1
|
Norollahi SE, Vahidi S, Shams S, Keymoradzdeh A, Soleymanpour A, Solymanmanesh N, Mirzajani E, Jamkhaneh VB, Samadani AA. Analytical and therapeutic profiles of DNA methylation alterations in cancer; an overview of changes in chromatin arrangement and alterations in histone surfaces. Horm Mol Biol Clin Investig 2023; 44:337-356. [PMID: 36799246 DOI: 10.1515/hmbci-2022-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 01/24/2023] [Indexed: 02/18/2023]
Abstract
DNA methylation is the most important epigenetic element that activates the inhibition of gene transcription and is included in the pathogenesis of all types of malignancies. Remarkably, the effectors of DNA methylation are DNMTs (DNA methyltransferases) that catalyze de novo or keep methylation of hemimethylated DNA after the DNA replication process. DNA methylation structures in cancer are altered, with three procedures by which DNA methylation helps cancer development which are including direct mutagenesis, hypomethylation of the cancer genome, and also focal hypermethylation of the promoters of TSGs (tumor suppressor genes). Conspicuously, DNA methylation, nucleosome remodeling, RNA-mediated targeting, and histone modification balance modulate many biological activities that are essential and indispensable to the genesis of cancer and also can impact many epigenetic changes including DNA methylation and histone modifications as well as adjusting of non-coding miRNAs expression in prevention and treatment of many cancers. Epigenetics points to heritable modifications in gene expression that do not comprise alterations in the DNA sequence. The nucleosome is the basic unit of chromatin, consisting of 147 base pairs (bp) of DNA bound around a histone octamer comprised of one H3/H4 tetramer and two H2A/H2B dimers. DNA methylation is preferentially distributed over nucleosome regions and is less increased over flanking nucleosome-depleted DNA, implying a connection between nucleosome positioning and DNA methylation. In carcinogenesis, aberrations in the epigenome may also include in the progression of drug resistance. In this report, we report the rudimentary notes behind these epigenetic signaling pathways and emphasize the proofs recommending that their misregulation can conclude in cancer. These findings in conjunction with the promising preclinical and clinical consequences observed with epigenetic drugs against chromatin regulators, confirm the important role of epigenetics in cancer therapy.
Collapse
Affiliation(s)
- Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shima Shams
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Arman Keymoradzdeh
- Department of Neurosurgery, School of Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armin Soleymanpour
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Nazanin Solymanmanesh
- Student Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Vida Baloui Jamkhaneh
- Department of Veterinary Medicine, Islamic Azad University of Babol Branch, Babol, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Guilan University of Medical Sciences, Rasht, Iran
| |
Collapse
|
2
|
Gonçalves E, Gonçalves-Reis M, Pereira-Leal JB, Cardoso J. DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies. Sci Rep 2022; 12:11512. [PMID: 35798798 PMCID: PMC9262906 DOI: 10.1038/s41598-022-15058-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is amongst the cancers with highest mortality rates and is the most common malignancy of the liver. Early detection is vital to provide the best treatment possible and liquid biopsies combined with analysis of circulating tumour DNA methylation show great promise as a non-invasive approach for early cancer diagnosis and monitoring with low false negative rates. To identify reliable diagnostic biomarkers of early HCC, we performed a systematic analysis of multiple hepatocellular studies and datasets comprising > 1500 genome-wide DNA methylation arrays, to define a methylation signature predictive of HCC in both tissue and cell-free DNA liquid biopsy samples. Our machine learning pipeline identified differentially methylated regions in HCC, some associated with transcriptional repression of genes related with cancer progression, that benchmarked positively against independent methylation signatures. Combining our signature of 38 DNA methylation regions, we derived a HCC detection score which confirmed the utility of our approach by identifying in an independent dataset 96% of HCC tissue samples with a precision of 98%, and most importantly successfully separated cfDNA of tumour samples from healthy controls. Notably, our risk score could identify cell-free DNA samples from patients with other tumours, including colorectal cancer. Taken together, we propose a comprehensive HCC DNA methylation fingerprint and an associated risk score for detection of HCC from tissue and liquid biopsies.
Collapse
Affiliation(s)
- Emanuel Gonçalves
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal.,INESC-ID, 1000-029, Lisbon, Portugal
| | - Maria Gonçalves-Reis
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal
| | - José B Pereira-Leal
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal
| | - Joana Cardoso
- Ophiomics, Pólo Tecnológico de 8, R. Cupertino de Miranda 9, 1600-513, Lisbon, Portugal.
| |
Collapse
|
3
|
Comprehensive Landscape of HOXA2, HOXA9, and HOXA10 as Potential Biomarkers for Predicting Progression and Prognosis in Prostate Cancer. J Immunol Res 2022; 2022:5740971. [PMID: 35372588 PMCID: PMC8970952 DOI: 10.1155/2022/5740971] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer (PCa) is recognized as a common malignancy in male patients. The homeobox A cluster (HOXA) family members have been confirmed to be implicated in the development of several types of tumors. However, the expression pattern and prognostic values of HOXA genes in PCa have not been investigated. In this study, we analyzed TCGA datasets and identified six HOXA family members which showed a dysregulated expression in PCa specimens compared with nontumor specimens. We also explored the potential mechanisms involved in the dysregulation of HOXA family members in PCa, and the results of Pearson's correlation revealed that most HOXA members were negatively related to the methylation degree. Moreover, we explored the prognostic values of HOXA family members and identified six survival-related HOXA members. Importantly, HOXA2, HOXA9, and HOXA10 were identified as critical PCa-related genes which were abnormally expressed in PCa and associated with clinical outcomes of PCa patients. Then, we explored the association between the above three genes and immune cell infiltration. We observed that the levels of HOXA2, HOXA9, and HOXA10 were associated with the levels of immune infiltration of several kinds of immune cells. Overall, our findings identified the potential values of the HOXA family for outcome prediction in PCa, which might facilitate personalized counselling and treatment in PCa.
Collapse
|
4
|
Zhou H, Gao Y, Li X, Shang S, Wang P, Zhi H, Guo S, Sun D, Liu H, Li X, Zhang Y, Ning S. Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer. J Transl Med 2021; 19:509. [PMID: 34906173 PMCID: PMC8672572 DOI: 10.1186/s12967-021-03179-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Emerging evidence has revealed that some long intergenic non-coding RNAs (lincRNAs) are likely to form clusters on the same chromosome, and lincRNA genomic clusters might play critical roles in the pathophysiological mechanism. However, the comprehensive investigation of lincRNA clustering is rarely studied, particularly the characterization of their functional significance across different cancer types. Methods In this study, we firstly constructed a computational method basing a sliding window approach for systematically identifying lincRNA genomic clusters. We then dissected these lincRNA genomic clusters to identify common characteristics in cooperative expression, conservation among divergent species, targeted miRNAs, and CNV frequency. Next, we performed comprehensive analyses in differentially-expressed patterns and overall survival outcomes for patients from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) across multiple cancer types. Finally, we explored the underlying mechanisms of lincRNA genomic clusters by functional enrichment analysis, pathway analysis, and drug-target interaction. Results We identified lincRNA genomic clusters according to the algorithm. Clustering lincRNAs tended to be co-expressed, highly conserved, targeted by more miRNAs, and with similar deletion and duplication frequency, suggesting that lincRNA genomic clusters may exert their effects by acting in combination. We further systematically explored conserved and cancer-specific lincRNA genomic clusters, indicating they were involved in some important mechanisms of disease occurrence through diverse approaches. Furthermore, lincRNA genomic clusters can serve as biomarkers with potential clinical significance and involve in specific pathological processes in the development of cancer. Moreover, a lincRNA genomic cluster named Cluster127 in DLK1-DIO3 imprinted locus was discovered, which contained MEG3, MEG8, MEG9, MIR381HG, LINC02285, AL132709.5, and AL132709.1. Further analysis indicated that Cluster127 may have the potential for predicting prognosis in cancer and could play their roles by participating in the regulation of PI3K-AKT signaling pathway. Conclusions Clarification of the lincRNA genomic clusters specific roles in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03179-5.
Collapse
Affiliation(s)
- Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| |
Collapse
|
5
|
Labade AS, Salvi A, Kar S, Karmodiya K, Sengupta K. Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation. J Cell Sci 2021; 134:273378. [PMID: 34746948 DOI: 10.1242/jcs.259307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/30/2021] [Indexed: 11/20/2022] Open
Abstract
Nucleoporins regulate nuclear transport and are also involved in DNA damage, repair, cell cycle, chromatin organization, and gene expression. Here, we studied the role of nucleoporin Nup93 and the chromatin organizer CTCF in regulating HOXA expression during differentiation. ChIP sequencing revealed a significant overlap between Nup93 and CTCF peaks. Interestingly, Nup93 and CTCF are associated with the 3' and 5'HOXA genes respectively. Depletions of Nup93 and CTCF antagonistically modulate expression levels of 3'and 5'HOXA genes in undifferentiated NT2/D1 cells. Nup93 also regulates the localization of the HOXA gene locus, which disengages from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. The dynamic association of Nup93 and CTCF with the HOXA locus during differentiation correlates with its spatial positioning and expression. While Nup93 tethers the HOXA locus to the nuclear periphery, CTCF potentially regulates looping of the HOXA gene cluster in a temporal manner. In summary, Nup93 and CTCF complement one another in modulating the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.
Collapse
Affiliation(s)
- Ajay S Labade
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Adwait Salvi
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Saswati Kar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Kundan Sengupta
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| |
Collapse
|
6
|
Lv H, Dao FY, Zhang D, Yang H, Lin H. Advances in mapping the epigenetic modifications of 5-methylcytosine (5mC), N6-methyladenine (6mA), and N4-methylcytosine (4mC). Biotechnol Bioeng 2021; 118:4204-4216. [PMID: 34370308 DOI: 10.1002/bit.27911] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/06/2021] [Indexed: 12/30/2022]
Abstract
DNA modification plays a pivotal role in regulating gene expression in cell development. As prevalent markers on DNA, 5-methylcytosine (5mC), N6-methyladenine (6mA), and N4-methylcytosine (4mC) can be recognized by specific methyltransferases, facilitating cellular defense and the versatile regulation of gene expression in eukaryotes and prokaryotes. Recent advances in DNA sequencing technology have permitted the positions of different modifications to be resolved at the genome-wide scale, which has led to the discovery of several novel insights into the complexity and functions of multiple methylations. In this review, we summarize differences in the various mapping approaches and discuss their pros and cons with respect to their relative read depths, speeds, and costs. We also discuss the development of future sequencing technologies and strategies for improving the detection resolution of current sequencing technologies. Lastly, we speculate on the potentially instrumental role that these sequencing technologies might play in future research.
Collapse
Affiliation(s)
- Hao Lv
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Fu-Ying Dao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hui Yang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
7
|
García-Cortés D, Hernández-Lemus E, Espinal-Enríquez J. Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations. Front Genet 2021; 12:629475. [PMID: 33959148 PMCID: PMC8096206 DOI: 10.3389/fgene.2021.629475] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Luminal A is the most common breast cancer molecular subtype in women worldwide. These tumors have characteristic yet heterogeneous alterations at the genomic and transcriptomic level. Gene co-expression networks (GCNs) have contributed to better characterize the cancerous phenotype. We have previously shown an imbalance in the proportion of intra-chromosomal (cis-) over inter-chromosomal (trans-) interactions when comparing cancer and healthy tissue GCNs. In particular, for breast cancer molecular subtypes (Luminal A included), the majority of high co-expression interactions connect gene-pairs in the same chromosome, a phenomenon that we have called loss of trans- co-expression. Despite this phenomenon has been described, the functional implication of this specific network topology has not been studied yet. To understand the biological role that communities of co-expressed genes may have, we constructed GCNs for healthy and Luminal A phenotypes. Network modules were obtained based on their connectivity patterns and they were classified according to their chromosomal homophily (proportion of cis-/trans- interactions). A functional overrepresentation analysis was performed on communities in both networks to observe the significantly enriched processes for each community. We also investigated possible mechanisms for which the loss of trans- co-expression emerges in cancer GCN. To this end we evaluated transcription factor binding sites, CTCF binding sites, differential gene expression and copy number alterations (CNAs) in the cancer GCN. We found that trans- communities in Luminal A present more significantly enriched categories than cis- ones. Processes, such as angiogenesis, cell proliferation, or cell adhesion were found in trans- modules. The differential expression analysis showed that FOXM1, CENPA, and CIITA transcription factors, exert a major regulatory role on their communities by regulating expression of their target genes in other chromosomes. Finally, identification of CNAs, displayed a high enrichment of deletion peaks in cis- communities. With this approach, we demonstrate that network topology determine, to at certain extent, the function in Luminal A breast cancer network. Furthermore, several mechanisms seem to be acting together to avoid trans- co-expression. Since this phenomenon has been observed in other cancer tissues, a remaining question is whether the loss of long distance co-expression is a novel hallmark of cancer.
