301
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Affiliation(s)
- Melvin M. Bonilla
- Department of Biology and Program in Ecology, Evolution and Conservation BiologyUniversity of NevadaRenoNVUSA
- Department of Environmental Health, T.H. Chan School of Public HealthHarvard UniversityBostonMAUSA
| | - Jeanne A. Zeh
- Department of Biology and Program in Ecology, Evolution and Conservation BiologyUniversity of NevadaRenoNVUSA
| | - David W. Zeh
- Department of Biology and Program in Ecology, Evolution and Conservation BiologyUniversity of NevadaRenoNVUSA
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302
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Kulp JL, Mamillapalli R, Taylor HS. Aberrant HOXA10 Methylation in Patients With Common Gynecologic Disorders: Implications for Reproductive Outcomes. Reprod Sci 2016; 23:455-63. [PMID: 26865543 DOI: 10.1177/1933719116630427] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
HomeoboxA10 (HOXA10) is a transcription factor that is crucial for the development and patterning of the uterus during embryogenesis. In the adult endometrium, HOXA10 expression is regulated by steroid hormones and embryonic signals. Expression of sufficient HOXA10 messenger RNA is essential to endometrial receptivity and embryo implantation. Aberrant methylation is believed to alter the expression of HOXA10. Methylation of this gene may be associated with decreased fertility, implantation defects, and/or reproductive wastage seen in certain disease states that affect the female reproductive tract. This study describes the differences in methylation patterns of HOXA10 gene in uterine myomas, endometriosis, uterine septum, Asherman syndrome, or uterine polyps of women undergoing hysteroscopic surgery. In the endometrium of uteri with polyps, submucosal myomas, and intramural myomas, there were CpG sites within the HOXA10 gene that were highly methylated compared to controls. The HOXA10 gene in women with endometriosis was hypomethylated compared to controls. DNA methylation may be a common molecular mechanism that results in reproductive dysfunction seen in gynecologic disease.
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Affiliation(s)
- Jennifer L Kulp
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Ramanaiah Mamillapalli
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
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303
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Nakazawa MS, Eisinger-Mathason TSK, Sadri N, Ochocki JD, Gade TPF, Amin RK, Simon MC. Epigenetic re-expression of HIF-2α suppresses soft tissue sarcoma growth. Nat Commun 2016; 7:10539. [PMID: 26837714 PMCID: PMC4742834 DOI: 10.1038/ncomms10539] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 12/21/2015] [Indexed: 12/17/2022] Open
Abstract
In soft tissue sarcomas (STS), low intratumoural O2 (hypoxia) is a poor prognostic indicator. HIF-1α mediates key transcriptional responses to hypoxia, and promotes STS metastasis; however, the role of the related HIF-2α protein is unknown. Surprisingly, here we show that HIF-2α inhibits high-grade STS cell growth in vivo, as loss of HIF-2α promotes sarcoma proliferation and increases calcium and mTORC1 signalling in undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma. We find that most human STS have lower levels of EPAS1 (the gene encoding HIF-2α) expression relative to normal tissue. Many cancers, including STS, contain altered epigenetics, and our findings define an epigenetic mechanism whereby EPAS1 is silenced during sarcoma progression. The clinically approved HDAC inhibitor Vorinostat specifically increases HIF-2α, but not HIF-1α, accumulation in multiple STS subtypes. Vorinostat inhibits STS tumour growth, an effect ameliorated by HIF-2α deletion, implicating HIF-2α as a biomarker for Vorinostat efficacy in STS.
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Affiliation(s)
- Michael S Nakazawa
- Abramson Family Cancer Research Institute, University of Pennsylvania, BRB II/III Room 456, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - T S Karin Eisinger-Mathason
- Abramson Family Cancer Research Institute, University of Pennsylvania, BRB II/III Room 456, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Navid Sadri
- Abramson Family Cancer Research Institute, University of Pennsylvania, BRB II/III Room 456, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joshua D Ochocki
- Abramson Family Cancer Research Institute, University of Pennsylvania, BRB II/III Room 456, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Terence P F Gade
- Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ruchi K Amin
- Howard Hughes Medical Institute, Philadelphia, Pennsylvania 19104, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania, BRB II/III Room 456, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Howard Hughes Medical Institute, Philadelphia, Pennsylvania 19104, USA
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304
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DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet 2016; 48:253-64. [PMID: 26780610 DOI: 10.1038/ng.3488] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022]
Abstract
Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.
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305
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Yan H, Tian S, Slager SL, Sun Z, Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol 2016; 183:96-109. [PMID: 26721890 DOI: 10.1093/aje/kwv187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/09/2015] [Indexed: 12/12/2022] Open
Abstract
Epigenetic information encoded in covalent modifications of DNA and histone proteins regulates fundamental biological processes through the action of chromatin regulators, transcription factors, and noncoding RNA species. Epigenetic plasticity enables an organism to respond to developmental and environmental signals without genetic changes. However, aberrant epigenetic control plays a key role in pathogenesis of disease. Normal epigenetic states could be disrupted by detrimental mutations and expression alteration of chromatin regulators or by environmental factors. In this primer, we briefly review the epigenetic basis of human disease and discuss how recent discoveries in this field could be translated into clinical diagnosis, prevention, and treatment. We introduce platforms for mapping genome-wide chromatin accessibility, nucleosome occupancy, DNA-binding proteins, and DNA methylation, primarily focusing on the integration of DNA methylation and chromatin immunoprecipitation-sequencing technologies into disease association studies. We highlight practical considerations in applying high-throughput epigenetic assays and formulating analytical strategies. Finally, we summarize current challenges in sample acquisition, experimental procedures, data analysis, and interpretation and make recommendations on further refinement in these areas. Incorporating epigenomic testing into the clinical research arsenal will greatly facilitate our understanding of the epigenetic basis of disease and help identify novel therapeutic targets.
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306
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Polycomb-dependent epigenetic landscape in adult T-cell leukemia. Blood 2016; 127:1790-802. [PMID: 26773042 DOI: 10.1182/blood-2015-08-662593] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/26/2015] [Indexed: 02/08/2023] Open
Abstract
Adult T-cell leukemia-lymphoma (ATL) shows global gene expression alterations that confer cellular characteristics and unfavorable prognosis. However, molecular mechanisms of the sustained expression changes are largely unknown, because there is no study addressing the relationship between landscapes of the gene expression and epigenetic modifications. Here, we analyzed ATL epigenome and integrated it with transcriptome from primary ATL cells and those from corresponding normal CD4(+)T cells to decipher ATL-specific "epigenetic code" that was critical for cell identity. We found that polycomb-repressive complex 2 (PRC2)-mediated trimethylation at histone H3Lys27 (H3K27me3) was significantly and frequently reprogrammed at half of genes in ATL cells. A large proportion of the abnormal gene downregulation was detected at the early stage of disease progression and was explained by H3K27me3 accumulation. The global H3K27me3 alterations involved ATL-specific gene expression changes that included several tumor suppressors, transcription factors, epigenetic modifiers, miRNAs, and developmental genes, suggesting diverse outcomes by the PRC2-dependent hierarchical regulation. Interestingly, a key enzyme, EZH2, was sensitive to promiscuous signaling network including the NF-κB pathway and was functionally affected by human T-cell leukemia virus type I (HTLV-1) Tax. The Tax-dependent immortalized cells showed H3K27me3 reprogramming that was significantly similar to that of ATL cells. Of note, a majority of the epigenetic silencing has occurred in leukemic cells from indolent ATL and also in HTLV-1-infected T cells from asymptomatic HTLV-1 carriers. Because pharmacologic inhibition of EZH2 reversed epigenetic disruption and selectively eliminated leukemic and HTLV-1-infected cells, targeting the epigenetic elements will hold great promise in treatment and prevention of the onset of ATL and HTLV-1-related diseases.
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307
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El-Araby AM, Fouad AA, Hanbal AM, Abdelwahab SM, Qassem OM, El-Araby ME. Epigenetic Pathways of Oncogenic Viruses: Therapeutic Promises. Arch Pharm (Weinheim) 2016; 349:73-90. [PMID: 26754591 DOI: 10.1002/ardp.201500375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/30/2015] [Accepted: 12/04/2015] [Indexed: 01/19/2023]
Abstract
Cancerous transformation comprises different events that are both genetic and epigenetic. The ultimate goal for such events is to maintain cell survival and proliferation. This transformation occurs as a consequence of different features such as environmental and genetic factors, as well as some types of infection. Many viral infections are considered to be causative agents of a number of different malignancies. To convert normal cells into cancerous cells, oncogenic viruses must function at the epigenetic level to communicate with their host cells. Oncogenic viruses encode certain epigenetic factors that lead to the immortality and proliferation of infected cells. The epigenetic effectors produced by oncogenic viruses constitute appealing targets to prevent and treat malignant diseases caused by these viruses. In this review, we highlight the importance of epigenetic reprogramming for virus-induced oncogenesis, with special emphasis on viral epigenetic oncoproteins as therapeutic targets. The discovery of molecular components that target epigenetic pathways, especially viral factors, is also discussed.
