addition to interactions between CLL cells and other cell types, such as stromal cells, T cells and nurse-like cells in the lymph nodes. The clinical progression of CLL is heterogeneous and ranges from patients who require treatment soon after diagnosis to others who do not require therapy for many years, if at all. Several factors, including the immunoglobulin heavy-chain variable region gene (IGHV) mutational status, genomic changes, patient age and the presence of comorbidities, should be considered when defining the optimal management strategies, which include chemotherapy, chemoimmunotherapy and/or drugs targeting B cell receptor signalling or inhibitors of apoptosis, such as BCL-2. Research on the biology of CLL has profoundly enhanced our ability to identify patients who are at higher risk for disease progression and our capacity to treat patients with drugs that selectively target distinctive phenotypic or physiological features of CLL. How these and other advances have shaped our current understanding and treatment of patients with CLL is the subject of this Primer.
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Affiliation(s)
- Thomas J Kipps
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Centre, University of California, San Diego, 3855 Health Sciences Drive M/C 0820, La Jolla, California 92093, USA
| | - Freda K Stevenson
- Southampton Cancer Research UK Centre, Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Catherine J Wu
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Carlo M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, Ohio, USA
| | - Graham Packham
- Southampton Cancer Research UK Centre, Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - William G Wierda
- Department of Hematology, MD Anderson Cancer Centre, Houston, Texas, USA
| | - Susan O'Brien
- Division of Hematology, Department of Medicine, University of California, Irvine, California, USA
| | - John Gribben
- Department of Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Kanti Rai
- CLL Research and Treatment Program, Feinstein Institute for Medical Research, Northwell Health, New Hyde Park, New York, USA
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Erratum: Corrigendum: Identification of a 5-Methylcytosine Site that may Regulate C/EBPβ Binding and Determine Tissue-Specific Expression of the BPI Gene in Piglets. Sci Rep 2016; 6:33772. [PMID: 27929030 PMCID: PMC5144098 DOI: 10.1038/srep33772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Targeting HSF1 disrupts HSP90 chaperone function in chronic lymphocytic leukemia. Oncotarget 2016; 6:31767-79. [PMID: 26397138 PMCID: PMC4741638 DOI: 10.18632/oncotarget.5167] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/28/2015] [Indexed: 12/01/2022] Open
Abstract
CLL is a disease characterized by chromosomal deletions, acquired copy number changes and aneuploidy. Recent studies have shown that overexpression of Heat Shock Factor (HSF) 1 in aneuploid tumor cells can overcome deficiencies in heat shock protein (HSP) 90-mediated protein folding and restore protein homeostasis. Interestingly, several independent studies have demonstrated that HSF1 expression and activity also affects the chaperoning of HSP90 kinase clients, although the mechanism underlying this observation is unclear. Here, we determined how HSF1 regulates HSP90 function using CLL as a model system. We report that HSF1 is overexpressed in CLL and treatment with triptolide (a small molecule inhibitor of HSF1) induces apoptosis in cultured and primary CLL B-cells. We demonstrate that knockdown of HSF1 or its inhibition with triptolide results in the reduced association of HSP90 with its kinase co-chaperone cell division cycle 37 (CDC37), leading to the partial depletion of HSP90 client kinases, Bruton's Tyrosine Kinase (BTK), c-RAF and cyclin-dependent kinase 4 (CDK4). Treatment with triptolide or HSF1 knockdown disrupts the cytosolic complex between HSF1, p97, HSP90 and the HSP90 deacetylase- Histone deacetylase 6 (HDAC6). Consequently, HSF1 inhibition results in HSP90 acetylation and abrogation of its chaperone function. Finally, tail vein injection of Mec-1 cells into Rag2−/−IL2Rγc−/− mice followed by treatment with minnelide (a pro-drug of triptolide), reduced leukemia, increased survival and attenuated HSP90-dependent survival signaling in vivo. In conclusion, our study provides a strong rationale to target HSF1 and test the activity of minnelide against human CLL.