Collapse
Affiliation(s)
- Diana García-Cortés
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
8
|
Paço A, Aparecida de Bessa Garcia S, Leitão Castro J, Costa-Pinto AR, Freitas R. Roles of the HOX Proteins in Cancer Invasion and Metastasis. Cancers (Basel) 2020; 13:E10. [PMID: 33375038 PMCID: PMC7792759 DOI: 10.3390/cancers13010010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Invasion and metastasis correspond to the foremost cause of cancer-related death, and the molecular networks behind these two processes are extremely complex and dependent on the intra- and extracellular conditions along with the prime of the premetastatic niche. Currently, several studies suggest an association between the levels of HOX genes expression and cancer cell invasion and metastasis, which favour the formation of novel tumour masses. The deregulation of HOX genes by HMGA2/TET1 signalling and the regulatory effect of noncoding RNAs generated by the HOX loci can also promote invasion and metastasis, interfering with the expression of HOX genes or other genes relevant to these processes. In this review, we present five molecular mechanisms of HOX deregulation by which the HOX clusters products may affect invasion and metastatic processes in solid tumours.
Collapse
Affiliation(s)
- Ana Paço
- BLC3—Biomassa Lenho-Celulósica de 3ª Geração, Campus of Technology and Innovation, 3405-169 Oliveira do Hospital, Portugal
| | - Simone Aparecida de Bessa Garcia
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Joana Leitão Castro
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Ana Rita Costa-Pinto
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| |
Collapse
|
9
|
Fiches GN, Zhou D, Kong W, Biswas A, Ahmed EH, Baiocchi RA, Zhu J, Santoso N. Profiling of immune related genes silenced in EBV-positive gastric carcinoma identified novel restriction factors of human gammaherpesviruses. PLoS Pathog 2020; 16:e1008778. [PMID: 32841292 PMCID: PMC7473590 DOI: 10.1371/journal.ppat.1008778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/04/2020] [Accepted: 07/05/2020] [Indexed: 12/24/2022] Open
Abstract
EBV-associated gastric cancer (EBVaGC) is characterized by high frequency of DNA methylation. In this study, we investigated how epigenetic alteration of host genome contributes to pathogenesis of EBVaGC through the analysis of transcriptomic and epigenomic datasets from NIH TCGA (The Cancer Genome Atlas) consortium. We identified that immune related genes (IRGs) is a group of host genes preferentially silenced in EBV-positive gastric cancers through DNA hypermethylation. Further functional characterizations of selected IRGs reveal their novel antiviral activity against not only EBV but also KSHV. In particular, we showed that metallothionein-1 (MT1) and homeobox A (HOXA) gene clusters are down-regulated via EBV-driven DNA hypermethylation. Several MT1 isoforms suppress EBV lytic replication and release of progeny virions as well as KSHV lytic reactivation, suggesting functional redundancy of these genes. In addition, single HOXA10 isoform exerts antiviral activity against both EBV and KSHV. We also confirmed the antiviral effect of other dysregulated IRGs, such as IRAK2 and MAL, in scenario of EBV and KSHV lytic reactivation. Collectively, our results demonstrated that epigenetic silencing of IRGs is a viral strategy to escape immune surveillance and promote viral propagation, which is overall beneficial to viral oncogenesis of human gamma-herpesviruses (EBV and KSHV), considering that these IRGs possess antiviral activities against these oncoviruses.
Collapse
Affiliation(s)
- Guillaume N. Fiches
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Dawei Zhou
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Weili Kong
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Ayan Biswas
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Elshafa H. Ahmed
- Division of Hematology, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Jian Zhu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Netty Santoso
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| |
Collapse
|
10
|
Hamilton MJ, Young M, Jang K, Sauer S, Neang VE, King AT, Girke T, Martinez E. HOTAIRM1 lncRNA is downregulated in clear cell renal cell carcinoma and inhibits the hypoxia pathway. Cancer Lett 2019; 472:50-58. [PMID: 31862408 DOI: 10.1016/j.canlet.2019.12.022] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022]
Abstract
HOXA Transcript Antisense RNA, Myeloid-Specific 1 (HOTAIRM1) is a conserved long non-coding RNA (lncRNA) involved in myeloid and neural differentiation that is deregulated in acute myeloid leukemia and other cancers. Previous studies focused on the nuclear unspliced HOTAIRM1 transcript, however cytoplasmic splice variants exist whose roles have remained unknown. Here, we report novel functions of HOTAIRM1 in the kidney. HOTAIRM1 transcripts are induced during renal lineage differentiation of embryonic stem cells and required for expression of specific renal differentiation genes. We show that the major HOTAIRM1 transcript in differentiated cells is the spliced cytoplasmic HM1-3 isoform and that HM1-3 is downregulated in >90% of clear cell renal cell carcinomas (ccRCCs). Knockdown of HM1-3 in renal cells deregulates hypoxia-responsive and angiogenic genes, including ANGPTL4. Furthermore, HOTAIRM1 transcripts are downregulated by hypoxia-mimetic stress and knockdown of the cytoplasmic HM1-3 isoform in normoxic cells post-transcriptionally induces Hypoxia-Inducible Factor 1α (HIF1α) protein, a key activator of ANGPTL4. Our results demonstrate the pervasive downregulation of the specific HOTAIRM1 cytoplasmic isoform HM1-3 in ccRCC and suggest possible roles of HOTAIRM1 in kidney differentiation and suppression of HIF1-dependent angiogenic pathways.
Collapse
Affiliation(s)
- Michael J Hamilton
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Matthew Young
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Kay Jang
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Silvia Sauer
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Vanessa E Neang
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Alexia T King
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Thomas Girke
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA, USA.
| |
Collapse
|
11
|
Choi M, Choi YM, An IS, Bae S, Jung JH, An S. E3 ligase RCHY1 negatively regulates HDAC2. Biochem Biophys Res Commun 2019; 521:37-41. [PMID: 31630802 DOI: 10.1016/j.bbrc.2019.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/04/2019] [Indexed: 11/18/2022]
Abstract
HDAC2, one of the class I histone deacetylase regulates epigenetic landscape through histone modification. Because HDAC2 is overexpressed in many cancers, cancer therapeutics against HDAC2 have been developed. Here we show novel mechanism of HDAC2 regulation by E3 ligase RCHY1. We found inverse correlation RCHY1 and HDAC2 levels in tumor tissue from six independent dataset using meta-analysis. Ectopic expression of RCHY1 decreased the level of HDAC2 from cancer cells including p53 wildtype, mutant and null cells. In addition, HDAC2 was increased by RCHY1 knockdown. RCHY1 directly interacts with HDAC2. Ectopic expression of wild type but not RING mutant RCHY1 increased HDAC2 levels. These data provide an evidence that RCHY1 negatively regulates HDAC2.
Collapse
Affiliation(s)
- Mina Choi
- Research Institute for Molecular-Targeted Drugs, Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Yeong Min Choi
- Korea Institute of Dermatological Science, GeneCellPharm Corporation, 375 Munjeong 2(i)-dong, Songpa-gu Seoul, 05836, South Korea
| | - In-Sook An
- Korea Institute of Dermatological Science, GeneCellPharm Corporation, 375 Munjeong 2(i)-dong, Songpa-gu Seoul, 05836, South Korea
| | - Seunghee Bae
- Research Institute for Molecular-Targeted Drugs, Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, South Korea
| | - Jin Hyuk Jung
- Korea Institute of Dermatological Science, GeneCellPharm Corporation, 375 Munjeong 2(i)-dong, Songpa-gu Seoul, 05836, South Korea.
| | - Sungkwan An
- Research Institute for Molecular-Targeted Drugs, Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, South Korea.
| |
Collapse
|
12
|
Escala-Garcia M, Guo Q, Dörk T, Canisius S, Keeman R, Dennis J, Beesley J, Lecarpentier J, Bolla MK, Wang Q, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Auer PL, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Boeckx B, Bojesen SE, Bonanni B, Børresen-Dale AL, Brauch H, Brenner H, Brentnall A, Brinton L, Broberg P, Brock IW, Brucker SY, Burwinkel B, Caldas C, Caldés T, Campa D, Canzian F, Carracedo A, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Cheng TYD, Chin SF, Clarke CL, Cordina-Duverger E, Couch FJ, Cox DG, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Dunn JA, Dunning AM, Durcan L, Dwek M, Earl HM, Ekici AB, Eliassen AH, Ellberg C, Engel C, Eriksson M, Evans DG, Figueroa J, Flesch-Janys D, Flyger H, Gabrielson M, Gago-Dominguez M, Galle E, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Georgoulias V, Giles GG, Glendon G, Goldgar DE, González-Neira A, Alnæs GIG, Grip M, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Hankinson S, Harkness EF, Harrington PA, Hart SN, Hartikainen JM, Hein A, Hillemanns P, Hiller L, Holleczek B, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Howell A, Huang G, Humphreys K, Hunter DJ, Janni W, John EM, Jones ME, Jukkola-Vuorinen A, Jung A, Kaaks R, Kabisch M, Kaczmarek K, Kerin MJ, Khan S, Khusnutdinova E, Kiiski JI, Kitahara CM, Knight JA, Ko YD, Koppert LB, Kosma VM, Kraft P, Kristensen VN, Krüger U, Kühl T, Lambrechts D, Le Marchand L, Lee E, Lejbkowicz F, Li L, Lindblom A, Lindström S, Linet M, Lissowska J, Lo WY, Loibl S, Lubiński J, Lux MP, MacInnis RJ, Maierthaler M, Maishman T, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Mavroudis D, McLean C, Meindl A, Middha P, Miller N, Milne RL, Moreno F, Mulligan AM, Mulot C, Nassir R, Neuhausen SL, Newman WT, Nielsen SF, Nordestgaard BG, Norman A, Olsson H, Orr N, Pankratz VS, Park-Simon TW, Perez JIA, Pérez-Barrios C, Peterlongo P, Petridis C, Pinchev M, Prajzendanc K, Prentice R, Presneau N, Prokofieva D, Pylkäs K, Rack B, Radice P, Ramachandran D, Rennert G, Rennert HS, Rhenius V, Romero A, Roylance R, Saloustros E, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schwentner L, Scott RJ, Scott C, Seynaeve C, Shah M, Simard J, Smeets A, Sohn C, Southey MC, Swerdlow AJ, Talhouk A, Tamimi RM, Tapper WJ, Teixeira MR, Tengström M, Terry MB, Thöne K, Tollenaar RAEM, Tomlinson I, Torres D, Truong T, Turman C, Turnbull C, Ulmer HU, Untch M, Vachon C, van Asperen CJ, van den Ouweland AMW, van Veen EM, Wendt C, Whittemore AS, Willett W, Winqvist R, Wolk A, Yang XR, Zhang Y, Easton DF, Fasching PA, Nevanlinna H, Eccles DM, Pharoah PDP, Schmidt MK. Genome-wide association study of germline variants and breast cancer-specific mortality. Br J Cancer 2019; 120:647-657. [PMID: 30787463 PMCID: PMC6461853 DOI: 10.1038/s41416-019-0393-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 01/02/2019] [Accepted: 01/14/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND We examined the associations between germline variants and breast cancer mortality using a large meta-analysis of women of European ancestry. METHODS Meta-analyses included summary estimates based on Cox models of twelve datasets using ~10.4 million variants for 96,661 women with breast cancer and 7697 events (breast cancer-specific deaths). Oestrogen receptor (ER)-specific analyses were based on 64,171 ER-positive (4116) and 16,172 ER-negative (2125) patients. We evaluated the probability of a signal to be a true positive using the Bayesian false discovery probability (BFDP). RESULTS We did not find any variant associated with breast cancer-specific mortality at P < 5 × 10-8. For ER-positive disease, the most significantly associated variant was chr7:rs4717568 (BFDP = 7%, P = 1.28 × 10-7, hazard ratio [HR] = 0.88, 95% confidence interval [CI] = 0.84-0.92); the closest gene is AUTS2. For ER-negative disease, the most significant variant was chr7:rs67918676 (BFDP = 11%, P = 1.38 × 10-7, HR = 1.27, 95% CI = 1.16-1.39); located within a long intergenic non-coding RNA gene (AC004009.3), close to the HOXA gene cluster. CONCLUSIONS We uncovered germline variants on chromosome 7 at BFDP < 15% close to genes for which there is biological evidence related to breast cancer outcome. However, the paucity of variants associated with mortality at genome-wide significance underpins the challenge in providing genetic-based individualised prognostic information for breast cancer patients.