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Affiliation(s)
- Amr M El-Araby
- Faculty of Pharmacy, Ain Shams University, Abbasia, Cairo, Egypt
| | | | - Amr M Hanbal
- Faculty of Pharmacy, Ain Shams University, Abbasia, Cairo, Egypt
| | | | - Omar M Qassem
- Faculty of Pharmacy, Ain Shams University, Abbasia, Cairo, Egypt
| | - Moustafa E El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanya, Jeddah, Saudi Arabia.,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Helwan University, Cairo, Egypt
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308
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Huang W, Qi CB, Lv SW, Xie M, Feng YQ, Huang WH, Yuan BF. Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry. Anal Chem 2016; 88:1378-84. [PMID: 26707930 DOI: 10.1021/acs.analchem.5b03962] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA methylation (5-methylcytosine, 5-mC) is the best characterized epigenetic mark that has regulatory roles in diverse biological processes. Recent investigation of RNA modifications also raises the possible functions of RNA adenine and cytosine methylations on gene regulation in the form of "RNA epigenetics." Previous studies demonstrated global DNA hypomethylation in tumor tissues compared to healthy controls. However, DNA and RNA methylation in circulating tumor cells (CTCs) that are derived from tumors are still a mystery due to the lack of proper analytical methods. In this respect, here we established an effective CTCs capture system conjugated with a combined strategy of sample preparation for the captured CTCs lysis, nucleic acids digestion, and nucleosides extraction in one tube. The resulting nucleosides were then further analyzed by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). With the developed method, we are able to detect DNA and RNA methylation (5-methyl-2'-deoxycytidine, 5-methylcytidine, and N(6)-methyladenosine) in a single cell. We then further successfully determined DNA and RNA methylation in CTCs from lung cancer patients. Our results demonstrated, for the first time, a significant decrease of DNA methylation (5-methyl-2'-deoxycytidine) and increase of RNA adenine and cytosine methylations (N(6)-methyladenosine and 5-methylcytidine) in CTCs compared with whole blood cells. The discovery of DNA hypomethylation and RNA hypermethylation in CTCs in the current study together with previous reports of global DNA hypomethylation in tumor tissues suggest that nucleic acid modifications play important roles in the formation and development of cancer cells. This work constitutes the first step for the investigation of DNA and RNA methylation in CTCs, which may facilitate uncovering the metastasis mechanism of cancers in the future.
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Affiliation(s)
- Wei Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Chu-Bo Qi
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China.,Department of Pathology, Hubei Cancer Hospital , Wuhan, Hubei 430079, Peoples' Republic of China
| | - Song-Wei Lv
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Min Xie
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Wei-Hua Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University , Wuhan 430072, Peoples' Republic of China
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309
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Kirchner H, Sinha I, Gao H, Ruby MA, Schönke M, Lindvall JM, Barrès R, Krook A, Näslund E, Dahlman-Wright K, Zierath JR. Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients. Mol Metab 2016; 5:171-183. [PMID: 26977391 PMCID: PMC4770265 DOI: 10.1016/j.molmet.2015.12.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 12/23/2015] [Accepted: 12/27/2015] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE Epigenetic modifications contribute to the etiology of type 2 diabetes. METHOD We performed genome-wide methylome and transcriptome analysis in liver from severely obese men with or without type 2 diabetes and non-obese men to discover aberrant pathways underlying the development of insulin resistance. Results were validated by pyrosequencing. RESULT We identified hypomethylation of genes involved in hepatic glycolysis and insulin resistance, concomitant with increased mRNA expression and protein levels. Pyrosequencing revealed the CpG-site within ATF-motifs was hypomethylated in four of these genes in liver of severely obese non-diabetic and type 2 diabetic patients, suggesting epigenetic regulation of transcription by altered ATF-DNA binding. CONCLUSION Severely obese non-diabetic and type 2 diabetic patients have distinct alterations in the hepatic methylome and transcriptome, with hypomethylation of several genes controlling glucose metabolism within the ATF-motif regulatory site. Obesity appears to shift the epigenetic program of the liver towards increased glycolysis and lipogenesis, which may exacerbate the development of insulin resistance.
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Affiliation(s)
- Henriette Kirchner
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Indranil Sinha
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Hui Gao
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Maxwell A Ruby
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Milena Schönke
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jessica M Lindvall
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Romain Barrès
- Section of Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Anna Krook
- Section of Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Näslund
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Karin Dahlman-Wright
- Department Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; SciLifeLab, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Juleen R Zierath
- Section of Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Section of Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Section of Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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310
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Kano H, Takayama T, Midorikawa Y, Nagase H. Promoter hypomethylation of RAR-related orphan receptor α 1 is correlated with unfavorable clinicopathological features in patients with colorectal cancer. Biosci Trends 2016; 10:202-9. [DOI: 10.5582/bst.2016.01097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Hisao Kano
- Department of Cancer Genetics, Nihon University School of Medicine
- Department of Digestive Surgery, Nihon University School of Medicine
| | | | - Yutaka Midorikawa
- Department of Digestive Surgery, Nihon University School of Medicine
| | - Hiroki Nagase
- Department of Cancer Genetics, Nihon University School of Medicine
- Division of Cancer Genetics, Chiba Cancer Center Research Institute
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311
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Paul DS, Jones A, Sellar RS, Mayor NP, Feber A, Webster AP, Afonso N, Sergeant R, Szydlo RM, Apperley JF, Widschwendter M, Mackinnon S, Marsh SGE, Madrigal JA, Rakyan VK, Peggs KS, Beck S. A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation. Genome Med 2015; 7:128. [PMID: 26669438 PMCID: PMC4681168 DOI: 10.1186/s13073-015-0246-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 11/12/2015] [Indexed: 02/07/2023] Open
Abstract
Background Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication following HSCT. Current diagnostic biomarkers that correlate with aGVHD severity, progression, and therapy response in graft recipients are insufficient. Here, we investigated whether epigenetic marks measured in peripheral blood of healthy graft donors stratify aGVHD severity in human leukocyte antigen (HLA)-matched sibling recipients prior to T cell-depleted HSCT. Methods We measured DNA methylation levels genome-wide at single-nucleotide resolution in peripheral blood of 85 HSCT donors, matched to recipients with various transplant outcomes, with Illumina Infinium HumanMethylation450 BeadChips. Results Using genome-wide DNA methylation profiling, we showed that epigenetic signatures underlying aGVHD severity in recipients correspond to immune pathways relevant to aGVHD etiology. We discovered 31 DNA methylation marks in donors that associated with aGVHD severity status in recipients, and demonstrated strong predictive performance of these markers in internal cross-validation experiments (AUC = 0.98, 95 % CI = 0.96–0.99). We replicated the top-ranked CpG classifier using an alternative, clinical DNA methylation assay (P = 0.039). In an independent cohort of 32 HSCT donors, we demonstrated the utility of the epigenetic classifier in the context of a T cell-replete conditioning regimen (P = 0.050). Conclusions Our findings suggest that epigenetic typing of HSCT donors in a clinical setting may be used in conjunction with HLA genotyping to inform both donor selection and transplantation strategy, with the ultimate aim of improving patient outcome. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0246-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dirk S Paul
- UCL Cancer Institute, University College London, London, UK.
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Rob S Sellar
- UCL Cancer Institute, University College London, London, UK.,Department of Haematology, University College London, University College London Hospital, London, UK
| | - Neema P Mayor
- UCL Cancer Institute, University College London, London, UK.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Andrew Feber
- UCL Cancer Institute, University College London, London, UK
| | - Amy P Webster
- UCL Cancer Institute, University College London, London, UK
| | - Neuza Afonso
- Department of Haematology, University College London, Royal Free Hospital, London, UK
| | - Ruhena Sergeant
- Clinical Immunology, Imperial NHS Trust Hammersmith Hospital, London, UK
| | - Richard M Szydlo
- Centre for Haematology, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK.,Department of Clinical Haematology, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Jane F Apperley
- Centre for Haematology, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK.,Department of Clinical Haematology, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, UK
| | - Stephen Mackinnon
- UCL Cancer Institute, University College London, London, UK.,Department of Haematology, University College London, Royal Free Hospital, London, UK
| | - Steven G E Marsh
- UCL Cancer Institute, University College London, London, UK.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - J Alejandro Madrigal
- UCL Cancer Institute, University College London, London, UK.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Vardhman K Rakyan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Karl S Peggs
- UCL Cancer Institute, University College London, London, UK. .,Department of Haematology, University College London, University College London Hospital, London, UK.
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK.
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312
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Affiliation(s)
- Miguel Vizoso
- a Cancer Epigenetics and Biology Program; Bellvitge Biomedical Research Institute ; Barcelona, Catalonia , Spain
| | - Manel Esteller
- a Cancer Epigenetics and Biology Program; Bellvitge Biomedical Research Institute ; Barcelona, Catalonia , Spain.,b Department of Physiological Sciences II ; School of Medicine; University of Barcelona ; Barcelona, Catalonia , Spain.,c Institucio Catalana de Recerca i Estudis Avançats ; Barcelona, Catalonia , Spain
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313
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Papadopoulou C, Guilbaud G, Schiavone D, Sale JE. Nucleotide Pool Depletion Induces G-Quadruplex-Dependent Perturbation of Gene Expression. Cell Rep 2015; 13:2491-2503. [PMID: 26686635 PMCID: PMC4695339 DOI: 10.1016/j.celrep.2015.11.039] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/28/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022] Open
Abstract
Nucleotide pool imbalance has been proposed to drive genetic instability in cancer. Here, we show that slowing replication forks by depleting nucleotide pools with hydroxyurea (HU) can also give rise to both transient and permanent epigenetic instability of a reporter locus, BU-1, in DT40 cells. HU induces stochastic formation of Bu-1(low) variants in dividing cells, which have lost the H3K4me3 present in untreated cells. This instability is potentiated by an intragenic G quadruplex, which also promotes local H2Ax phosphorylation and transient heterochromatinization. Genome-wide, gene expression changes induced by HU significantly overlap with those resulting from loss of the G4-helicases FANCJ, WRN, and BLM. Thus, the effects of global replication stress induced by nucleotide pool depletion can be focused by local replication impediments caused by G quadruplex formation to induce epigenetic instability and changes in gene expression, a mechanism that may contribute to selectable transcriptional changes in cancer.