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Upchurch GM, Haney SL, Opavsky R. Aberrant Promoter Hypomethylation in CLL: Does It Matter for Disease Development? Front Oncol 2016; 6:182. [PMID: 27563627 PMCID: PMC4980682 DOI: 10.3389/fonc.2016.00182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Over the last 30 years, studies of aberrant DNA methylation in hematologic malignancies have been dominated by the primary focus of understanding promoter hypermethylation. These efforts not only resulted in a better understanding of the basis of epigenetic silencing of tumor suppressor genes but also resulted in approval of hypomethylating agents for the treatment of several malignancies, such as myelodysplastic syndrome and acute myeloid leukemia. Recent advances in global methylation profiling coupled with the use of mouse models suggest that aberrant promoter hypomethylation is also a frequent event in hematologic malignancies, particularly in chronic lymphocytic leukemia (CLL). Promoter hypomethylation affects gene expression and, therefore, may play an important role in disease pathogenesis. Here, we review recent findings and discuss the potential involvement of aberrant promoter hypomethylation in CLL.
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Affiliation(s)
- Garland Michael Upchurch
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, NE , USA
| | - Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center , Omaha, NE , USA
| | - Rene Opavsky
- Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA; Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE, USA
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Ryu D, Xu H, George V, Su S, Wang X, Shi H, Podolsky RH. Differential methylation tests of regulatory regions. Stat Appl Genet Mol Biol 2016; 15:237-51. [PMID: 26982617 DOI: 10.1515/sagmb-2015-0037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Differential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at http://www.augusta.edu/mcg/biostatepi/people/software/gift.html.
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Shull AY, Noonepalle SK, Awan FT, Liu J, Pei L, Bollag RJ, Salman H, Ding Z, Shi H. RPPA-based protein profiling reveals eIF4G overexpression and 4E-BP1 serine 65 phosphorylation as molecular events that correspond with a pro-survival phenotype in chronic lymphocytic leukemia. Oncotarget 2016; 6:14632-45. [PMID: 25999352 PMCID: PMC4546493 DOI: 10.18632/oncotarget.4104] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/08/2015] [Indexed: 12/22/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL), the most common adult leukemia, remains incurable despite advancements in treatment regimens over the past decade. Several expression profile studies have been pursued to better understand CLL pathogenesis. However, these large-scale studies only provide information at the transcriptional level. To better comprehend the differential protein changes that take place in CLL, we performed a reverse-phase protein array (RPPA) analysis using 167 different antibodies on B-cell lysates from 18 CLL patients and 6 normal donors. From our analysis, we discovered an enrichment of protein alterations involved with mRNA translation, specifically upregulation of the translation initiator eIF4G and phosphorylation of the cap-dependent translation inhibitor 4E-BP1 at serine 65. Interestingly, 4E-BP1 phosphorylation occurred independently of AKT phosphorylation, suggesting a disconnect between PI3K/AKT pathway activation and 4E-BP1 phosphorylation. Based on these results, we treated primary CLL samples with NVP-BEZ235, a PI3K/mTOR dual inhibitor, and compared its apoptotic-inducing potential against the BTK inhibitor Ibrutinib and the PI3Kδ inhibitor Idelalisib. We demonstrated that treatment with NVP-BEZ235 caused greater apoptosis, greater apoptotic cleavage of eIF4G, and greater dephosphorylation of 4E-BP1 in primary CLL cells. Taken together, these results highlight the potential dependence of eIF4G overexpression and 4E-BP1 phosphorylation in CLL survival.
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Affiliation(s)
- Austin Y Shull
- Department of Biochemistry & Molecular Biology, Georgia Regents University, Augusta, Georgia, USA.,GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Satish K Noonepalle
- Department of Biochemistry & Molecular Biology, Georgia Regents University, Augusta, Georgia, USA.,GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Farrukh T Awan
- The Ohio State Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Jimei Liu
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Lirong Pei
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
| | - Roni J Bollag
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA.,Department of Pathology, Georgia Regents University, Augusta, Georgia, USA
| | - Huda Salman
- GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA.,Deparment of Medicine, Georgia Regents University, Augusta, Georgia, USA
| | - Zhiyong Ding
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Huidong Shi
- Department of Biochemistry & Molecular Biology, Georgia Regents University, Augusta, Georgia, USA.,GRU Cancer Center, Georgia Regents University, Augusta, Georgia, USA
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Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing. Sci Rep 2016; 6:22138. [PMID: 26912189 PMCID: PMC4766444 DOI: 10.1038/srep22138] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 02/08/2016] [Indexed: 12/16/2022] Open
Abstract
Substantial evidence has shown that DNA methylation regulates the initiation of ovarian and sexual maturation. Here, we investigated the genome-wide profile of DNA methylation in porcine ovaries at single-base resolution using reduced representation bisulfite sequencing. The biological variation was minimal among the three ovarian replicates. We found hypermethylation frequently occurred in regions with low gene abundance, while hypomethylation in regions with high gene abundance. The DNA methylation around transcriptional start sites was negatively correlated with their own CpG content. Additionally, the methylation level in the bodies of genes was higher than that in their 5′ and 3′ flanking regions. The DNA methylation pattern of the low CpG content promoter genes differed obviously from that of the high CpG content promoter genes. The DNA methylation level of the porcine ovary was higher than that of the porcine intestine. Analyses of the genome-wide DNA methylation in porcine ovaries would advance the knowledge and understanding of the porcine ovarian methylome.