Collapse
Affiliation(s)
- Maria Escala-Garcia
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
| | - Qi Guo
- University of Cambridge, Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Cambridge, UK.
| | - Thilo Dörk
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Sander Canisius
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Division of Molecular Carcinogenesis, Amsterdam, The Netherlands
| | - Renske Keeman
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
| | - Joe Dennis
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Jonathan Beesley
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Queensland, Australia
| | - Julie Lecarpentier
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Manjeet K Bolla
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Qin Wang
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Jean Abraham
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- University of Cambridge NHS Foundation Hospitals, Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON, Canada
- University of Toronto, Department of Molecular Genetics, Toronto, ON, Canada
| | - Hoda Anton-Culver
- University of California Irvine, Department of Epidemiology, Genetic Epidemiology Research Institute, Irvine, CA, USA
| | - Volker Arndt
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
| | - Paul L Auer
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Seattle, WA, USA
- University of Wisconsin-Milwaukee, Zilber School of Public Health, Milwaukee, WI, USA
| | - Matthias W Beckmann
- University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
| | - Sabine Behrens
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Javier Benitez
- Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Marina Bermisheva
- Ufa Scientific Center of Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, Russia
| | - Leslie Bernstein
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Carl Blomqvist
- University of Helsinki, Department of Oncology, Helsinki University Hospital, Helsinki, Finland
- Örebro University Hospital, Department of Oncology, Örebro, Sweden
| | - Bram Boeckx
- VIB, VIB Center for Cancer Biology, Leuven, Belgium
- University of Leuven, Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium
| | - Stig E Bojesen
- Copenhagen University Hospital, Copenhagen General Population Study, Herlevand Gentofte Hospital, Herlev, Denmark
- Copenhagen University Hospital, Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology IRCCS Milan, Milan, 20141, Italy
| | - Anne-Lise Børresen-Dale
- Oslo University Hospital-Radiumhospitalet, Department of Cancer Genetics, Institute for Cancer Research, Oslo, Norway
- University of Oslo, Institute of Clinical Medicine, Faculty of Medicine, Oslo, Norway
- Department of Research, Vestre Viken Hospital, Drammen, Norway; Section for Breast- and Endocrine Surgery, Department of Cancer, Division of Surgery, Cancer and Transplantation Medicine, Oslo University Hospital-Ullevål, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
- Department of Pathology at Akershus University hospital, Lørenskog, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Division of Surgery and Cancer and Transplantation Medicine, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- National Advisory Unit on Late Effects after Cancer Treatment, Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Breast Cancer Research Consortium, Oslo University Hospital, Oslo, Norway
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hermann Brenner
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Division of Preventive Oncology, Heidelberg, Germany
| | - Adam Brentnall
- Queen Mary University of London, Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, London, UK
| | - Louise Brinton
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Per Broberg
- Lund University, Department of Cancer Epidemiology, Clinical Sciences, Lund, Sweden
| | - Ian W Brock
- University of Sheffield, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, Sheffield, UK
| | - Sara Y Brucker
- University of Tübingen, Department of Gynecology and Obstetrics, Tübingen, Germany
| | - Barbara Burwinkel
- University of Heidelberg, Department of Obstetrics and Gynecology, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Molecular Epidemiology Group, C080, Heidelberg, Germany
| | - Carlos Caldas
- Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- University of Cambridge NHS Foundation Hospitals, Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- The Institute of Cancer Research, Section of Cancer Genetics, London, UK
| | - Trinidad Caldés
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Medical Oncology Department, Hospital Cl'nico San Carlos, Madrid, Spain
| | - Daniele Campa
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
- University of Pisa, Department of Biology, Pisa, Italy
| | - Federico Canzian
- German Cancer Research Center (DKFZ), Molecular Epidemiology Group, C080, Heidelberg, Germany
| | - Angel Carracedo
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Genomic Medicine Group, Galician Foundation of Genomic Medicine, SERGAS, Santiago de Compostela, Spain
- Universidad de Santiago de Compostela, Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago De Compostela, Spain
- King Abdulaziz University, Center of Excellence in Genomic Medicine, Jeddah, Kingdom of Saudi Arabia
| | - Brian D Carter
- American Cancer Society, Epidemiology Research Program, Atlanta, GA, USA
| | - Jose E Castelao
- Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Oncology and Genetics Unit, Vigo, Spain
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
- University Medical Center Hamburg-Eppendorf, Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Georgia Chenevix-Trench
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, Queensland, Australia
| | - Ting-Yuan David Cheng
- Roswell Park Cancer Institute, Division of Cancer Prevention and Control, Buffalo, NY, USA
| | - Suet-Feung Chin
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Christine L Clarke
- University of Sydney, Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Emilie Cordina-Duverger
- INSERM, University Paris-Sud, University Paris-Saclay, Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), Villejuif, France
| | - Fergus J Couch
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - David G Cox
- Imperial College London, Department of Epidemiology and Biostatistics, School of Public Health, London, UK
- Cancer Research Center of Lyon, INSERM U1052, Lyon, France
| | - Angela Cox
- University of Sheffield, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, Sheffield, UK
| | - Simon S Cross
- University of Sheffield, Academic Unit of Pathology, Department of Neuroscience, Sheffield, UK
| | - Kamila Czene
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Mary B Daly
- Fox Chase Cancer Center, Department of Clinical Genetics, Philadelphia, PA, USA
| | - Peter Devilee
- Leiden University Medical Center, Department of Pathology, Leiden, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Janet A Dunn
- University of Warwick, Warwick Clinical Trials Unit, Coventry, UK
| | - Alison M Dunning
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Lorraine Durcan
- University of Southampton, Southampton Clinical Trials Unit, Faculty of Medicine, Southampton, UK
- University of Southampton, Cancer Sciences Academic Unit, Faculty of Medicine, Southampton, UK
| | - Miriam Dwek
- University of Westminster, Department of Biomedical Sciences, Faculty of Science and Technology, London, UK
| | - Helena M Earl
- University of Cambridge NHS Foundation Hospitals, Cambridge Breast Unit and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- University of Cambridge, Department of Oncology, Cambridge, UK
| | - Arif B Ekici
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - A Heather Eliassen
- Harvard Medical School, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
| | - Carolina Ellberg
- Lund University, Department of Cancer Epidemiology, Clinical Sciences, Lund, Sweden
| | - Christoph Engel
- University of Leipzig, Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- University of Leipzig, LIFE - Leipzig Research Centre for Civilization Diseases, Leipzig, Germany
| | - Mikael Eriksson
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - D Gareth Evans
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
- St Marys Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Jonine Figueroa
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
- The University of Edinburgh Medical School, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Edinburgh, UK
| | - Dieter Flesch-Janys
- University Medical Centre Hamburg-Eppendorf, Institute for Medical Biometrics and Epidemiology, Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf, Department of Cancer Epidemiology, Clinical Cancer Registry, Hamburg, Germany
| | - Henrik Flyger
- Copenhagen University Hospital, Department of Breast Surgery, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Marike Gabrielson
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Genomic Medicine Group, Galician Foundation of Genomic Medicine, SERGAS, Santiago de Compostela, Spain
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Eva Galle
- VIB, VIB Center for Cancer Biology, Leuven, Belgium
- University of Leuven, Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium
| | - Susan M Gapstur
- American Cancer Society, Epidemiology Research Program, Atlanta, GA, USA
| | - Montserrat García-Closas
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
- Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | - José A García-Sáenz
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Medical Oncology Department, Hospital Cl'nico San Carlos, Madrid, Spain
| | - Mia M Gaudet
- American Cancer Society, Epidemiology Research Program, Atlanta, GA, USA
| | - Angela George
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
- The Royal Marsden NHS Foundation Trust, Cancer Genetics Unit, London, UK
| | | | - Graham G Giles
- Cancer Council Victoria, Cancer Epidemiology & Intelligence Division, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne School of Population and Global Health, Centre for Epidemiology and Biostatistics, Melbourne, VIC, Australia
- Monash University, Department of Epidemiology and Preventive Medicine, Melbourne, VIC, Australia
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON, Canada
| | - David E Goldgar
- Huntsman Cancer Institute, University of Utah School of Medicine, Department of Dermatology, Salt Lake City, UT, USA
| | - Anna González-Neira
- Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain
| | - Grethe I Grenaker Alnæs
- Oslo University Hospital-Radiumhospitalet, Department of Cancer Genetics, Institute for Cancer Research, Oslo, Norway
| | - Mervi Grip
- University of Oulu, Department of Surgery, Oulu University Hospital, Oulu, Finland
| | - Pascal Guénel
- INSERM, University Paris-Sud, University Paris-Saclay, Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), Villejuif, France
| | - Lothar Haeberle
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Centre Erlangen-EMN, Department of Gynaecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Eric Hahnen
- University Hospital of Cologne, Centre for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- University of Cologne, Centre for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Christopher A Haiman
- University of Southern California, Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA, USA
| | - Niclas Håkansson
- Karolinska Institutet, Institute of Environmental Medicine, Stockholm, Sweden
| | - Per Hall
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
- South General Hospital, Department of Oncology, Stockholm, Sweden
| | - Ute Hamann
- German Cancer Research Centre (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Susan Hankinson
- University of Massachusetts, Amherst, Department of Biostatistics & Epidemiology, Amherst, MA, USA
| | - Elaine F Harkness
- University of Manchester, Manchester Academic Health Science Centre, Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Nightingale Breast Screening Centre, Manchester, UK
- Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Unit, Manchester, UK
| | - Patricia A Harrington
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Steven N Hart
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Jaana M Hartikainen
- University of Eastern Finland, Translational Cancer Research Area, Kuopio, Finland
- University of Eastern Finland, Institute of Clinical Medicine, Pathology and Forensic Medicine, Kuopio, Finland
- Kuopio University Hospital, Imaging Centre, Department of Clinical Pathology, Kuopio, Finland
| | - Alexander Hein
- University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
| | - Peter Hillemanns
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Louise Hiller
- University of Warwick, Warwick Clinical Trials Unit, Coventry, UK
| | | | - Antoinette Hollestelle
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
| | - Maartje J Hooning
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
| | - Robert N Hoover
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - John L Hopper
- The University of Melbourne, Melbourne School of Population and Global Health, Centre for Epidemiology and Biostatistics, Melbourne, VIC, Australia
| | - Anthony Howell
- University of Manchester, Institute of Cancer studies, Manchester, UK
| | - Guanmengqian Huang
- German Cancer Research Centre (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Keith Humphreys
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm, Sweden
| | - David J Hunter
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Program in Genetic Epidemiology and Statistical Genetics, Boston, MA, USA
- University of Oxford, Nuffield Department of Population Health, Oxford, UK
| | | | - Esther M John
- Cancer Prevention Institute of California, Department of Epidemiology, Fremont, CA, USA
- Stanford University School of Medicine, Department of Health Research and Policy - Epidemiology, Stanford, CA, USA
- Stanford University School of Medicine, Department of Biomedical Data Science, Stanford, CA, USA
| | - Michael E Jones
- Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | | | - Audrey Jung
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Rudolf Kaaks
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Maria Kabisch
- German Cancer Research Centre (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Katarzyna Kaczmarek
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
| | - Michael J Kerin
- National University of Ireland, Surgery, School of Medicine, Galway, Ireland
| | - Sofia Khan
- University of Helsinki, Department of Obstetrics and Gynaecology, Helsinki University Hospital, Helsinki, Finland
| | - Elza Khusnutdinova
- Ufa Scientific Center of Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, Russia
- Bashkir State University, Department of Genetics and Fundamental Medicine, Ufa, Russia
| | - Johanna I Kiiski
- University of Helsinki, Department of Obstetrics and Gynaecology, Helsinki University Hospital, Helsinki, Finland
| | - Cari M Kitahara
- National Cancer Institute, Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Prosserman Centre for Population Health Research, Toronto, ON, Canada
- University of Toronto, Division of Epidemiology, Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Yon-Dschun Ko
- Johanniter Krankenhaus, Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Bonn, Germany
| | - Linetta B Koppert
- Erasmus MC Cancer Institute, Department of Surgical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
| | - Veli-Matti Kosma
- University of Eastern Finland, Translational Cancer Research Area, Kuopio, Finland
- University of Eastern Finland, Institute of Clinical Medicine, Pathology and Forensic Medicine, Kuopio, Finland
- Kuopio University Hospital, Imaging Centre, Department of Clinical Pathology, Kuopio, Finland
| | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Program in Genetic Epidemiology and Statistical Genetics, Boston, MA, USA
| | - Vessela N Kristensen
- Oslo University Hospital-Radiumhospitalet, Department of Cancer Genetics, Institute for Cancer Research, Oslo, Norway