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Affiliation(s)
- Charikleia Papadopoulou
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Guillaume Guilbaud
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Davide Schiavone
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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314
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CellMethy: Identification of a focal concordantly methylated pattern of CpGs revealed wide differences between normal and cancer tissues. Sci Rep 2015; 5:18037. [PMID: 26659027 PMCID: PMC4674876 DOI: 10.1038/srep18037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/10/2015] [Indexed: 12/11/2022] Open
Abstract
DNA methylation patterns may serve as a key in determining cell phenotypes and functions. Adjacent CpG patterns may provide insight into methylation functional mechanisms. Some regions display different DNA methylation patterns between normal and cancer tissues, but the same average methylation level. Here, we developed a method (CellMethy) to infer a region in which all CpGs exhibit concordant methylation (CM) and to quantify the extent of CM in the region. Using simulation data, CellMethy showed high performance in discovering the concordant methylation patterns (AUC = 0.89). CellMethy was then applied to RRBS data including 11 normal tissues and 12 tumors. We found that the extent of CM exhibited wider differentials among tissues than did the average methylation levels from the CM regions, with 45% of CM regions occurring specifically in one tissue and mainly in tumors. Then, we identified CM regions through genome wide bisulfite sequencing (GWBS) data on breast cancer. Approximately 82% of CM regions revealed a significantly different extent of CM between cancer and normal tissues. CellMethy can accurately describe concordantly methylated regions, and the results suggest that CM might also serve as a stable marker of cell sub-populations.
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315
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Atrian F, Lelièvre SA. Mining the epigenetic landscape of tissue polarity in search of new targets for cancer therapy. Epigenomics 2015; 7:1313-25. [PMID: 26646365 DOI: 10.2217/epi.15.83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The epigenetic nature of cancer encourages the development of inhibitors of epigenetic pathways. Yet, the clinical use for solid tumors of approved epigenetic drugs is meager. We argue that this situation might improve upon understanding the coinfluence between epigenetic pathways and tissue architecture. We present emerging information on the epigenetic control of the polarity axis, a central feature of epithelial architecture created by the orderly distribution of multiprotein complexes at cell-cell and cell-extracellular matrix contacts and altered upon cancer onset (with apical polarity loss), invasive progression (with basolateral polarity loss) and metastatic development (with basoapical polarity imbalance). This information combined with the impact of polarity-related proteins on epigenetic mechanisms of cancer enables us to envision how to guide the choice of drugs specific for distinct epigenetic modifiers, in order to halt cancer development and counter the consequences of polarity alterations.
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Affiliation(s)
- Farzaneh Atrian
- Department of Basic Medical Sciences and Center for Cancer Research, Purdue University, 625 Harrison Street, Lynn Hall, West Lafayette, IN 47906, USA
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences and Center for Cancer Research, Purdue University, 625 Harrison Street, Lynn Hall, West Lafayette, IN 47906, USA
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316
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Shinjo K, Kondo Y. Targeting cancer epigenetics: Linking basic biology to clinical medicine. Adv Drug Deliv Rev 2015; 95:56-64. [PMID: 26494398 DOI: 10.1016/j.addr.2015.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 02/06/2023]
Abstract
Recent studies provide compelling evidence that epigenetic dysregulation is involved in almost every step of tumor development and progression. Differences in tumor behavior, which ultimately reflects clinical outcome, can be explained by variations in gene expression patterns generated by epigenetic mechanisms, such as DNA methylation. Therefore, epigenetic abnormalities are considered potential biomarkers and therapeutic targets. DNA methylation is stable at certain specific loci in cancer cells and predominantly reflects the characteristic clinicopathological features. Thus, it is an ideal biomarker for cancer screening, classification and prognostic purposes. Epigenetic treatment for cancers is based on the pharmacologic targeting of various core transcriptional programs that sustains cancer cell identity. Therefore, targeting aberrant epigenetic modifiers may be effective for multiple processes compared with using a selective inhibitor of aberrant single signaling pathway. This review provides an overview of the epigenetic alterations in human cancers and discusses about novel therapeutic strategies targeting epigenetic alterations.
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Affiliation(s)
- Keiko Shinjo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Yutaka Kondo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
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317
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Abstract
DNA demethylating agents are approved for some blood malignancies and are under active investigation in solid tumors, but how these drugs work has remained unclear. In this issue of Cell, two groups show that these agents activate a toxic cellular antiviral program through transcriptional activation of endogenous retroviral sequences.
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Affiliation(s)
- Jonathan D Licht
- Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, 303 East Superior Street, Lurie 5-123, Chicago, IL 60611, USA.
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318
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Horning AM, Awe JA, Wang CM, Liu J, Lai Z, Wang VY, Jadhav RR, Louie AD, Lin CL, Kroczak T, Chen Y, Jin VX, Abboud-Werner SL, Leach RJ, Hernandez J, Thompson IM, Saranchuk J, Drachenberg D, Chen CL, Mai S, Huang THM. DNA methylation screening of primary prostate tumors identifies SRD5A2 and CYP11A1 as candidate markers for assessing risk of biochemical recurrence. Prostate 2015; 75:1790-801. [PMID: 26332453 DOI: 10.1002/pros.23052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/02/2015] [Indexed: 01/18/2023]
Abstract
BACKGROUND Altered DNA methylation in CpG islands of gene promoters has been implicated in prostate cancer (PCa) progression and can be used to predict disease outcome. In this study, we determine whether methylation changes of androgen biosynthesis pathway (ABP)-related genes in patients' plasma cell-free DNA (cfDNA) can serve as prognostic markers for biochemical recurrence (BCR). METHODS Methyl-binding domain capture sequencing (MBDCap-seq) was used to identify differentially methylated regions (DMRs) in primary tumors of patients who subsequently developed BCR or not, respectively. Methylation pyrosequencing of candidate loci was validated in cfDNA samples of 86 PCa patients taken at and/or post-radical prostatectomy (RP) using univariate and multivariate prediction analyses. RESULTS Putative DMRs in 13 of 30 ABP-related genes were found between tumors of BCR (n = 12) versus no evidence of disease (NED) (n = 15). In silico analysis of The Cancer Genome Atlas data confirmed increased DNA methylation of two loci-SRD5A2 and CYP11A1, which also correlated with their decreased expression, in tumors with subsequent BCR development. Their aberrant cfDNA methylation was also associated with detectable levels of PSA taken after patients' post-RP. Multivariate analysis of the change in cfDNA methylation at all of CpG sites measured along with patient's treatment history predicted if a patient will develop BCR with 77.5% overall accuracy. CONCLUSIONS Overall, increased DNA methylation of SRD5A2 and CYP11A1 related to androgen biosynthesis functions may play a role in BCR after patients' RP. The correlation between aberrant cfDNA methylation and detectable PSA in post-RP further suggests their utility as predictive markers for PCa recurrence. .
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Affiliation(s)
- Aaron M Horning
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Julius A Awe
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Joseph Liu
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Zhao Lai
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas
| | - Vickie Yao Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Rohit R Jadhav
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Anna D Louie
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Tad Kroczak
- Manitoba Prostate Center, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Yidong Chen
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas
- Department of Epidemiology & Biostatistics, University of Texas Health Science Center, San Antonio, Texas
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
- Department of Epidemiology & Biostatistics, University of Texas Health Science Center, San Antonio, Texas
| | | | - Robin J Leach
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
- Department of Urology, University of Texas Health Science Center, San Antonio, Texas
| | - Javior Hernandez
- Department of Urology, University of Texas Health Science Center, San Antonio, Texas
| | - Ian M Thompson
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
- Department of Urology, University of Texas Health Science Center, San Antonio, Texas
| | - Jeff Saranchuk
- Manitoba Prostate Center, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darrel Drachenberg
- Manitoba Prostate Center, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Sabine Mai
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas
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319
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Moarii M, Boeva V, Vert JP, Reyal F. Changes in correlation between promoter methylation and gene expression in cancer. BMC Genomics 2015; 16:873. [PMID: 26510534 PMCID: PMC4625954 DOI: 10.1186/s12864-015-1994-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/06/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Methylation of high-density CpG regions known as CpG Islands (CGIs) has been widely described as a mechanism associated with gene expression regulation. Aberrant promoter methylation is considered a hallmark of cancer involved in silencing of tumor suppressor genes and activation of oncogenes. However, recent studies have also challenged the simple model of gene expression control by promoter methylation in cancer, and the precise mechanism of and role played by changes in DNA methylation in carcinogenesis remains elusive. RESULTS Using a large dataset of 672 matched cancerous and healthy methylomes, gene expression, and copy number profiles accross 3 types of tissues from The Cancer Genome Atlas (TCGA), we perform a detailed meta-analysis to clarify the interplay between promoter methylation and gene expression in normal and cancer samples. On the one hand, we recover the existence of a CpG island methylator phenotype (CIMP) with prognostic value in a subset of breast, colon and lung cancer samples, where a common subset of promoter CGIs hypomethylated in normal samples become hypermethylated. However, this hypermethylation is not accompanied by a decrease in expression of the corresponding genes, which are already lowly expressed in the normal genes. On the other hand, we identify tissue-specific sets of genes, different between normal and cancer samples, whose inter-individual variation in expression is significantly correlated with the variation in methylation of the 3' flanking regions of the promoter CGIs. These subsets of genes are not the same in the different tissues, nor between normal and cancerous samples, but transcription factors are over-represented in all subsets. CONCLUSION Our results suggest that epigenetic reprogramming in cancer does not contribute to cancer development via direct inhibition of gene expression through promoter hypermethylation. It may instead modify how the expression of a few specific genes, particularly transcription factors, are associated with DNA methylation variations in a tissue-dependent manner.