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48
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dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. Sci Rep 2016; 6:19340. [PMID: 26777304 PMCID: PMC4726101 DOI: 10.1038/srep19340] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/02/2015] [Indexed: 12/23/2022] Open
Abstract
We have developed a database called dbEM (database of Epigenetic Modifiers) to maintain the genomic information of about 167 epigenetic modifiers/proteins, which are considered as potential cancer targets. In dbEM, modifiers are classified on functional basis and comprise of 48 histone methyl transferases, 33 chromatin remodelers and 31 histone demethylases. dbEM maintains the genomic information like mutations, copy number variation and gene expression in thousands of tumor samples, cancer cell lines and healthy samples. This information is obtained from public resources viz. COSMIC, CCLE and 1000-genome project. Gene essentiality data retrieved from COLT database further highlights the importance of various epigenetic proteins for cancer survival. We have also reported the sequence profiles, tertiary structures and post-translational modifications of these epigenetic proteins in cancer. It also contains information of 54 drug molecules against different epigenetic proteins. A wide range of tools have been integrated in dbEM e.g. Search, BLAST, Alignment and Profile based prediction. In our analysis, we found that epigenetic proteins DNMT3A, HDAC2, KDM6A, and TET2 are highly mutated in variety of cancers. We are confident that dbEM will be very useful in cancer research particularly in the field of epigenetic proteins based cancer therapeutics. This database is available for public at URL: http://crdd.osdd.net/raghava/dbem.
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Wang H, He C, Kushwaha G, Xu D, Qiu J. A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. BMC Bioinformatics 2016; 17 Suppl 1:7. [PMID: 26818685 PMCID: PMC4895387 DOI: 10.1186/s12859-015-0850-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Backgroud DNA methylation is an epigenetic modification that plays important roles on gene regulation. Study of whole-genome bisulfite sequencing and reduced representation bisulfite sequencing brings the availability of DNA methylation at single CpG resolution. The main interest of study on DNA methylation data is to test the methylation difference under two conditions of biological samples. However, the high cost and complexity of this sequencing experiment limits the number of biological replicates, which brings challenges to the development of statistical methods. Results Bayesian modeling is well known to be able to borrow strength across the genome, and hence is a powerful tool for high-dimensional- low-sample- size data. In order to provide accurate identification of methylation loci, especially for low coverage data, we propose a full Bayesian partition model to detect differentially methylated loci under two conditions of scientific study. Since hypo-methylation and hyper-methylation have distinct biological implication, it is desirable to differentiate these two types of differential methylation. The advantage of our Bayesian model is that it can produce one-step output of each locus being either equal-, hypo- or hyper-methylated locus without further post-hoc analysis. An R package named as MethyBayes implementing the proposed full Bayesian partition model will be submitted to the bioconductor website upon publication of the manuscript. Conclusions The proposed full Bayesian partition model outperforms existing methods in terms of power while maintaining a low false discovery rate based on simulation studies and real data analysis including bioinformatics analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0850-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Henan Wang
- Department of Statistics, University of Missouri, Columbia, Missouri, USA.
| | - Chong He
- Department of Statistics, University of Missouri, Columbia, Missouri, USA.
| | - Garima Kushwaha
- Department of Computer Science and Informatics Institute, Columbia, USA.
| | - Dong Xu
- Department of Computer Science and Informatics Institute, Columbia, USA.
| | - Jing Qiu
- Department of Applied Economics and Statistics, University of Delaware, Newark, DE, USA.
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50
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Klein HU, Hebestreit K. An evaluation of methods to test predefined genomic regions for differential methylation in bisulfite sequencing data. Brief Bioinform 2015; 17:796-807. [DOI: 10.1093/bib/bbv095] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Indexed: 12/24/2022] Open
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