- University of Oslo, Institute of Clinical Medicine, Faculty of Medicine, Oslo, Norway
- Department of Research, Vestre Viken Hospital, Drammen, Norway; Section for Breast- and Endocrine Surgery, Department of Cancer, Division of Surgery, Cancer and Transplantation Medicine, Oslo University Hospital-Ullevål, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
- Department of Pathology at Akershus University hospital, Lørenskog, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Division of Surgery and Cancer and Transplantation Medicine, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- National Advisory Unit on Late Effects after Cancer Treatment, Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Breast Cancer Research Consortium, Oslo University Hospital, Oslo, Norway
| | - Ute Krüger
- Lund University, Department of Cancer Epidemiology, Clinical Sciences, Lund, Sweden
| | - Tabea Kühl
- University Medical Center Hamburg-Eppendorf, Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), Hamburg, Germany
| | - Diether Lambrechts
- VIB, VIB Center for Cancer Biology, Leuven, Belgium
- University of Leuven, Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Epidemiology Program, Honolulu, HI, USA
| | - Eunjung Lee
- University of Southern California, Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA, USA
| | - Flavio Lejbkowicz
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Lian Li
- Tianjin Medical University Cancer Institute and Hospital, Department of Epidemiology, Tianjin, China
| | - Annika Lindblom
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden
| | - Sara Lindström
- University of Washington School of Public Health, Department of Epidemiology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - Martha Linet
- National Cancer Institute, Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Jolanta Lissowska
- M. Sklodowska-Curie Cancer Centre, Oncology Institute, Department of Cancer Epidemiology and Prevention, Warsaw, Poland
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | | | - Jan Lubiński
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
| | - Michael P Lux
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Centre Erlangen-EMN, Department of Gynaecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Robert J MacInnis
- Cancer Council Victoria, Cancer Epidemiology & Intelligence Division, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne School of Population and Global Health, Centre for Epidemiology and Biostatistics, Melbourne, VIC, Australia
| | - Melanie Maierthaler
- German Cancer Research Center (DKFZ), Molecular Epidemiology Group, C080, Heidelberg, Germany
| | - Tom Maishman
- University of Southampton, Southampton Clinical Trials Unit, Faculty of Medicine, Southampton, UK
- University of Southampton, Cancer Sciences Academic Unit, Faculty of Medicine, Southampton, UK
| | - Enes Makalic
- The University of Melbourne, Melbourne School of Population and Global Health, Centre for Epidemiology and Biostatistics, Melbourne, VIC, Australia
| | - Arto Mannermaa
- University of Eastern Finland, Translational Cancer Research Area, Kuopio, Finland
- University of Eastern Finland, Institute of Clinical Medicine, Pathology and Forensic Medicine, Kuopio, Finland
- Kuopio University Hospital, Imaging Centre, Department of Clinical Pathology, Kuopio, Finland
| | - Mehdi Manoochehri
- German Cancer Research Centre (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Siranoush Manoukian
- Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Unit of Medical Genetics, Department of Medical Oncology and Haematology, Milan, Italy
| | - Sara Margolin
- Karolinska Institutet, Department of Clinical Science and Education, Sšdersjukhuset, Stockholm, Sweden
| | - Maria Elena Martinez
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
- University of California San Diego, Department of Family Medicine and Public Health, La Jolla, CA, USA
| | - Dimitrios Mavroudis
- University Hospital of Heraklion, Department of Medical Oncology, Heraklion, Greece
| | - Catriona McLean
- The Alfred Hospital, Anatomical Pathology, Melbourne, VIC, Australia
| | - Alfons Meindl
- Ludwig Maximilian University of Munich, Department of Gynaecology and Obstetrics, Munich, Germany
| | - Pooja Middha
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
- University of Heidelberg, Faculty of Medicine, Heidelberg, Germany
| | - Nicola Miller
- National University of Ireland, Surgery, School of Medicine, Galway, Ireland
| | - Roger L Milne
- Cancer Council Victoria, Cancer Epidemiology & Intelligence Division, Melbourne, VIC, Australia
- The University of Melbourne, Melbourne School of Population and Global Health, Centre for Epidemiology and Biostatistics, Melbourne, VIC, Australia
| | - Fernando Moreno
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Medical Oncology Department, Hospital Cl'nico San Carlos, Madrid, Spain
| | - Anna Marie Mulligan
- University of Toronto, Department of Laboratory Medicine and Pathobiology, Toronto, ON, Canada
- University Health Network, Laboratory Medicine Program, Toronto, ON, Canada
| | - Claire Mulot
- INSERM UMR-S1147, Université Paris Sorbonne Cité, Paris, France
| | - Rami Nassir
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, CA, USA
| | - Susan L Neuhausen
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - William T Newman
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
- St Marys Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Sune F Nielsen
- Copenhagen University Hospital, Copenhagen General Population Study, Herlevand Gentofte Hospital, Herlev, Denmark
- Copenhagen University Hospital, Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Børge G Nordestgaard
- Copenhagen University Hospital, Copenhagen General Population Study, Herlevand Gentofte Hospital, Herlev, Denmark
- Copenhagen University Hospital, Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Aaron Norman
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Håkan Olsson
- Lund University, Department of Cancer Epidemiology, Clinical Sciences, Lund, Sweden
| | - Nick Orr
- Queen's University Belfast, Centre for Cancer Research and Cell Biology, Belfast, Ireland, UK
| | - V Shane Pankratz
- University of New Mexico, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | - Jose I A Perez
- Hospital Monte Naranco, Servicio de Cirug'a General y Especialidades, Oviedo, Spain
| | - Clara Pérez-Barrios
- Hospital Universitario Puerta de Hierro, Medical Oncology Department, Madrid, Spain
| | - Paolo Peterlongo
- The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, IFOM, Milan, Italy
| | - Christos Petridis
- King's College London, Research Oncology, Guy's Hospital, London, UK
| | - Mila Pinchev
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Karoliona Prajzendanc
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
| | - Ross Prentice
- Fred Hutchinson Cancer Research Center, Cancer Prevention Program, Seattle, WA, USA
| | - Nadege Presneau
- University of Westminster, Department of Biomedical Sciences, Faculty of Science and Technology, London, UK
| | - Darya Prokofieva
- Bashkir State University, Department of Genetics and Fundamental Medicine, Ufa, Russia
| | - Katri Pylkäs
- University of Oulu, Laboratory of Cancer Genetics and Tumour Biology, Cancer and Translational Medicine Research Unit, Biocentre Oulu, Oulu, Finland
- Northern Finland Laboratory Centre Oulu, Laboratory of Cancer Genetics and Tumour Biology, Oulu, Finland
| | - Brigitte Rack
- Ludwig Maximilian University of Munich, Department of Gynaecology and Obstetrics, Munich, Germany
| | - Paolo Radice
- Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Milan, Italy
| | | | - Gadi Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Hedy S Rennert
- Carmel Medical Center and Technion Faculty of Medicine, Clalit National Cancer Control Center, Haifa, Israel
| | - Valerie Rhenius
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Atocha Romero
- Hospital Universitario Puerta de Hierro, Medical Oncology Department, Madrid, Spain
| | | | | | - Elinor J Sawyer
- King's College London, Research Oncology, Guy's Hospital, London, UK
| | - Daniel F Schmidt
- The University of Melbourne, Melbourne School of Population and Global Health, Centre for Epidemiology and Biostatistics, Melbourne, VIC, Australia
| | - Rita K Schmutzler
- University Hospital of Cologne, Centre for Hereditary Breast and Ovarian Cancer, Cologne, Germany
- University of Cologne, Centre for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Andreas Schneeweiss
- University of Heidelberg, Department of Obstetrics and Gynecology, Heidelberg, Germany
- University of Heidelberg, National Centre for Tumour Diseases, Heidelberg, Germany
| | - Minouk J Schoemaker
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | - Fredrick Schumacher
- Case Western Reserve University, Department of Population and Quantitative Health Sciences, Cleveland, OH, USA
| | | | - Rodney J Scott
- John Hunter Hospital, Division of Molecular Medicine, Pathology North, Newcastle, NSW, Australia
- University of Newcastle, Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, Callaghan, NSW, Australia
- John Hunter Hospital, Hunter Medical Research Institute, Newcastle, NSW, Australia
- University of Newcastle, Centre for Information Based Medicine, Callaghan, Newcastle, NSW, Australia
| | - Christopher Scott
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Caroline Seynaeve
- Erasmus MC Cancer Institute, Department of Medical Oncology, Family Cancer Clinic, Rotterdam, The Netherlands
| | - Mitul Shah
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec - Université Laval Research Centre, Genomics Centre, Québec City, QC, Canada
| | - Ann Smeets
- University Hospitals Leuven, Department of Surgical Oncology, Leuven, Belgium
| | - Christof Sohn
- University of Heidelberg, National Centre for Tumour Diseases, Heidelberg, Germany
| | - Melissa C Southey
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, Victoria, Australia
- The University of Melbourne, Department of Clinical Pathology, Melbourne, VIC, Australia
| | - Anthony J Swerdlow
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
- The Institute of Cancer Research, Division of Breast Cancer Research, London, UK
| | - Aline Talhouk
- BC Cancer Agency and University of British Columbia, British Columbia's Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, Vancouver, BC, Canada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
- University of British Columbia, Department of Obstetrics and Gynaecology, Vancouver, BC, Canada
| | - Rulla M Tamimi
- Harvard Medical School, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Program in Genetic Epidemiology and Statistical Genetics, Boston, MA, USA
| | | | - Manuel R Teixeira
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
- University of Porto, Biomedical Sciences Institute (ICBAS), Porto, Portugal
| | - Maria Tengström
- University of Eastern Finland, Translational Cancer Research Area, Kuopio, Finland
- Kuopio University Hospital, Cancer Centre, Kuopio, Finland
- University of Eastern Finland, Institute of Clinical Medicine, Oncology, Kuopio, Finland
| | - Mary Beth Terry
- Columbia University, Department of Epidemiology, Mailman School of Public Health, New York, NY, USA
| | - Kathrin Thöne
- University Medical Center Hamburg-Eppendorf, Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), Hamburg, Germany
| | - Rob A E M Tollenaar
- Leiden University Medical Centre, Department of Surgery, Leiden, The Netherlands
| | - Ian Tomlinson
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, UK
- University of Oxford, Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Diana Torres
- German Cancer Research Centre (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
- Pontificia Universidad Javeriana, Institute of Human Genetics, Bogota, Colombia
| | - Thérèse Truong
- INSERM, University Paris-Sud, University Paris-Saclay, Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), Villejuif, France
| | - Constance Turman
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
| | - Clare Turnbull
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | | | - Michael Untch
- Helios Clinics Berlin-Buch, Department of Gynaecology and Obstetrics, Berlin, Germany
| | - Celine Vachon
- Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Christi J van Asperen
- Leiden University Medical Centre, Department of Clinical Genetics, Leiden, The Netherlands
| | | | - Elke M van Veen
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
- St Marys Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Camilla Wendt
- Karolinska Institutet, Department of Clinical Science and Education, Södersjukhuset, Stockholm, Sweden
| | - Alice S Whittemore
- Stanford University School of Medicine, Department of Health Research and Policy - Epidemiology, Stanford, CA, USA
- Stanford University School of Medicine, Department of Biomedical Data Science, Stanford, CA, USA
| | - Walter Willett
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Department of Nutrition, Boston, MA, USA
- Brigham and Women's Hospital and Harvard Medical School, Channing Division of Network Medicine, Boston, MA, USA
| | - Robert Winqvist
- University of Oulu, Laboratory of Cancer Genetics and Tumour Biology, Cancer and Translational Medicine Research Unit, Biocentre Oulu, Oulu, Finland
- Northern Finland Laboratory Centre Oulu, Laboratory of Cancer Genetics and Tumour Biology, Oulu, Finland
| | - Alicja Wolk
- Karolinska Institutet, Department of Environmental Medicine, Division of Nutritional Epidemiology, Stockholm, Sweden
| | - Xiaohong R Yang
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Yan Zhang
- German Cancer Research Center (DKFZ), Division of Clinical Epidemiology and Aging Research, Heidelberg, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Douglas F Easton
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Peter A Fasching
- University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
- University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, Los Angeles, CA, USA
| | - Heli Nevanlinna
- University of Helsinki, Department of Obstetrics and Gynaecology, Helsinki University Hospital, Helsinki, Finland
| | - Diana M Eccles
- University of Southampton, Cancer Sciences Academic Unit, Faculty of Medicine, Southampton, UK
| | - Paul D P Pharoah
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Marjanka K Schmidt
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Division of Molecular Pathology, Amsterdam, The Netherlands
- The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Division of Psychosocial Research and Epidemiology, Amsterdam, The Netherlands
| |
Collapse
|
13
|
Chai P, Jia R, Jia R, Pan H, Wang S, Ni H, Wang H, Zhou C, Shi Y, Ge S, Zhang H, Fan X. Dynamic chromosomal tuning of a novel GAU1 lncing driver at chr12p13.32 accelerates tumorigenesis. Nucleic Acids Res 2018; 46:6041-6056. [PMID: 29741668 PMCID: PMC6158754 DOI: 10.1093/nar/gky366] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/02/2018] [Accepted: 04/26/2018] [Indexed: 12/11/2022] Open
Abstract
Aberrant chromatin transformation dysregulates gene expression and may be an important driver of tumorigenesis. However, the functional role of chromosomal dynamics in tumorigenesis remains to be elucidated. Here, using in vitro and in vivo experiments, we reveal a novel long noncoding (lncing) driver at chr12p13.3, in which a novel lncRNA GALNT8 Antisense Upstream 1 (GAU1) is initially activated by an open chromatin status, triggering recruitment of the transcription elongation factor TCEA1 at the oncogene GALNT8 promoter and cis-activates the expression of GALNT8. Analysis of The Cancer Genome Atlas (TCGA) clinical database revealed that the GAU1/GALNT8 driver serves as an important indicative biomarker, and targeted silencing of GAU1 via the HKP-encapsulated method exhibited therapeutic efficacy in orthotopic xenografts. Our study presents a novel oncogenetic mechanism in which aberrant tuning of the chromatin state at specific chromosomal loci exposes factor-binding sites, leading to recruitment of trans-factor and activation of oncogenetic driver, thereby provide a novel alternative concept of chromatin dynamics in tumorigenesis.