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Affiliation(s)
- Matahi Moarii
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Valentina Boeva
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Jean-Philippe Vert
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Fabien Reyal
- UMR932, Immunity and Cancer Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France. .,Department of Translational Research, Residual Tumor and Response to Treatment Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France. .,Department of Surgery, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France.
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320
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Peng D, Kryczek I, Nagarsheth N, Zhao L, Wei S, Wang W, Sun Y, Zhao E, Vatan L, Szeliga W, Kotarski J, Tarkowski R, Dou Y, Cho K, Hensley-Alford S, Munkarah A, Liu R, Zou W. Epigenetic silencing of TH1-type chemokines shapes tumour immunity and immunotherapy. Nature 2015; 527:249-53. [PMID: 26503055 PMCID: PMC4779053 DOI: 10.1038/nature15520] [Citation(s) in RCA: 825] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 08/24/2015] [Indexed: 12/14/2022]
Abstract
Epigenetic silencing including histone modifications and DNA methylation is an important tumorigenic mechanism1 However, its role in cancer immunopathology and immunotherapy is poorly understood. Using ovarian cancers as our model, we found that enhancer of zeste homolog 2 (EZH2)-mediated histone H3 lysine 27 trimethylation (H3K27me3) and DNA methyltransferase (DNMT) 1-mediated DNA methylation repress the tumor production of Th1-type chemokines CXCL9 and CXCL10, and subsequently determine effector T cell trafficking to the tumor microenvironment. Treatment with epigenetic modulators removes the repression and increases effector T cell tumor infiltration, slows down tumor progression, and improves therapeutic efficacy of PD-L1 (B7-H1) checkpoint blockade2–4 and adoptive T cell transfusion5 in tumor bearing mice. Moreover, tumor EZH2 and DNMT1 are negatively associated with tumor infiltrating CD8+ T cells and patient outcome. Thus, epigenetic silencing of Th1-type chemokine is a novel tumor immune evasion mechanism. Selective epigenetic reprogramming alters T cell landscape6 in cancer and may enhance clinical efficacy of cancer therapy.
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Affiliation(s)
- Dongjun Peng
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Ilona Kryczek
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA.,Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nisha Nagarsheth
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA.,Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Weimin Wang
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Yuqing Sun
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Ende Zhao
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Linda Vatan
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Wojciech Szeliga
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Jan Kotarski
- The First Department of Gynecologic Oncology and Gynecology, Medical University in Lublin, Lublin 20-081, Poland
| | - Rafał Tarkowski
- The First Department of Gynecologic Oncology and Gynecology, Medical University in Lublin, Lublin 20-081, Poland
| | - Yali Dou
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Kathleen Cho
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA.,The University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sharon Hensley-Alford
- Department of Women's Health Services, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Adnan Munkarah
- Department of Women's Health Services, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Rebecca Liu
- The University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA
| | - Weiping Zou
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan 48109, USA.,Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA.,The University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA.,Graduate Program in Tumor Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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321
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Abstract
Alterations of epigenetic marks are linked to normal development and cellular differentiation as well as to the progression of common chronic diseases. The plasticity of these marks provides potential for disease therapies and prevention strategies. Macro- and micro-nutrients have been shown to modulate disease risk in part via effects on the epigenome. The essential micronutrient selenium affects human health outcomes, e.g., cancers, cardiovascular and autoimmune diseases, via selenoproteins and through a range of biologically active dietary selenocompounds and metabolism products thereof. This review provides an assessment of the current literature regarding epigenetic effects of dietary and synthetic selenocompounds, which include the modulation of marks and editors of epigenetic information and interference with one-carbon metabolism, which provides the methyl donor for DNA methylation. The relevance of a selenium-epigenome interaction for human health is discussed, and we also indicate where future studies will be helpful to gain a deeper understanding of epigenetic effects elicited by selenium.
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Affiliation(s)
- Bodo Speckmann
- a German Institute of Human Nutrition Potsdam-Rehbruecke ; Department of Molecular Toxicology ; Nuthetal , Germany
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322
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Abstract
A wealth of genomic and epigenomic data has identified abnormal regulation of epigenetic processes as a prominent theme in hematologic malignancies. Recurrent somatic alterations in myeloid malignancies of key proteins involved in DNA methylation, post-translational histone modification and chromatin remodeling have highlighted the importance of epigenetic regulation of gene expression in the initiation and maintenance of various malignancies. The rational use of targeted epigenetic therapies requires a thorough understanding of the underlying mechanisms of malignant transformation driven by aberrant epigenetic regulators. In this review we provide an overview of the major protagonists in epigenetic regulation, their aberrant role in myeloid malignancies, prognostic significance and potential for therapeutic targeting.
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Affiliation(s)
- Chun Yew Fong
- Cancer Epigenetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Jessica Morison
- Cancer Epigenetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne
| | - Mark A Dawson
- Cancer Epigenetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
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323
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Hudler P. Challenges of deciphering gastric cancer heterogeneity. World J Gastroenterol 2015; 21:10510-10527. [PMID: 26457012 PMCID: PMC4588074 DOI: 10.3748/wjg.v21.i37.10510] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 06/19/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer is in decline in most developed countries; however, it still accounts for a notable fraction of global mortality and morbidity related to cancer. High-throughput methods are rapidly changing our view and understanding of the molecular basis of gastric carcinogenesis. Today, it is widely accepted that the molecular complexity and heterogeneity, both inter- and intra-tumour, of gastric adenocarcinomas present significant obstacles in elucidating specific biomarkers for early detection of the disease. Although genome-wide sequencing and gene expression studies have revealed the intricate nature of the molecular changes that occur in tumour landscapes, the collected data and results are complex and sometimes contradictory. Several aberrant molecules have already been tested in clinical trials, although their diagnostic and prognostic utilities have not been confirmed thus far. The gold standard for the detection of sporadic gastric cancer is still the gastric endoscopy, which is considered invasive. In addition, genome-wide association studies have confirmed that genetic variations are important contributors to increased cancer risk and could participate in the initiation of malignant transformation. This hypothesis could in part explain the late onset of sporadic gastric cancers. The elaborate interplay of polymorphic low penetrance genes and lifestyle and environmental risk factors requires additional research to decipher their relative impacts on tumorigenesis. The purpose of this article is to present details of the molecular heterogeneity of sporadic gastric cancers at the DNA, RNA, and proteome levels and to discuss issues relevant to the translation of basic research data to clinically valuable tools. The focus of this work is the identification of relevant molecular changes that could be detected non-invasively.
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324
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Beaver JE, Peacor BC, Bain JV, James LI, Waters ML. Contributions of pocket depth and electrostatic interactions to affinity and selectivity of receptors for methylated lysine in water. Org Biomol Chem 2015; 13:3220-6. [PMID: 25437861 DOI: 10.1039/c4ob02231a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dynamic combinatorial chemistry was used to generate a set of receptors for peptides containing methylated lysine (KMen, n = 0-3) and study the contribution of electrostatic effects and pocket depth to binding affinity and selectivity. We found that changing the location of a carboxylate resulted in an increase in preference for KMe2, presumably based on ability to form a salt bridge with KMe2. The number of charged groups on either the receptor or peptide guest systematically varied the binding affinities to all guests by approximately 1-1.5 kcal mol(-1), with little influence on selectivity. Lastly, formation of a deeper pocket led to both increased affinity and selectivity for KMe3 over the lower methylation states. From these studies, we identified that the tightest binder was a receptor with greater net charge, with a Kd of 0.2 μM, and the receptor with the highest selectivity was the one with the deepest pocket, providing 14-fold selectivity between KMe3 and KMe2 and a Kd for KMe3 of 0.3 μM. This work provides key insights into approaches to improve binding affinity and selectivity in water, while also demonstrating the versatility of dynamic combinatorial chemistry for rapidly exploring the impact of subtle changes in receptor functionality on molecular recognition in water.