Collapse
MESH Headings
- Adult
- Animals
- Biomarkers, Tumor
- Carcinogenesis/genetics
- Cell Line
- Cells, Cultured
- Chromatin/metabolism
- Chromosomes, Human, Pair 12
- Disease Progression
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Mice, Inbred BALB C
- Mice, Nude
- N-Acetylgalactosaminyltransferases/genetics
- N-Acetylgalactosaminyltransferases/metabolism
- Neuroblastoma/genetics
- Neuroblastoma/metabolism
- Promoter Regions, Genetic
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Retinal Neoplasms/genetics
- Retinal Neoplasms/metabolism
- Retinal Neoplasms/pathology
- Retinoblastoma/genetics
- Retinoblastoma/metabolism
- Retinoblastoma/pathology
- Transcriptional Elongation Factors/metabolism
- Polypeptide N-acetylgalactosaminyltransferase
Collapse
Affiliation(s)
- Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Ruobing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Hui Pan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Shaoyun Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Hongyan Ni
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Huixue Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Chuandi Zhou
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Yingyun Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - He Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| |
Collapse
|
14
|
Homeobox A11 hypermethylation indicates unfavorable prognosis in breast cancer. Oncotarget 2018; 8:9794-9805. [PMID: 28038461 PMCID: PMC5354771 DOI: 10.18632/oncotarget.14216] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 12/05/2016] [Indexed: 01/17/2023] Open
Abstract
Homeobox A11 (HOXA11) is one of the hypermethylated genes in breast cancer and its function in breast tumorigenesis remains elusive. In this study, we analyzed the methylation status of HOXA11 in 264 paired breast cancer and normal tissue as well as in matched serum samples by MethyLight assay. Further, the function of HOXA11 in breast tumorigenesis was analyzed by cell proliferation and migration assays. We found that HOXA11 was hypermethylated in cancer tissues (45.08%), especially in invasive ductal carcinomas (P<0.001), patients with a family history of cancer (P=0.033), cases with metastatic lymph nodes (P=0.004) and P53 positive group (P=0.017). Kaplan-Meier survival analysis and Cox regression analysis revealed that HOXA11 hypermethylation is an independent predictor of poor outcomes. The over expression of HOXA11 suppressed cell growth in MDA-MB-231, MCF7, SKBR3 and BT474 cells. In conclusion, the hypermethylation of HOXA11 is an independent prognostic biomarker in breast cancer. Additionally, HOXA11 can be a potential tumor suppressor.
Collapse
|
15
|
Watanabe Y, Saito M, Saito K, Matsumoto Y, Kanke Y, Onozawa H, Hayase S, Sakamoto W, Ishigame T, Momma T, Ohki S, Takenoshita S. Upregulated HOXA9 expression is associated with lymph node metastasis in colorectal cancer. Oncol Lett 2017; 15:2756-2762. [PMID: 29435001 PMCID: PMC5778893 DOI: 10.3892/ol.2017.7650] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/30/2017] [Indexed: 12/19/2022] Open
Abstract
Homeobox A (HOXA) cluster genes, members of the HOX family, perform an important role in normal organ development. It has previously been reported that HOXA gene expression in various types of cancer is associated with poor patient outcomes. However, the role of HOXA genes, as well as their expression, in colorectal cancers (CRC) remains unknown. Therefore, the present study investigated HOXA gene expression in patients with CRC and revealed that HOXA9 expression was significantly increased in tumor tissues compared with non-tumor tissues. Additionally, the functional role of HOXA9 was assessed by knocking down the HOXA9 gene in CRC cells and by evaluating cell growth. Regarding gene expression, cases with positive HOXA9 expression (as detected by immunohistochemical staining) were significantly associated with higher TNM stage and positive lymph node metastasis, although no association was observed between increased HOXA9 levels and the rate of overall survival in the present cohort. Regarding the functional role, HOXA9 expression was demonstrated to be upregulated in patients with CRC and was associated with lymph node metastasis.
Collapse
Affiliation(s)
- Yohei Watanabe
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Motonobu Saito
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Katsuharu Saito
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Yoshiko Matsumoto
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Yasuyuki Kanke
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Hisashi Onozawa
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Suguru Hayase
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Wataru Sakamoto
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Teruhide Ishigame
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Tomoyuki Momma
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Shinji Ohki
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| | - Seiichi Takenoshita
- Department of Organ Regulatory Surgery, Fukushima Medical University School of Medicine, Fukushima 960-1295, Japan
| |
Collapse
|
16
|
Bahrami A, Joodi M, Maftooh M, Ferns GA, M. Ahmadi M, Hassanian SM, Avan A. The genetic factors contributing to the development of Wilm's tumor and their clinical utility in its diagnosis and prognosis. J Cell Physiol 2017; 233:2882-2888. [DOI: 10.1002/jcp.26021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/19/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Afsane Bahrami
- Department of Modern Sciences and Technologies; Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
- Student Research Committee; Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
| | - Marjan Joodi
- Department of Pediatric Surgery; Faculty of Medicine; Mashhad University of Medical Sciences; Mashhad Iran
- Endoscopic and Minimally Invasive Surgery Research Center; Sarvar Children's Hospital; Mashhad Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Gordon A. Ferns
- Division of Medical Education, Falmer, Brighton; Brighton and Sussex Medical School; Sussex UK
| | - Mehrdad M. Ahmadi
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Seyed M. Hassanian
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| | - Amir Avan
- Metabolic Syndrome Research Center; Mashhad University of Medical Sciences; Mashhad Iran
- Cancer Research Center; Mashhad University of Medical Sciences; Mashhad Iran
| |
Collapse
|
17
|
Qu XL, Ming-Zhang, Yuan-Fang, Wang H, Zhang YZ. Effect of 2,3',4,4',5-Pentachlorobiphenyl Exposure on Endometrial Receptivity and the Methylation of HOXA10. Reprod Sci 2017. [PMID: 28631552 DOI: 10.1177/1933719117711258] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Polychlorinated biphenyls (PCBs) are one of the most common endocrine-disrupting chemicals and have obvious toxicity on human reproductive development. The aim of our study was to investigate the toxicity of chronic 2,3',4,4',5-pentachlorobiphenyl (PCB 118) exposure on embryo implantation and endometrial receptivity, with the possible mechanism of DNA methylation involved. Virgin CD-1 female mice (3 weeks old) were housed and orally treated with PCB 118 (0, 1, 10, 100 μg/kg) for a month. After mating with fertile males, the pregnant mice were killed on gestation day 4.5. Compared with the control group, implantation failures were observed in 1 μg/kg PCB 118- and 100 μg/kg PCB 118-treated groups. Abnormal endometrial morphology with open uterine lumens and densely compact stromal cells and poorly developed pinopodes were substantially in response to PCB 118 doses above, as well as the significant downregulation of implantation-associated genes (estrogen receptor 1, homeobox A10 [HOXA10], integrin subunit beta 3) and hypermethylation in the promoter region of HOXA10 further. It was confirmed that chronic exposure to PCB 118 produced an increased number of implantation failures in association with a defective uterine morphology during the implantation period. Alterations in methylation of HOXA10 could explain, at least in part, the mechanism of effects of PCB 118 exposure on the implantation process.
Collapse
Affiliation(s)
- Xin-Lan Qu
- 1 The Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,2 Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China.,3 Hubei Provincial Key Laboratory of Developmentally Originated Diseases, Wuhan, China
| | - Ming-Zhang
- 1 The Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,2 Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China.,3 Hubei Provincial Key Laboratory of Developmentally Originated Diseases, Wuhan, China
| | - Yuan-Fang
- 4 Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Wang
- 3 Hubei Provincial Key Laboratory of Developmentally Originated Diseases, Wuhan, China.,5 Department of Pharmacology, Basic Medical School of Wuhan University, Wuhan, China
| | - Yuan-Zhen Zhang
- 1 The Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,2 Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, China.,3 Hubei Provincial Key Laboratory of Developmentally Originated Diseases, Wuhan, China
| |
Collapse
|
18
|
Gonzalez-Cortes T, Recio-Vega R, Lantz RC, Chau BT. DNA methylation of extracellular matrix remodeling genes in children exposed to arsenic. Toxicol Appl Pharmacol 2017; 329:140-147. [PMID: 28579250 DOI: 10.1016/j.taap.2017.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022]
Abstract
Several novel mechanistic findings regarding to arsenic's pathogenesis has been reported and some of them suggest that the etiology of some arsenic induced diseases are due in part to heritable changes to the genome via epigenetic processes such as DNA methylation, histone maintenance, and mRNA expression. Recently, we reported that arsenic exposure during in utero and early life was associated with impairment in the lung function and abnormal receptor for advanced glycation endproducts (RAGE), matrix metalloproteinase-9 (MMP-9) and tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) sputum levels. Based on our results and the reported arsenic impacts on DNA methylation, we designed this study in our cohort of children exposed in utero and early childhood to arsenic with the aim to associate DNA methylation of MMP9, TIMP1 and RAGE genes with its protein sputum levels and with urinary and toenail arsenic levels. The results disclosed hypermethylation in MMP9 promotor region in the most exposed children; and an increase in the RAGE sputum levels among children with the mid methylation level; there were also positive associations between MMP9 DNA methylation with arsenic toenail concentrations; RAGE DNA methylation with iAs, and %DMA; and finally between TIMP1 DNA methylation with the first arsenic methylation. A negative correlation between MMP9 sputum levels with its DNA methylation was registered. In conclusion, arsenic levels were positive associated with the DNA methylation of extracellular matrix remodeling genes;, which in turn could modifies the biological process in which they are involved causing or predisposing to lung diseases.
Collapse
Affiliation(s)
- Tania Gonzalez-Cortes
- Department of Environmental Health, Biomedical Research Center, School of Medicine, University of Coahuila, Torreon, Coahuila, Mexico
| | - Rogelio Recio-Vega
- Department of Environmental Health, Biomedical Research Center, School of Medicine, University of Coahuila, Torreon, Coahuila, Mexico.
| | - Robert Clark Lantz
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States; Southwest Environmental Health Science Center, University of Arizona, Tucson, AZ, United States
| | - Binh T Chau
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
19
|
Staševskij Z, Gibas P, Gordevičius J, Kriukienė E, Klimašauskas S. Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. Mol Cell 2017; 65:554-564.e6. [PMID: 28111014 DOI: 10.1016/j.molcel.2016.12.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 10/13/2016] [Accepted: 12/15/2016] [Indexed: 12/17/2022]
Abstract
Modification of CG dinucleotides in DNA is part of epigenetic regulation of gene function in vertebrates and is associated with complex human disease. Bisulfite sequencing permits high-resolution analysis of cytosine modification in mammalian genomes; however, its utility is often limited due to substantial cost. Here, we describe an alternative epigenome profiling approach, named TOP-seq, which is based on covalent tagging of individual unmodified CG sites followed by non-homologous priming of the DNA polymerase action at these sites to directly produce adjoining regions for their sequencing and precise genomic mapping. Pilot TOP-seq analyses of bacterial and human genomes showed a better agreement of TOP-seq with published bisulfite sequencing maps as compared to widely used MBD-seq and MRE-seq and permitted identification of long-range and gene-level differential methylation among human tissues and neuroblastoma cell types. Altogether, we propose an affordable single CG-resolution technique well suited for large-scale epigenome studies.
Collapse
Affiliation(s)
- Zdislav Staševskij
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Juozas Gordevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania; Department of Systems Analysis, Institute of Mathematics and Informatics, Vilnius University, Vilnius LT-08663, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania.
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania.
| |
Collapse
|
20
|
Abstract
microRNAs (miRNAs) and DNA methylation are the 2 epigenetic modifications that have emerged in recent years as the most critical players in the regulation of gene expression. Compelling evidence has indicated the roles of miRNAs and DNA methylation in modulating cellular transformation and tumorigenesis. miRNAs act as negative regulators of gene expression and are involved in the regulation of both physiologic conditions and during diseases, such as cancer, inflammatory diseases, and psychiatric disorders, among others. Meanwhile, aberrant DNA methylation manifests in both global genome changes and in localized gene promoter changes, which influences the transcription of cancer genes. In this review, we described the mutual regulation of miRNAs and DNA methylation in human cancers. miRNAs regulate DNA methylation by targeting DNA methyltransferases or methylation-related proteins. On the other hand, both hyper- and hypo-methylation of miRNAs occur frequently in human cancers and represent a new level of complexity in gene regulation. Therefore, understanding the mechanisms underlying the mutual regulation of miRNAs and DNA methylation may provide helpful insights in the development of efficient therapeutic approaches.
Collapse
Affiliation(s)
- Sumei Wang
- a Department of Oncology , Guangdong Provincial Hospital of Chinese Medicine , Guangzhou, Guangdong , P. R. China.,b Department of Systems Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Wanyin Wu
- a Department of Oncology , Guangdong Provincial Hospital of Chinese Medicine , Guangzhou, Guangdong , P. R. China
| | - Francois X Claret
- b Department of Systems Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA.,c Experimental Therapeutics Academic Program and Cancer Biology Program , The University of Texas Graduate School of Biomedical Sciences at Houston , Houston , TX , USA
| |
Collapse
|
21
|
Labade AS, Karmodiya K, Sengupta K. HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205. Epigenetics Chromatin 2016; 9:54. [PMID: 27980680 PMCID: PMC5135769 DOI: 10.1186/s13072-016-0106-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
Background The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown. Results Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster. Conclusions This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0106-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ajay S Labade
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| | - Krishanpal Karmodiya
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| |
Collapse
|
22
|
Verma M. Genome-wide association studies and epigenome-wide association studies go together in cancer control. Future Oncol 2016; 12:1645-64. [PMID: 27079684 PMCID: PMC5551540 DOI: 10.2217/fon-2015-0035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/22/2016] [Indexed: 02/07/2023] Open
Abstract
Completion of the human genome a decade ago laid the foundation for: using genetic information in assessing risk to identify individuals and populations that are likely to develop cancer, and designing treatments based on a person's genetic profiling (precision medicine). Genome-wide association studies (GWAS) completed during the past few years have identified risk-associated single nucleotide polymorphisms that can be used as screening tools in epidemiologic studies of a variety of tumor types. This led to the conduct of epigenome-wide association studies (EWAS). This article discusses the current status, challenges and research opportunities in GWAS and EWAS. Information gained from GWAS and EWAS has potential applications in cancer control and treatment.
Collapse
Affiliation(s)
- Mukesh Verma
- Methods & Technologies Branch, Epidemiology & Genomics Research Program, Division of Cancer Control & Population Sciences, National Cancer Institute (NCI), NIH, 9609 Medical Center Drive, Suite 4E102, Rockville, MD 20850, USA
| |
Collapse
|
23
|
Fan H, Zhao H, Pang L, Liu L, Zhang G, Yu F, Liu T, Xu C, Xiao Y, Li X. Systematically Prioritizing Functional Differentially Methylated Regions (fDMRs) by Integrating Multi-omics Data in Colorectal Cancer. Sci Rep 2015; 5:12789. [PMID: 26239918 PMCID: PMC4523937 DOI: 10.1038/srep12789] [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: 03/23/2015] [Accepted: 07/08/2015] [Indexed: 01/06/2023] Open
Abstract
While genome-wide differential DNA methylation regions (DMRs) have been extensively identified, the comprehensive prioritization of their functional importance is still poorly explored. Here, we aggregated multiple data resources rooted in the genome, epigenome and transcriptome to systematically prioritize functional DMRs (fDMRs) in colorectal cancer (CRC). As demonstrated, the top-ranked fDMRs from all of the data resources showed a strong enrichment for known methylated genes. Additionally, we analyzed those top 5% DMR-coupled coding genes using functional enrichment, which resulted in significant disease-related biological functions in contrast to the tail 5% genes. To further confirm the functional importance of the top-ranked fDMRs, we applied chromatin modification alterations of CRC cell lines to characterize their functional regulation. Specifically, we extended the utility of the top-ranked DMR-coupled genes to serve as classification and survival biomarkers, which showed a robust performance across diverse independent data sets. Collectively, our results established an integrative framework to prioritize fDMRs, which could help characterize aberrant DNA methylation-induced potential mechanisms underlying tumorigenesis and uncover epigenome-based biomarkers for clinical diagnosis and prognosis.
Collapse
Affiliation(s)
- Huihui Fan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Hongying Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Ling Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Guanxiong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Tingting Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| |
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
Theophilou G, Paraskevaidi M, Lima KMG, Kyrgiou M, Martin-Hirsch PL, Martin FL. Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology. Expert Rev Mol Diagn 2015; 15:693-713. [DOI: 10.1586/14737159.2015.1028372] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
26
|
Jadhav RR, Ye Z, Huang RL, Liu J, Hsu PY, Huang YW, Rangel LB, Lai HC, Roa JC, Kirma NB, Huang THM, Jin VX. Genome-wide DNA methylation analysis reveals estrogen-mediated epigenetic repression of metallothionein-1 gene cluster in breast cancer. Clin Epigenetics 2015; 7:13. [PMID: 25763113 PMCID: PMC4355986 DOI: 10.1186/s13148-015-0045-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 01/13/2015] [Indexed: 12/23/2022] Open
Abstract
Background Recent genome-wide analysis has shown that DNA methylation spans long stretches of chromosome regions consisting of clusters of contiguous CpG islands or gene families. Hypermethylation of various gene clusters has been reported in many types of cancer. In this study, we conducted methyl-binding domain capture (MBDCap) sequencing (MBD-seq) analysis on a breast cancer cohort consisting of 77 patients and 10 normal controls, as well as a panel of 38 breast cancer cell lines. Results Bioinformatics analysis determined seven gene clusters with a significant difference in overall survival (OS) and further revealed a distinct feature that the conservation of a large gene cluster (approximately 70 kb) metallothionein-1 (MT1) among 45 species is much lower than the average of all RefSeq genes. Furthermore, we found that DNA methylation is an important epigenetic regulator contributing to gene repression of MT1 gene cluster in both ERα positive (ERα+) and ERα negative (ERα−) breast tumors. In silico analysis revealed much lower gene expression of this cluster in The Cancer Genome Atlas (TCGA) cohort for ERα + tumors. To further investigate the role of estrogen, we conducted 17β-estradiol (E2) and demethylating agent 5-aza-2′-deoxycytidine (DAC) treatment in various breast cancer cell types. Cell proliferation and invasion assays suggested MT1F and MT1M may play an anti-oncogenic role in breast cancer. Conclusions Our data suggests that DNA methylation in large contiguous gene clusters can be potential prognostic markers of breast cancer. Further investigation of these clusters revealed that estrogen mediates epigenetic repression of MT1 cluster in ERα + breast cancer cell lines. In all, our studies identify thousands of breast tumor hypermethylated regions for the first time, in particular, discovering seven large contiguous hypermethylated gene clusters. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0045-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rohit R Jadhav
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Zhenqing Ye
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan
| | - Joseph Liu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Pei-Yin Hsu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, 9200 West Wisconsin Avenue, Froedtert Medical College Lab Building (FMCLB) 258, Milwaukee, 53226 WI USA
| | - Leticia B Rangel
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Pharmaceutical Sciences, Biotechnology Program/RENORBIO, Health Sciences Center, Universidade Federal do Espirito Santo, Av. Marechal Campos, 1468, Maruipe, 29040-090 Vitoria ES Brazil ; Programa Ciencias Sem Fronteiras, CNPq, Brasilia, Brazil
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Taipei Medical University Shuang Ho Hospital, New Taipei City, 23561 Taiwan ; School of Medicine, Taipei Medical University, No. 250, Wu-Hsing Street, Taipei, 110 Taiwan ; Graduate Institute of Life Sciences, Department and Graduate Institute of Biochemistry, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Juan Carlos Roa
- Departamento de Pathologı'a, Universidad de la Frontera, Claro Solar 115, Temuco, Chile
| | - Nameer B Kirma
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| | - Victor X Jin
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, STRF, Room 225, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Cancer Therapy and Research Center, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA ; Department of Epidemiology and Biostatistics, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, 78229 TX USA
| |
Collapse
|
27
|
Xia R, Jin FY, Lu K, Wan L, Xie M, Xu TP, De W, Wang ZX. SUZ12 promotes gastric cancer cell proliferation and metastasis by regulating KLF2 and E-cadherin. Tumour Biol 2015; 36:5341-51. [PMID: 25672609 DOI: 10.1007/s13277-015-3195-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 01/30/2015] [Indexed: 12/31/2022] Open
Abstract
SUZ12 is a core component of the polycomb repressive complex 2 (PRC2), which could silence gene transcription by generating trimethylation on lysine 27 residue of histone H3 (H3K27Me3). Meanwhile, SUZ12 has been found to be overexpressed in multiple cancers; however, the clinical significance and molecular mechanisms of SUZ12 controlling gastric cancer cell proliferation and metastasis are unclear. In this study, we found that SUZ12 expression was significantly increased in 64 gastric tumor tissues compared with normal tissues. Additionally, SUZ12 expression was associated with pathological stage, metastasis distance, and shorter overall survival of gastric cancer patients. Knockdown of SUZ12 expression impaired cell proliferation and invasion in vitro, leading to the inhibition of metastasis in vivo. Upregulation of SUZ12 was found to play a key role in gastric cancer cell proliferation and metastasis through the regulation of EMT and KLF2 expression.