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Affiliation(s)
- Joshua E Beaver
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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325
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Abstract
DNA methylation plays a significant role in gastric carcinogenesis. The CpG island methylator phenotype (CIMP) characterizes distinct subtypes of gastric cancer (GC) and the relationship between specific methylation patterns and clinicopathological features has been evaluated. Altered DNA methylation is also observed in Helicobacter pylori-infected gastric mucosa, and its potential utility for GC risk estimation has been suggested. The ability to detect small amounts of methylated DNA among tissues allows us to use DNA methylation as a molecular biomarker in GC in a variety of samples, including serum, plasma and gastric washes. The DNA methylation status of nontargeted tissue, particularly blood, has been associated with predisposition to GC. We focus on the recent development of DNA methylation-based biomarkers in GC.
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Affiliation(s)
- Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, 1-98 Dengakugakubo Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Tomiyasu Arisawa
- Department of Gastroenterology, Kanazawa Medical University, Ishikawa, Japan
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326
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Labbé DP, Zadra G, Ebot EM, Mucci LA, Kantoff PW, Loda M, Brown M. Role of diet in prostate cancer: the epigenetic link. Oncogene 2015; 34:4683-91. [PMID: 25531313 PMCID: PMC4476943 DOI: 10.1038/onc.2014.422] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 12/12/2022]
Abstract
Diet is hypothesized to be a critical environmentally related risk factor for prostate cancer (PCa) development, and specific diets and dietary components can also affect PCa progression; however, the mechanisms underlying these associations remain elusive. As for a maturing organism, PCa's epigenome is plastic and evolves from the pre-neoplastic to the metastatic stage. In particular, epigenetic remodeling relies on substrates or cofactors obtained from the diet. Here we review the evidence that bridges dietary modulation to alterations in the prostate epigenome. We propose that such diet-related effects offer a mechanistic link between the impact of different diets and the course of PCa development and progression.
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Affiliation(s)
- D P Labbé
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - G Zadra
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - E M Ebot
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - L A Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - P W Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - M Loda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
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327
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Siegel EM, Berglund AE, Riggs BM, Eschrich SA, Putney RM, Ajidahun AO, Coppola D, Shibata D. Expanding epigenomics to archived FFPE tissues: an evaluation of DNA repair methodologies. Cancer Epidemiol Biomarkers Prev 2015; 23:2622-31. [PMID: 25472669 DOI: 10.1158/1055-9965.epi-14-0464] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Epigenome-wide association studies are emerging in the field of cancer epidemiology with the rapid development of large-scale methylation array platforms. Until recently, these methods were only valid for DNA from flash frozen (FF) tissues. Novel techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissues have emerged; however, a direct comparison of FFPE DNA repair methods before analysis on genome-wide methylation array to matched FF tissues has not been conducted. METHODS We conducted a systematic performance comparison of two DNA repair methods (REPLI-g Ligase vs. Infinium HD Restore Kit) on FFPE-DNA compared with matched FF tissues on the Infinium 450K array. A threshold of discordant methylation between FF-FFPE pairs was set at Δβ > 0.3. The correlations of β-values from FF-FFPE pairs were compared across methods and experimental conditions. RESULTS The Illumina Restore kit outperformed the REPLI-g ligation method with respect to reproducibility of replicates (R(2) > 0.970), highly correlated β-values between FF-FFPE (R(2) > 0.888), and fewest discordant loci between FF-FFPE (≤0.61%). The performance of the Restore kit was validated in an independent set of 121 FFPE tissues. CONCLUSIONS The Restore kit outperformed RELPI-g ligation in restoring FFPE-derived DNA before analysis on the Infinium 450K methylation array. Our findings provide critical guidance that may significantly enhance the breadth of diseases that can be studied by methylomic profiling. IMPACT Epigenomic studies using FFPE tissues should now be considered among cancers that have not been fully characterized from an epigenomic standpoint. These findings promote novel epigenome-wide studies focused on cancer etiology, identification of novel biomarkers, and developing targeted therapies. See all the articles in this CEBP Focus section, "Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology."
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Affiliation(s)
- Erin M Siegel
- Department of Cancer Epidemiology, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Bridget M Riggs
- Department of Cancer Epidemiology, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ryan M Putney
- Department of Biostatistics and Bioinformatics, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Abidemi O Ajidahun
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Domenico Coppola
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - David Shibata
- Department of Cancer Epidemiology, Division of Population Sciences, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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328
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Hlady RA, Tiedemann RL, Puszyk W, Zendejas I, Roberts LR, Choi JH, Liu C, Robertson KD. Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis. Oncotarget 2015; 5:9425-43. [PMID: 25294808 PMCID: PMC4253444 DOI: 10.18632/oncotarget.2444] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the second most common cause of cancer deaths worldwide. Deregulated DNA methylation landscapes are ubiquitous in human cancers. Interpretation of epigenetic aberrations in HCC is confounded by multiple etiologic drivers and underlying cirrhosis. We globally profiled the DNA methylome of 34 normal and 122 liver disease tissues arising in settings of hepatitis B (HBV) or C (HCV) viral infection, alcoholism (EtOH), and other causes to examine how these environmental agents impact DNA methylation in a manner that contributes to liver disease. Our results demonstrate that each 'exposure' leaves unique and overlapping signatures on the methylome. CpGs aberrantly methylated in cirrhosis-HCV and conserved in HCC were enriched for cancer driver genes, suggesting a pathogenic role for HCV-induced methylation changes. Additionally, large genomic regions displaying stepwise hypermethylation or hypomethylation during disease progression were identified. HCC-HCV/EtOH methylomes overlap highly with cryptogenic HCC, suggesting shared epigenetically deregulated pathways for hepatocarcinogenesis. Finally, overlapping methylation abnormalities between primary and cultured tumors unveil conserved epigenetic signatures in HCC. Taken together, this study reveals profound epigenome deregulation in HCC beginning during cirrhosis and influenced by common environmental agents. These results lay the foundation for defining epigenetic drivers and clinically useful methylation markers for HCC.
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Affiliation(s)
- Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Rochelle L Tiedemann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. Cancer Center, Georgia Regents University, Augusta, GA, USA
| | - William Puszyk
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Ivan Zendejas
- Department of Surgery, University of Florida, Gainesville, FL, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | | | - Chen Liu
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
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329
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Rafique S, Thomas JS, Sproul D, Bickmore WA. Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer. Genome Biol 2015; 16:145. [PMID: 26235388 PMCID: PMC4536608 DOI: 10.1186/s13059-015-0719-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/06/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic changes are being increasingly recognized as a prominent feature of cancer. This occurs not only at individual genes, but also over larger chromosomal domains. To investigate this, we set out to identify large chromosomal domains of epigenetic dysregulation in breast cancers. RESULTS We identify large regions of coordinate down-regulation of gene expression, and other regions of coordinate activation, in breast cancers and show that these regions are linked to tumor subtype. In particular we show that a group of coordinately regulated regions are expressed in luminal, estrogen-receptor positive breast tumors and cell lines. For one of these regions of coordinate gene activation, we show that regional epigenetic regulation is accompanied by visible unfolding of large-scale chromatin structure and a repositioning of the region within the nucleus. In MCF7 cells, we show that this depends on the presence of estrogen. CONCLUSIONS Our data suggest that the liganded estrogen receptor is linked to long-range changes in higher-order chromatin organization and epigenetic dysregulation in cancer. This may suggest that as well as drugs targeting histone modifications, it will be valuable to investigate the inhibition of protein complexes involved in chromatin folding in cancer cells.
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Affiliation(s)
- Sehrish Rafique
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Jeremy S Thomas
- Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK. .,Edinburgh Breakthrough Research Unit and Edinburgh Cancer Centre, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, Scotland, EH4 2XU, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
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330
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Discovery of substituted 1,4-dihydroquinolines as novel class of ABCB1 modulators. Bioorg Med Chem 2015; 23:5015-5021. [DOI: 10.1016/j.bmc.2015.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 11/18/2022]
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331
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Yang Z, Jones A, Widschwendter M, Teschendorff AE. An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer. Genome Biol 2015; 16:140. [PMID: 26169266 PMCID: PMC4501092 DOI: 10.1186/s13059-015-0699-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 06/19/2015] [Indexed: 12/20/2022] Open
Abstract
Background One of the most important recent findings in cancer genomics is the identification of novel driver mutations which often target genes that regulate genome-wide chromatin and DNA methylation marks. Little is known, however, as to whether these genes exhibit patterns of epigenomic deregulation that transcend cancer types. Results Here we conduct an integrative pan-cancer-wide analysis of matched RNA-Seq and DNA methylation data across ten different cancer types. We identify seven tumor suppressor and eleven oncogenic epigenetic enzymes which display patterns of deregulation and association with genome-wide cancer DNA methylation patterns, which are largely independent of cancer type. In doing so, we provide evidence that genome-wide cancer hyper- and hypo- DNA methylation patterns are independent processes, controlled by distinct sets of epigenetic enzyme genes. Using causal network modeling, we predict a number of candidate drivers of cancer DNA hypermethylation and hypomethylation. Finally, we show that the genomic loci whose DNA methylation levels associate most strongly with expression of these putative drivers are highly consistent across cancer types. Conclusions This study demonstrates that there exist universal patterns of epigenomic deregulation that transcend cancer types, and that intra-tumor levels of genome-wide DNA hypomethylation and hypermethylation are controlled by distinct processes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0699-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Allison Jones
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Andrew E Teschendorff
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China. .,Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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332
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Hughes D, Andersson DI. Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms. Nat Rev Genet 2015; 16:459-71. [DOI: 10.1038/nrg3922] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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333
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Affiliation(s)
- Lucio Luzzatto
- From the Istituto Toscano Tumori and University of Firenze, Florence, Italy (L.L.); and the Cancer Research Institute and Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston (P.P.P.)
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Abstract
SIGNIFICANCE Epigenetic inactivation of pivotal genes involved in cell growth is a hallmark of human pathologies, in particular cancer. Histone acetylation balance obtained through opposing actions of histone deacetylases (HDACs) and histone acetyltransferases is one epigenetic mechanism controlling gene expression and is, thus, associated with disease etiology and progression. Interfering pharmacologically with HDAC activity can correct abnormalities in cell proliferation, migration, vascularization, and death. RECENT ADVANCES Histone deacetylase inhibitors (HDACi) represent a new class of cytostatic agents that interfere with the function of HDACs and are able to increase gene expression by indirectly inducing histone acetylation. Several HDACi, alone or in combination with DNA-demethylating agents, chemopreventive, or classical chemotherapeutic drugs, are currently being used in clinical trials for solid and hematological malignancies, and are, thus, promising candidates for cancer therapy. CRITICAL ISSUES (i) Non-specific (off-target) HDACi effects due to activities unassociated with HDAC inhibition. (ii) Advantages/disadvantages of non-selective or isoform-directed HDACi. (iii) Limited number of response-predictive biomarkers. (iv) Toxicity leading to dysfunction of critical biological processes. FUTURE DIRECTIONS Selective HDACi could achieve enhanced clinical utility by reducing or eliminating the serious side effects associated with current first-generation non-selective HDACi. Isoform-selective and pan-HDACi candidates might benefit from the identification of biomarkers, enabling better patient stratification and prediction of response to treatment.
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Affiliation(s)
- Rosaria Benedetti
- 1 Department of Biochemistry, Biophysics, and General Pathology, Seconda Università degli Studi di Napoli , Napoli, Italy
| | - Mariarosaria Conte
- 1 Department of Biochemistry, Biophysics, and General Pathology, Seconda Università degli Studi di Napoli , Napoli, Italy
| | - Lucia Altucci
- 1 Department of Biochemistry, Biophysics, and General Pathology, Seconda Università degli Studi di Napoli , Napoli, Italy .,2 Istituto di Genetica e Biofisica "Adriano Buzzati-Traverso," Napoli, Italy
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335
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Vizoso M, Ferreira HJ, Lopez-Serra P, Carmona FJ, Martínez-Cardús A, Girotti MR, Villanueva A, Guil S, Moutinho C, Liz J, Portela A, Heyn H, Moran S, Vidal A, Martinez-Iniesta M, Manzano JL, Fernandez-Figueras MT, Elez E, Muñoz-Couselo E, Botella-Estrada R, Berrocal A, Pontén F, Oord JVD, Gallagher WM, Frederick DT, Flaherty KT, McDermott U, Lorigan P, Marais R, Esteller M. Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR. Nat Med 2015; 21:741-50. [PMID: 26030178 PMCID: PMC4968631 DOI: 10.1038/nm.3863] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/17/2015] [Indexed: 12/11/2022]
Abstract
Metastasis is responsible for most cancer-related deaths, and, among common tumor types, melanoma is one with great potential to metastasize. Here we study the contribution of epigenetic changes to the dissemination process by analyzing the changes that occur at the DNA methylation level between primary cancer cells and metastases. We found a hypomethylation event that reactivates a cryptic transcript of the Rab GTPase activating protein TBC1D16 (TBC1D16-47 kDa; referred to hereafter as TBC1D16-47KD) to be a characteristic feature of the metastatic cascade. This short isoform of TBC1D16 exacerbates melanoma growth and metastasis both in vitro and in vivo. By combining immunoprecipitation and mass spectrometry, we identified RAB5C as a new TBC1D16 target and showed that it regulates EGFR in melanoma cells. We also found that epigenetic reactivation of TBC1D16-47KD is associated with poor clinical outcome in melanoma, while conferring greater sensitivity to BRAF and MEK inhibitors.
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Affiliation(s)
- Miguel Vizoso
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Humberto J Ferreira
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Paula Lopez-Serra
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - F Javier Carmona
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Anna Martínez-Cardús
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Maria Romina Girotti
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester, UK
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Catia Moutinho
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Julia Liz
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Anna Portela
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - August Vidal
- Department of Pathological Anatomy, Bellvitge University Hospital, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Maria Martinez-Iniesta
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Jose L Manzano
- Medical Oncology Service, Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | | | - Elena Elez
- Medical Oncology Service, Vall d'Hebron University Hospital, Barcelona, Catalonia, Spain
| | - Eva Muñoz-Couselo
- Medical Oncology Service, Vall d'Hebron University Hospital, Barcelona, Catalonia, Spain
| | | | | | - Fredrik Pontén
- Department of Pathology, University Hospital of Uppsala, Uppsala, Sweden
| | - Joost van den Oord
- Translational Cell &Tissue Pathology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - William M Gallagher
- University College Dublin School of Biomolecular and Biomedical Science, University College Dublin Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Dennie T Frederick
- Center for Melanoma, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Keith T Flaherty
- Center for Melanoma, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Paul Lorigan
- University of Manchester, Christie National Health Service Foundation Trust, Manchester, UK
| | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester, UK
| | - Manel Esteller
- 1] Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain. [2] Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain. [3] Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
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336
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Eriksson A, Lennartsson A, Lehmann S. Epigenetic aberrations in acute myeloid leukemia: Early key events during leukemogenesis. Exp Hematol 2015; 43:609-24. [PMID: 26118500 DOI: 10.1016/j.exphem.2015.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 12/17/2022]
Abstract
As a result of the introduction of new sequencing technologies, the molecular landscape of acute myeloid leukemia (AML) is rapidly evolving. From karyotyping, which detects only large genomic aberrations of metaphase chromosomes, we have moved into an era when sequencing of each base pair allows us to define the AML genome at highest resolution. This has revealed a new complex landscape of genetic aberrations where addition of mutations in epigenetic regulators has been one of the most important contributions to the understanding of the pathogenesis of AML. These findings, together with new insights into epigenetic mechanisms, have placed dysregulated epigenetic mechanisms at the forefront of AML development. Not only have several new mutations in genes directly involved in epigenetic regulatory mechanisms been discovered, but also previously well-known gene fusions have been found to exert aberrant effects through epigenetic mechanisms. In addition, mutations in epigenetic regulators such as DNMT3A, TET2, and ASXL1 have recently been found to be the earliest known events during AML evolution and to be present as preleukemic lesions before the onset of AML. In this article, we review epigenetic changes in AML also in relation to what is known about their mechanism of action and their prognostic role.
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Affiliation(s)
- Anna Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Centre of Hematology, HERM, Department of Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.
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337
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Paska AV, Hudler P. Aberrant methylation patterns in cancer: a clinical view. Biochem Med (Zagreb) 2015; 25:161-76. [PMID: 26110029 PMCID: PMC4470106 DOI: 10.11613/bm.2015.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/30/2015] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms, such as DNA methylation, DNA hydroxymethylation, post-translational modifications (PTMs) of histone proteins affecting nucleosome remodelling, and regulation by small and large non-coding RNAs (ncRNAs) work in concert with cis and trans acting elements to drive appropriate gene expression. Advances in detection methods and development of dedicated platforms and methylation arrays resulted in an explosion of information on aberrantly methylated sequences linking deviations in epigenetic landscape with the initiation and progression of complex diseases. Here, we consider how DNA methylation changes in malignancies, such as breast, pancreatic, colorectal, and gastric cancer could be exploited for the purpose of developing specific diagnostic tools. DNA methylation changes can be applicable as biomarkers for detection of malignant disease in easily accessible tissues. Methylation signatures are already proving to be an important marker for determination of drug sensitivity. Even more, promoter methylation patterns of some genes, such as MGMT, SHOX2, and SEPT9, have already been translated into commercial clinical assays aiding in patient assessment as adjunct diagnostic tools. In conclusion, the changes in DNA methylation patterns in tumour cells are slowly gaining entrance into routine diagnostic tests as promising biomarkers and as potential therapeutic targets.
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Affiliation(s)
- Alja Videtic Paska
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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338
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Pang B, de Jong J, Qiao X, Wessels LFA, Neefjes J. Chemical profiling of the genome with anti-cancer drugs defines target specificities. Nat Chem Biol 2015; 11:472-80. [PMID: 25961671 DOI: 10.1038/nchembio.1811] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 04/08/2015] [Indexed: 01/05/2023]
Abstract
Many anticancer drugs induce DNA breaks to eliminate tumor cells. The anthracycline topoisomerase II inhibitors additionally cause histone eviction. Here, we performed genome-wide high-resolution mapping of chemotherapeutic effects of various topoisomerase I and II (TopoI and II) inhibitors and integrated this mapping with established maps of genomic or epigenomic features to show their activities in different genomic regions. The TopoI inhibitor topotecan and the TopoII inhibitor etoposide are similar in inducing DNA damage at transcriptionally active genomic regions. The anthracycline daunorubicin induces DNA breaks and evicts histones from active chromatin, thus quenching local DNA damage responses. Another anthracycline, aclarubicin, has a different genomic specificity and evicts histones from H3K27me3-marked heterochromatin, with consequences for diffuse large B-cell lymphoma cells with elevated levels of H3K27me3. Modifying anthracycline structures may yield compounds with selectivity for different genomic regions and activity for different tumor types.