Collapse
Affiliation(s)
- Rui Xia
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Vallot C, Hérault A, Boyle S, Bickmore WA, Radvanyi F. PRC2-independent chromatin compaction and transcriptional repression in cancer. Oncogene 2015; 34:741-51. [PMID: 24469045 DOI: 10.1038/onc.2013.604] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 12/10/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022]
Abstract
The silencing of large chromosomal regions by epigenetic mechanisms has been reported to occur frequently in cancer. Epigenetic marks, such as histone methylation and acetylation, are altered at these loci. However, the mechanisms of formation of such aberrant gene clusters remain largely unknown. Here, we show that, in cancer cells, the epigenetic remodeling of chromatin into hypoacetylated domains covered with histone H3K27 trimethylation is paralleled by changes in higher-order chromatin structures. Using fluorescence in situ hybridization, we demonstrate that regional epigenetic silencing corresponds to the establishment of compact chromatin domains. We show that gene repression is tightly correlated to the state of chromatin compaction and not to the levels of H3K27me3-its removal through the knockdown of EZH2 does not induce significant gene expression nor chromatin decompaction. Moreover, transcription can occur with intact high-H3K27me3 levels; treatment with histone deacetylase inhibitors can relieve chromatin compaction and gene repression, without altering H3K27me3 levels. Our findings imply that compaction and subsequent repression of large chromatin domains are not direct consequences of PRC2 deregulation in cancer cells. By challenging the role of EZH2 in aberrant gene silencing in cancer, these findings have therapeutical implications, notably for the choice of epigenetic drugs for tumors with multiple regional epigenetic alterations.
Collapse
Affiliation(s)
- C Vallot
- 1] CNRS, UMR 144 - Cell Biology Department, Institut Curie, Paris, France [2] Institut Curie, Centre de Recherche, Paris, France
| | - A Hérault
- 1] CNRS, UMR 144 - Cell Biology Department, Institut Curie, Paris, France [2] Institut Curie, Centre de Recherche, Paris, France
| | - S Boyle
- Chromosome and Gene Expression Section, MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Scotland, UK
| | - W A Bickmore
- 1] Chromosome and Gene Expression Section, MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Scotland, UK [2] Breakthrough Breast Cancer Research Unit, University of Edinburgh, Scotland, UK
| | - F Radvanyi
- 1] CNRS, UMR 144 - Cell Biology Department, Institut Curie, Paris, France [2] Institut Curie, Centre de Recherche, Paris, France
| |
Collapse
|
29
|
Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nat Genet 2014; 47:22-30. [PMID: 25485837 DOI: 10.1038/ng.3165] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/17/2014] [Indexed: 12/14/2022]
Abstract
Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.
Collapse
Affiliation(s)
- Lei Gu
- 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra C Frommel
- 1] Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland. [2] Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Christopher C Oakes
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Grupp
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cristina Y Gerig
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Dominik Bär
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- 1] Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland. [2] Swiss Institute of Bioinformatics (SIB), University of Zurich, Zurich, Switzerland
| | - Constance Baer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Weiss
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthieu Schapira
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Ruprecht Kuner
- Unit of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center of Tumour Diseases, Heidelberg, Germany
| | - Holger Sültmann
- Unit of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center of Tumour Diseases, Heidelberg, Germany
| | - Maurizio Provenzano
- Oncology Research Unit, Division of Urology, University Hospital of Zurich, Zurich, Switzerland
| | | | | | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thorsten Schlomm
- Martini Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roland Eils
- 1] Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [2] Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raffaella Santoro
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
30
|
Minning C, Mokhtar NM, Abdullah N, Muhammad R, Emran NA, Ali SAMD, Harun R, Jamal R. Exploring breast carcinogenesis through integrative genomics and epigenomics analyses. Int J Oncol 2014; 45:1959-68. [PMID: 25175708 DOI: 10.3892/ijo.2014.2625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 07/18/2014] [Indexed: 11/05/2022] Open
Abstract
There have been many DNA methylation studies on breast cancer which showed various methylation patterns involving tumour suppressor genes and oncogenes but only a few of those studies link the methylation data with gene expression. More data are required especially from the Asian region and to analyse how the epigenome data correlate with the transcriptome. DNA methylation profiling was carried out on 76 fresh frozen primary breast tumour tissues and 25 adjacent non-cancerous breast tissues using the Illumina Infinium(®) HumanMethylation27 BeadChip. Validation of methylation results was performed on 7 genes using either MS-MLPA or MS-qPCR. Gene expression profiling was done on 15 breast tumours and 5 adjacent non-cancerous breast tissues using the Affymetrix GeneChip(®) Human Gene 1.0 ST array. The overlapping genes between DNA methylation and gene expression datasets were further mapped to the KEGG database to identify the molecular pathways that linked these genes together. Supervised hierarchical cluster analysis revealed 1,389 hypermethylated CpG sites and 22 hypomethylated CpG sites in cancer compared to the normal samples. Gene expression microarray analysis using a fold-change of at least 1.5 and a false discovery rate (FDR) at p>0.05 identified 404 upregulated and 463 downregulated genes in cancer samples. Integration of both datasets identified 51 genes with hypermethylation with low expression (negative association) and 13 genes with hypermethylation with high expression (positive association). Most of the overlapping genes belong to the focal adhesion and extracellular matrix-receptor interaction that play important roles in breast carcinogenesis. The present study displayed the value of using multiple datasets in the same set of tissues and how the integrative analysis can create a list of well-focused genes as well as to show the correlation between epigenetic changes and gene expression. These gene signatures can help us understand the epigenetic regulation of gene expression and could be potential targets for therapeutic intervention in the future.
Collapse
Affiliation(s)
- Chin Minning
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Norlia Abdullah
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rohaizak Muhammad
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nor Aina Emran
- Department of Surgery, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Siti Aishah M D Ali
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Roslan Harun
- Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| |
Collapse
|
31
|
Xavier FCA, Destro MFDSS, Duarte CME, Nunes FD. Epigenetic repression of HOXB cluster in oral cancer cell lines. Arch Oral Biol 2014; 59:783-9. [DOI: 10.1016/j.archoralbio.2014.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 03/25/2014] [Accepted: 05/02/2014] [Indexed: 12/12/2022]
|
32
|
Marcato P, Dean CA, Liu RZ, Coyle KM, Bydoun M, Wallace M, Clements D, Turner C, Mathenge EG, Gujar SA, Giacomantonio CA, Mackey JR, Godbout R, Lee PWK. Aldehyde dehydrogenase 1A3 influences breast cancer progression via differential retinoic acid signaling. Mol Oncol 2014; 9:17-31. [PMID: 25106087 DOI: 10.1016/j.molonc.2014.07.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/12/2014] [Accepted: 07/13/2014] [Indexed: 01/08/2023] Open
Abstract
Aldehyde dehydrogenase (ALDH) 1A enzymes produce retinoic acid (RA), a transcription induction molecule. To investigate if ALDH1A1 or ALDH1A3-mediated RA signaling has an active role in breast cancer tumorigenesis, we performed gene expression and tumor xenograft studies. Analysis of breast patient tumors revealed that high levels of ALDH1A3 correlated with expression of RA-inducible genes with retinoic acid response elements (RAREs), poorer patient survival and triple-negative breast cancers. This suggests a potential link between ALDH1A3 expression and RA signaling especially in aggressive and/or triple-negative breast cancers. In MDA-MB-231, MDA-MB-468 and MDA-MB-435 cells, ALDH1A3 and RA increased expression of RA-inducible genes. Interestingly, ALDH1A3 had opposing effects in tumor xenografts, increasing tumor growth and metastasis of MDA-MB-231 and MDA-MB-435 cells, but decreasing tumor growth of MDA-MB-468 cells. Exogenous RA replaced ALDH1A3 in inducing the same opposing tumor growth and metastasis effects, suggesting that ALDH1A3 mediates these effects by promoting RA signaling. Genome expression analysis revealed that ALDH1A3 induced largely divergent gene expression in MDA-MB-231 and MDA-MB-468 cells which likely resulted in the opposing tumor growth effects. Treatment with DNA methylation inhibitor 5-aza-2'deoxycytidine restored uniform RA-inducibility of RARE-containing HOXA1 and MUC4 in MDA-MB-231 and MDA-MB-468 cells, suggesting that differences in epigenetic modifications contribute to differential ALDH1A3/RA-induced gene expression in breast cancer. In summary, ALDH1A3 induces differential RA signaling in breast cancer cells which affects the rate of breast cancer progression.
Collapse
Affiliation(s)
- Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS, Canada; Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada.
| | - Cheryl A Dean
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada
| | - Rong-Zong Liu
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Krysta M Coyle
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Moamen Bydoun
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Melissa Wallace
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Derek Clements
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Colin Turner
- Department of Surgery, Dalhousie University, Halifax, NS, Canada
| | | | - Shashi A Gujar
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada; Strategy and Organizational Performance, IWK Health Centre, Halifax, NS, Canada
| | | | - John R Mackey
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Patrick W K Lee
- Department of Pathology, Dalhousie University, Halifax, NS, Canada; Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada.
| |
Collapse
|
33
|
Genomic and transcriptomic analyses match medulloblastoma mouse models to their human counterparts. Acta Neuropathol 2014; 128:123-36. [PMID: 24871706 DOI: 10.1007/s00401-014-1297-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/08/2014] [Accepted: 05/19/2014] [Indexed: 12/15/2022]
Abstract
Medulloblastoma is a malignant embryonal brain tumor with highly variable outcome. In order to study the biology of this tumor and to perform preclinical treatment studies, a lot of effort has been put into the generation of appropriate mouse models. The usage of these models, however, has become debatable with the advances in human medulloblastoma subgrouping. This study brings together multiple relevant mouse models and matches genetic alterations and gene expression data of 140 murine tumors with 423 human medulloblastomas in a global way. Using AGDEX analysis and k-means clustering, we show that the Blbp-cre::Ctnnb1(ex3)(Fl/+)Trp53 (Fl/Fl) mouse model fits well to human WNT medulloblastoma, and that, among various Myc- or Mycn-based mouse medulloblastomas, tumors in Glt1-tTA::TRE-MYCN/Luc mice proved to be most specific for human group 3 medulloblastoma. None of the analyzed models displayed a significant match to group 4 tumors. Intriguingly, mice with Ptch1 or Smo mutations selectively modeled SHH medulloblastomas of adulthood, although such mutations occur in all human age groups. We therefore suggest that the infantile or adult gene expression pattern of SHH MBs are not solely determined by specific mutations. This is supported by the observation that human medulloblastomas with PTCH1 mutations displayed more similarities to PTCH1 wild-type tumors of the same age group than to PTCH1-mutated tumors of the other age group. Together, we provide novel insights into previously unrecognized specificity of distinct models and suggest these findings as a solid basis to choose the appropriate model for preclinical studies on medulloblastoma.
Collapse
|
34
|
Busuttil RA, George J, Tothill RW, Ioculano K, Kowalczyk A, Mitchell C, Lade S, Tan P, Haviv I, Boussioutas A. A signature predicting poor prognosis in gastric and ovarian cancer represents a coordinated macrophage and stromal response. Clin Cancer Res 2014; 20:2761-72. [PMID: 24658156 DOI: 10.1158/1078-0432.ccr-13-3049] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE Gene-expression profiling has revolutionized the way we think about cancer and confers the ability to observe the synchronous expression of thousands of genes. The use of putative genome-level expression profiles has allowed biologists to observe the complex interactions of genes that constitute recognized biologic pathways. We used gastric and ovarian datasets to identify gene-expression signatures and determine any functional significance. EXPERIMENTAL DESIGN Microarray data of 94-tumor and 45-benign samples derived from patients with gastric cancer were interrogated using Hierarchical Ordered Partitioning and Collapsing Hybrid analysis identifying clusters of coexpressed genes. Clusters were further characterized with respect to biologic significance, gene ontology, and ability to discriminate between normal and tumor tissue. Tumor tissues were separated into epithelial and stromal compartments and immunohistochemical analysis performed to further elucidate specific cell lineages expressing genes contained in the signature. RESULTS We identified a "stromal-response" expression signature, highly enriched for inflammatory, extracellular matrix, cytokine, and growth factor proteins. The majority of genes in the signature are expressed in the tumor-associated stroma but were absent in associated premalignant conditions. In gastric cancer, this module almost perfectly differentiates tumor from nonmalignant gastric tissue and hence can be regarded as a highly tumor-specific gene-expression signature. CONCLUSIONS We show that these genes are consistently coexpressed across a range of independent gastric datasets as well as other cancer types suggesting a conserved functional role in cancer. In addition, we show that this signature can be a surrogate marker for M2 macrophage activity and has significant prognostic implications in gastric and ovarian high-grade serous cancer.