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Affiliation(s)
- Baoxu Pang
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiaohang Qiao
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jacques Neefjes
- 1] Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, the Netherlands. [2] Institute for Chemical Immunology, the Netherlands
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339
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Vaca-Paniagua F, Alvarez-Gomez RM, Maldonado-Martínez HA, Pérez-Plasencia C, Fragoso-Ontiveros V, Lasa-Gonsebatt F, Herrera LA, Cantú D, Bargallo-Rocha E, Mohar A, Durand G, Forey N, Voegele C, Vallée M, Le Calvez-Kelm F, McKay J, Ardin M, Villar S, Zavadil J, Olivier M. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PLoS One 2015; 10:e0126762. [PMID: 25961742 PMCID: PMC4427337 DOI: 10.1371/journal.pone.0126762] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 12/27/2022] Open
Abstract
Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.
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Affiliation(s)
- Felipe Vaca-Paniagua
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Rosa María Alvarez-Gomez
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Carlos Pérez-Plasencia
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | - Veronica Fragoso-Ontiveros
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Luis Alonso Herrera
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - David Cantú
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Enrique Bargallo-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, México D.F., México
| | - Alejandro Mohar
- Departamento de Epidemiología, Instituto Nacional de Cancerología, México D.F., México
| | - Geoffroy Durand
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Forey
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maxime Vallée
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Florence Le Calvez-Kelm
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - James McKay
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maude Ardin
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Stéphanie Villar
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Jiri Zavadil
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Magali Olivier
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
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340
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Solé RV, Valverde S, Rodriguez-Caso C, Sardanyés J. Can a minimal replicating construct be identified as the embodiment of cancer? Bioessays 2015; 36:503-12. [PMID: 24723412 DOI: 10.1002/bies.201300098] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Genomic instability is a hallmark of cancer. Cancer cells that exhibit abnormal chromosomes are characteristic of most advanced tumours, despite the potential threat represented by accumulated genetic damage. Carcinogenesis involves a loss of key components of the genetic and signalling molecular networks; hence some authors have suggested that this is part of a trend of cancer cells to behave as simple, minimal replicators. In this study, we explore this conjecture and suggest that, in the case of cancer, genomic instability has an upper limit that is associated with a minimal cancer cell network. Such a network would include (for a given microenvironment) the basic molecular components that allow cells to replicate and respond to selective pressures. However, it would also exhibit internal fragilities that could be exploited by appropriate therapies targeting the DNA repair machinery. The implications of this hypothesis are discussed.
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Affiliation(s)
- Ricard V Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona, Spain; Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain; Santa Fe Institute, Santa Fe, NM, USA
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341
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Smith EN, Ghia EM, DeBoever CM, Rassenti LZ, Jepsen K, Yoon KA, Matsui H, Rozenzhak S, Alakus H, Shepard PJ, Dai Y, Khosroheidari M, Bina M, Gunderson KL, Messer K, Muthuswamy L, Hudson TJ, Harismendy O, Barrett CL, Jamieson CHM, Carson DA, Kipps TJ, Frazer KA. Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development. Blood Cancer J 2015; 5:e303. [PMID: 25860294 PMCID: PMC4450323 DOI: 10.1038/bcj.2015.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 01/01/2023] Open
Abstract
We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.
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Affiliation(s)
- E N Smith
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - E M Ghia
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - C M DeBoever
- Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA
| | - L Z Rassenti
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K Jepsen
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K-A Yoon
- Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA
| | - H Matsui
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - S Rozenzhak
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - H Alakus
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - P J Shepard
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Y Dai
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - M Khosroheidari
- Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - M Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - K L Gunderson
- Illumina, Inc., 5200 Illumina Way, San Diego, CA, USA
| | - K Messer
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - L Muthuswamy
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - T J Hudson
- 1] Ontario Institute for Cancer Research, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - O Harismendy
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C L Barrett
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - C H M Jamieson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA [3] Stem Cell Program, University of California San Diego, La Jolla, CA, USA
| | - D A Carson
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - T J Kipps
- 1] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [2] Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - K A Frazer
- 1] Pediatrics and Rady's Children's Hospital, University of California at San Diego, La Jolla, CA, USA [2] Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA [3] Bioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, CA, USA [4] Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
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342
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Tesfay L, Clausen KA, Kim JW, Hegde P, Wang X, Miller LD, Deng Z, Blanchette N, Arvedson T, Miranti CK, Babitt JL, Lin HY, Peehl DM, Torti FM, Torti SV. Hepcidin regulation in prostate and its disruption in prostate cancer. Cancer Res 2015; 75:2254-63. [PMID: 25858146 DOI: 10.1158/0008-5472.can-14-2465] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/19/2015] [Indexed: 12/29/2022]
Abstract
Hepcidin is a circulating peptide hormone made by the liver that is a central regulator of systemic iron uptake and recycling. Here, we report that prostate epithelial cells also synthesize hepcidin, and that synthesis and secretion of hepcidin are markedly increased in prostate cancer cells and tissue. Prostatic hepcidin functions as an autocrine hormone, decreasing cell surface ferroportin, an iron exporter, increasing intracellular iron retention, and promoting prostate cancer cell survival. Synthesis of hepcidin in prostate cancer is controlled by a unique intersection of pathways that involves BMP4/7, IL6, Wnt, and the dual BMP and Wnt antagonist, SOSTDC1. Epigenetic silencing of SOSTDC1 through methylation is increased in prostate cancer and is associated with accelerated disease progression in patients with prostate cancer. These results establish a new connection between iron metabolism and prostate cancer, and suggest that prostatic dysregulation of hepcidin contributes to prostate cancer growth and progression.
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Affiliation(s)
- Lia Tesfay
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut
| | | | - Jin Woo Kim
- Panagene Inc., Yuseong-gu, Daejeon, Republic of Korea
| | - Poornima Hegde
- Department of Pathology, University of Connecticut Health Center, Farmington, Connecticut
| | - Xiaohong Wang
- Department of Pathology, University of Connecticut Health Center, Farmington, Connecticut
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, North Carolina
| | - Zhiyong Deng
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut
| | - Nicole Blanchette
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut
| | - Tara Arvedson
- Department of Inflammation, Amgen Inc., Seattle, Washington
| | - Cindy K Miranti
- Laboratory of Integrin Signaling, Program in Skeletal Disease and Tumor Microenvironment, Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Jodie L Babitt
- Program in Anemia Signaling Research, Division of Nephrology, Program in Membrane Biology, Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Herbert Y Lin
- Program in Anemia Signaling Research, Division of Nephrology, Program in Membrane Biology, Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Donna M Peehl
- Department of Urology, Stanford University School of Medicine, Stanford, California
| | - Frank M Torti
- Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut
| | - Suzy V Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut.
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343
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Genome-wide methylation study on depression: differential methylation and variable methylation in monozygotic twins. Transl Psychiatry 2015; 5:e557. [PMID: 25918994 PMCID: PMC4462612 DOI: 10.1038/tp.2015.49] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/02/2015] [Accepted: 03/09/2015] [Indexed: 12/13/2022] Open
Abstract
Depressive disorders have been shown to be highly influenced by environmental pathogenic factors, some of which are believed to exert stress on human brain functioning via epigenetic modifications. Previous genome-wide methylomic studies on depression have suggested that, along with differential DNA methylation, affected co-twins of monozygotic (MZ) pairs have increased DNA methylation variability, probably in line with theories of epigenetic stochasticity. Nevertheless, the potential biological roots of this variability remain largely unexplored. The current study aimed to evaluate whether DNA methylation differences within MZ twin pairs were related to differences in their psychopathological status. Data from the Illumina Infinium HumanMethylation450 Beadchip was used to evaluate peripheral blood DNA methylation of 34 twins (17 MZ pairs). Two analytical strategies were used to identify (a) differentially methylated probes (DMPs) and (b) variably methylated probes (VMPs). Most DMPs were located in genes previously related to neuropsychiatric phenotypes. Remarkably, one of these DMPs (cg01122889) was located in the WDR26 gene, the DNA sequence of which has been implicated in major depressive disorder from genome-wide association studies. Expression of WDR26 has also been proposed as a biomarker of depression in human blood. Complementarily, VMPs were located in genes such as CACNA1C, IGF2 and the p38 MAP kinase MAPK11, showing enrichment for biological processes such as glucocorticoid signaling. These results expand on previous research to indicate that both differential methylation and differential variability have a role in the etiology and clinical manifestation of depression, and provide clues on specific genomic loci of potential interest in the epigenetics of depression.
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344
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Roos L, Spector TD, Bell CG. Using epigenomic studies in monozygotic twins to improve our understanding of cancer. Epigenomics 2015; 6:299-309. [PMID: 25111484 DOI: 10.2217/epi.14.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cancer is a set of diseases that exhibit not only genetic mutations but also a profoundly distorted epigenetic landscape. Over the last two decades, great advances have been made in identifying these alterations and their importance in the initiation and progression of cancer. Epigenetic changes can be seen from the very early stages in tumorigenesis and dysregulation of the epigenome has an increasingly acknowledged pathogenic role. Epigenomic twin studies have great potential to contribute to our understanding of complex diseases, such as cancer. This is because the use of monozygotic twins discordant for cancer enables epigenetic variation analysis without the confounding influence of the constitutive genetic background, age or cohort effects. It therefore allows the identification of susceptibility loci that may be sensitive to modification by the environment. These studies into cancer etiology will potentially lead to robust epigenetic markers for the detection and risk assessment of cancer.
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Affiliation(s)
- Leonie Roos
- Department of Twin Research & Genetic Epidemiology, St Thomas' Hospital, King's College London, London, SE1 7EH, UK
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345
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Abu-Remaileh M, Bender S, Raddatz G, Ansari I, Cohen D, Gutekunst J, Musch T, Linhart H, Breiling A, Pikarsky E, Bergman Y, Lyko F. Chronic inflammation induces a novel epigenetic program that is conserved in intestinal adenomas and in colorectal cancer. Cancer Res 2015; 75:2120-30. [PMID: 25808873 DOI: 10.1158/0008-5472.can-14-3295] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/12/2015] [Indexed: 12/13/2022]
Abstract
Chronic inflammation represents a major risk factor for tumor formation, but the underlying mechanisms have remained largely unknown. Epigenetic mechanisms can record the effects of environmental challenges on the genome level and could therefore play an important role in the pathogenesis of inflammation-associated tumors. Using single-base methylation maps and transcriptome analyses of a colitis-induced mouse colon cancer model, we identified a novel epigenetic program that is characterized by hypermethylation of DNA methylation valleys that are characterized by low CpG density and active chromatin marks. This program is conserved and functional in mouse intestinal adenomas and results in silencing of active intestinal genes that are involved in gastrointestinal homeostasis and injury response. Further analyses reveal that the program represents a prominent feature of human colorectal cancer and can be used to correctly classify colorectal cancer samples with high accuracy. Together, our results show that inflammatory signals establish a novel epigenetic program that silences a specific set of genes that contribute to inflammation-induced cellular transformation.
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Affiliation(s)
- Monther Abu-Remaileh
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ihab Ansari
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Daphne Cohen
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Heinz Linhart
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany. Salem Medical Center, University of Heidelberg, Heidelberg, Germany. Department of Hematology/Oncology, University of Heidelberg Medical Center, Heidelberg, Germany
| | - Achim Breiling
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Eli Pikarsky
- The Lautenberg Center for Immunology, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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346
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Abstract
Wilms' tumor, or nephroblastoma, is the most common pediatric renal cancer. The tumors morphologically resemble embryonic kidneys with a disrupted architecture and are associated with undifferentiated metanephric precursors. Here, we discuss genetic and epigenetic findings in Wilms' tumor in the context of renal development. Many of the genes implicated in Wilms' tumorigenesis are involved in the control of nephron progenitors or the microRNA (miRNA) processing pathway. Whereas the first group of genes has been extensively studied in normal development, the second finding suggests important roles for miRNAs in general-and specific miRNAs in particular-in normal kidney development that still await further analysis. The recent identification of Wilms' tumor cancer stem cells could provide a framework to integrate these pathways and translate them into new or improved therapeutic interventions.
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Affiliation(s)
- Peter Hohenstein
- The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom; MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom;
| | - Kathy Pritchard-Jones
- UCL Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
| | - Jocelyn Charlton
- UCL Institute of Child Health, University College London, London WC1N 1EH, United Kingdom
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347
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Szumiel I. From radioresistance to radiosensitivity: In vitro evolution of L5178Y lymphoma. Int J Radiat Biol 2015; 91:465-71. [PMID: 25651039 DOI: 10.3109/09553002.2014.996263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
PURPOSE To discuss the possible reasons for the loss of tumourigenicity and the acquisition of new phenotypic features (among them, sensitivity to X and UVC radiations) as a result of in vitro cultivation of L5178Y lymphoma cells. RESULTS Ten years ago the phenotypic differences between LY-R (original L5178Y maintained in vivo and examined in vitro) and LY-S lines were reviewed in detail by the author. The loss of tumourigenicity of LY-R cells upon in vitro cultivation accompanying the acquirement of the LY-S phenotype had been described earlier by Beer et al. (1983). In spite of their common origin, the sublines were shown to differ in their relative sensitivity to a number of DNA damaging agents and in numerous other features. Here, selected differences between LY-R and LY-S lines are briefly reviewed. It is proposed that Wallace's concept (2010a) that mitochondria are the interface between environmental conditions and the genome may explain the LY-R-LY-S conversion under prolonged in vitro cultivation. CONCLUSION The differences between the LY lines were probably of epigenetic rather than genetic character. The properties of LY-R cells changed as a result of exposure to an oxic in vitro milieu. The changes could be preconditioned by heteroplasmy and the selection of cells endowed with mitochondria best fitted to a high oxygen-low carbon dioxide environment.
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Affiliation(s)
- Irena Szumiel
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology , Warsaw , Poland
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348
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Affiliation(s)
- Steven A. Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico 87108;
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349
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Charlton J, Williams RD, Sebire NJ, Popov S, Vujanic G, Chagtai T, Alcaide-German M, Morris T, Butcher LM, Guilhamon P, Beck S, Pritchard-Jones K. Comparative methylome analysis identifies new tumour subtypes and biomarkers for transformation of nephrogenic rests into Wilms tumour. Genome Med 2015; 7:11. [PMID: 25763109 PMCID: PMC4354990 DOI: 10.1186/s13073-015-0136-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/21/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Wilms tumours (WTs) are characterised by several hallmarks that suggest epimutations such as aberrant DNA methylation are involved in tumour progression: loss of imprinting at 11p15, lack of recurrent mutations and formation of nephrogenic rests (NRs), which are lesions of retained undifferentiated embryonic tissue that can give rise to WTs. METHODS To identify such epimutations, we performed a comprehensive methylome analysis on 20 matched trios of micro-dissected WTs, NRs and surrounding normal kidneys (NKs) using Illumina Infinium HumanMethylation450 Bead Chips and functionally validated findings using RNA sequencing. RESULTS Comparison of NRs with NK revealed prominent tissue biomarkers: 629 differentially methylated regions, of which 55% were hypermethylated and enriched for domains that are bivalent in embryonic stem cells and for genes expressed during development (P = 2.49 × 10(-5)). Comparison of WTs with NRs revealed two WT subgroups; group-2 WTs and NRs were epigenetically indistinguishable whereas group-1 WTs showed an increase in methylation variability, hypomethylation of renal development genes, hypermethylation and relative loss of expression of cell adhesion genes and known and potential new WT tumour suppressor genes (CASP8, H19, MIR195, RB1 and TSPAN32) and was strongly associated with bilateral disease (P = 0.032). Comparison of WTs and NRs to embryonic kidney highlighted the significance of polycomb target methylation in Wilms tumourigenesis. CONCLUSIONS Methylation levels vary during cancer evolution. We have described biomarkers related to WT evolution from its precursor NRs which may be useful to differentiate between these tissues for patients with bilateral disease.
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Affiliation(s)
- Jocelyn Charlton
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Richard D Williams
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Neil J Sebire
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Sergey Popov
- />The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG UK
| | - Gordan Vujanic
- />Department of Pathology, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN UK
| | - Tasnim Chagtai
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Marisa Alcaide-German
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
| | - Tiffany Morris
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Lee M Butcher
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Paul Guilhamon
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Stephan Beck
- />UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT UK
| | - Kathy Pritchard-Jones
- />UCL Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH UK
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350
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Mayor R, Izquierdo-Bouldstridge A, Millán-Ariño L, Bustillos A, Sampaio C, Luque N, Jordan A. Genome distribution of replication-independent histone H1 variants shows H1.0 associated with nucleolar domains and H1X associated with RNA polymerase II-enriched regions. J Biol Chem 2015; 290:7474-91. [PMID: 25645921 DOI: 10.1074/jbc.m114.617324] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unlike core histones, the linker histone H1 family is more evolutionarily diverse, and many organisms have multiple H1 variants or subtypes. In mammals, the H1 family includes seven somatic H1 variants; H1.1 to H1.5 are expressed in a replication-dependent manner, whereas H1.0 and H1X are replication-independent. Using ChIP-sequencing data and cell fractionation, we have compared the genomic distribution of H1.0 and H1X in human breast cancer cells, in which we previously observed differential distribution of H1.2 compared with the other subtypes. We have found H1.0 to be enriched at nucleolus-associated DNA repeats and chromatin domains, whereas H1X is associated with coding regions, RNA polymerase II-enriched regions, and hypomethylated CpG islands. Further, H1X accumulates within constitutive or included exons and retained introns and toward the 3' end of expressed genes. Inducible H1X knockdown does not affect cell proliferation but dysregulates a subset of genes related to cell movement and transport. In H1X-depleted cells, the promoters of up-regulated genes are not occupied specifically by this variant, have a lower than average H1 content, and, unexpectedly, do not form an H1 valley upon induction. We conclude that H1 variants are not distributed evenly across the genome and may participate with some specificity in chromatin domain organization or gene regulation.
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Affiliation(s)
- Regina Mayor
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Andrea Izquierdo-Bouldstridge
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Lluís Millán-Ariño
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Alberto Bustillos
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Cristina Sampaio
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Neus Luque
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
| | - Albert Jordan
- From the Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia 08028 Spain
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