Collapse
Affiliation(s)
- Rita A Busuttil
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Fa
| | - Joshy George
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, Israel
| | - Richard W Tothill
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, Israel
| | - Kylie Ioculano
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, Israel
| | - Adam Kowalczyk
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, Israel
| | - Catherine Mitchell
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, Israel
| | - Stephen Lade
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, Israel
| | - Patrick Tan
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Fa
| | - Izhak Haviv
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Fa
| | - Alex Boussioutas
- Authors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Faculty of Medicine in the Galilee, Bar Ilan University, Zfat, IsraelAuthors' Affiliations: Cancer Genetics and Genomics Laboratory; Molecular Genomics Core Facility; Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne; Sir Peter MacCallum Department of Oncology; Department of Medicine, Royal Melbourne Hospital; National ICT Australia (NICTA); Department of Pathology, The University of Melbourne, Parkville, Australia; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School; Cellular and Molecular Research, National Cancer Centre; Cancer Science Institute of Singapore, National University of Singapore; Genome Institute of Singapore, Singapore; and Fa
| |
Collapse
|
35
|
Hatzfeld M, Wolf A, Keil R. Plakophilins in Desmosomal Adhesion and Signaling. ACTA ACUST UNITED AC 2014; 21:25-42. [DOI: 10.3109/15419061.2013.876017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
36
|
Kanduri M, Sander B, Ntoufa S, Papakonstantinou N, Sutton LA, Stamatopoulos K, Kanduri C, Rosenquist R. A key role for EZH2 in epigenetic silencing of HOX genes in mantle cell lymphoma. Epigenetics 2013; 8:1280-8. [PMID: 24107828 DOI: 10.4161/epi.26546] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The chromatin modifier EZH2 is overexpressed and associated with inferior outcome in mantle cell lymphoma (MCL). Recently, we demonstrated preferential DNA methylation of HOX genes in MCL compared with chronic lymphocytic leukemia (CLL), despite these genes not being expressed in either entity. Since EZH2 has been shown to regulate HOX gene expression, to gain further insight into its possible role in differential silencing of HOX genes in MCL vs. CLL, we performed detailed epigenetic characterization using representative cell lines and primary samples. We observed significant overexpression of EZH2 in MCL vs. CLL. Chromatin immune precipitation (ChIP) assays revealed that EZH2 catalyzed repressive H3 lysine 27 trimethylation (H3K27me3), which was sufficient to silence HOX genes in CLL, whereas in MCL H3K27me3 is accompanied by DNA methylation for a more stable repression. More importantly, hypermethylation of the HOX genes in MCL resulted from EZH2 overexpression and subsequent recruitment of the DNA methylation machinery onto HOX gene promoters. The importance of EZH2 upregulation in this process was further underscored by siRNA transfection and EZH2 inhibitor experiments. Altogether, these observations implicate EZH2 in the long-term silencing of HOX genes in MCL, and allude to its potential as a therapeutic target with clinical impact.
Collapse
Affiliation(s)
- Meena Kanduri
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; Gothenburg University; Gothenburg, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine; Division of Pathology; Karolinska Institutet and Karolinska University Hospital; Huddinge, Sweden
| | - Stavroula Ntoufa
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Nikos Papakonstantinou
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
| | - Kostas Stamatopoulos
- Hematology Department and HCT Unit G. Papanicolaou Hospital; Thessaloniki, Greece; Institute of Applied Biosciences; CERTH; Thessaloniki, Greece
| | - Chandrasekhar Kanduri
- Department of Medical and Clinical Genetics; Department of Biomedicine; The Sahlgrenska Academy; Gothenburg University; Gothenburg, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology; Uppsala University; Uppsala, Sweden
| |
Collapse
|
37
|
Mitchell NE, Wilson ML, Bray MS, Crossman DK, Tollefsbol TO. Real-time methylomic aberrations during initiation and progression of induced human mammary epithelial cell tumorigenesis. Epigenomics 2013; 5:155-65. [PMID: 23566093 DOI: 10.2217/epi.13.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AIM Neoplastic transformation provides one of the few existing opportunities to analyze molecular changes in real time during the initiation and progression of breast cancer. MATERIALS & METHODS Human mammary epithelial cells underwent neoplastic reprogramming, generating one line of semitransformed, premalignant cells and two separate, temporal lines of fully transformed human mammary epithelial cells (THMECs). An Illumina Infinium HumanMethylation27 BeadChip was used to analyze DNA methylation alterations in 27,578 CpG loci at three consecutive time points over an 80-day (d) transformation period. RESULTS The mean β value for semitransformed human mammary epithelial cells CpG loci (0.245) was much greater than for either THMEC-40d (0.055) or THMEC-80d (0.066), indicating a large loss of methylation after neoplastic induction. In addition, 54% of CpG loci were hypermethylated during the THMEC-40d to THMEC-80d transition. We observed that the CpG loci exhibiting DNA methylation changes during early oncogenesis were enriched for biological functions like cellular movement; this was distinctly different than in the later, more progressive stages of the transformation process enriched for processes involving differentiation. CONCLUSION The timing of major methylomic changes may be important in directing the cell toward a more cancerous phenotype. In addition, gene-specific hypermethylation appears to silence developmentally related genes, leading to dedifferentiation.
Collapse
Affiliation(s)
- Natalie E Mitchell
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA
| | | | | | | | | |
Collapse
|
38
|
Sun M, Song CX, Huang H, Frankenberger CA, Sankarasharma D, Gomes S, Chen P, Chen J, Chada KK, He C, Rosner MR. HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis. Proc Natl Acad Sci U S A 2013; 110:9920-5. [PMID: 23716660 PMCID: PMC3683728 DOI: 10.1073/pnas.1305172110] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ten-eleven translocation (TET) family of methylcytosine dioxygenases initiates demethylation of DNA and is associated with tumorigenesis in many cancers; however, the mechanism is mostly unknown. Here we identify upstream activators and downstream effectors of TET1 in breast cancer using human breast cancer cells and a genetically engineered mouse model. We show that depleting the architectural transcription factor high mobility group AT-hook 2 (HMGA2) induces TET1. TET1 binds and demethylates its own promoter and the promoter of homeobox A (HOXA) genes, enhancing its own expression and stimulating expression of HOXA genes including HOXA7 and HOXA9. Both TET1 and HOXA9 suppress breast tumor growth and metastasis in mouse xenografts. The genes comprising the HMGA2-TET1-HOXA9 pathway are coordinately regulated in breast cancer and together encompass a prognostic signature for patient survival. These results implicate the HMGA2-TET1-HOX signaling pathway in the epigenetic regulation of human breast cancer and highlight the importance of targeting methylation in specific subpopulations as a potential therapeutic strategy.
Collapse
Affiliation(s)
- Miao Sun
- Ben May Department for Cancer Research
- Committee on Genetics, Genomics, and Systems Biology
| | - Chun-Xiao Song
- Department of Chemistry and Institute for Biophysical Dynamics, and
| | - Hao Huang
- Department of Medicine, University of Chicago, Chicago, IL 60637; and
| | | | - Devipriya Sankarasharma
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854
| | | | - Ping Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637; and
| | - Jianjun Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637; and
| | - Kiran K. Chada
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, and
| | - Marsha R. Rosner
- Ben May Department for Cancer Research
- Committee on Genetics, Genomics, and Systems Biology
| |
Collapse
|
39
|
miRNA gene promoters are frequent targets of aberrant DNA methylation in human breast cancer. PLoS One 2013; 8:e54398. [PMID: 23342147 PMCID: PMC3547033 DOI: 10.1371/journal.pone.0054398] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/12/2012] [Indexed: 12/19/2022] Open
Abstract
miRNAs are important regulators of gene expression that are frequently deregulated in cancer, with aberrant DNA methylation being an epigenetic mechanism involved in this process. We previously identified miRNA promoter regions active in normal mammary cell types and here we analyzed which of these promoters are targets of aberrant DNA methylation in human breast cancer cell lines and breast tumor specimens. Using 5-methylcytosine immunoprecipitation coupled to miRNA tiling microarray hybridization, we performed comprehensive evaluation of DNA methylation of miRNA gene promoters in breast cancer. We found almost one third (55/167) of miRNA promoters were targets for aberrant methylation in breast cancer cell lines. Breast tumor specimens displayed DNA methylation of majority of these miRNA promoters, indicating that these changes in DNA methylation might be clinically relevant. Aberrantly methylated miRNA promoters were, similar to protein coding genes, enriched for promoters targeted by polycomb in normal cells. Detailed analysis of selected miRNA promoters revealed decreased expression of miRNA linked to increased promoter methylation for mir-31, mir-130a, let-7a-3/let-7b, mir-155, mir-137 and mir-34b/mir-34c genes. The proportion of miRNA promoters we found aberrantly methylated in breast cancer is several fold larger than that observed for protein coding genes, indicating an important role of DNA methylation in miRNA deregulation in cancer.
Collapse
|
40
|
Hirayama T, Yagi T. Clustered protocadherins and neuronal diversity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 116:145-67. [PMID: 23481194 DOI: 10.1016/b978-0-12-394311-8.00007-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Neuronal diversity is a fundamental requirement for complex neuronal networks and brain function. The clustered protocadherin (Pcdh) family possesses several characteristic features that are important for the molecular basis of neuronal diversity. Clustered Pcdhs are expressed predominantly in the central nervous system, in neurites, growth cones, and synapses. They consist of about 60 isoforms, and their expression is stochastically and combinatorially regulated in individual neurons. The multiple clustered Pcdhs expressed in individual neurons form heteromultimeric protein complexes that exhibit homophilic adhesion properties. Theoretically, the clustered Pcdhs could generate more than 3×10(10) possible variations in each neuron and 12,720 types of cis-tetramers per neuron. The clustered Pcdhs are important for normal neuronal development. The clustered Pcdh genes have also attracted attention as a target for epigenetic regulation.
Collapse
Affiliation(s)
- Teruyoshi Hirayama
- KOKORO Biology Group and JST-CREST, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | | |
Collapse
|
41
|
Futscher BW. Epigenetic changes during cell transformation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:179-94. [PMID: 22956502 DOI: 10.1007/978-1-4419-9967-2_9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Malignant cancer emerges from normal healthy cells in a multistep -process that involves both genetic and epigenetic lesions. Both genetic and environmental inputs participate in driving the epigenetic changes that occur during human carcinogenesis. The pathologic changes seen in DNA methylation and histone posttranslational modifications are complex, deeply intertwined, and act in concert to produce malignant transformation. To better understand the causes and consequences of the pathoepigenetic changes in cancer formation, a variety of experimentally tractable human cell line model systems that accurately reflect the molecular alterations seen in the clinical disease have been developed. Results from studies using these cell line model systems suggest that early critical epigenetic events occur in a stepwise fashion prior to cell immortalization. These epigenetic steps coincide with the cell's transition through well-defined cell proliferation barriers of stasis and telomere dysfunction. Following cell immortalization, stressors, such as environmental toxicants, can induce malignant transformation in a process in which the epigenetic changes occur in a smoother progressive fashion, in contrast to the stark stepwise epigenetic changes seen prior to cell immortalization. It is hoped that developing a clearer understanding of the identity, timing, and consequences of these epigenetic lesions will prove useful in future clinical applications that range from early disease detection to therapeutic intervention in malignant cancer.
Collapse
Affiliation(s)
- Bernard W Futscher
- Department of Pharmacology and Toxicology, College of Pharmacy and The University of Arizona Cancer Center, The University of Arizona, Tucson, AZ 85724-5024, USA.
| |
Collapse
|
42
|
Novak P, Stampfer MR, Munoz-Rodriguez JL, Garbe JC, Ehrich M, Futscher BW, Jensen TJ. Cell-type specific DNA methylation patterns define human breast cellular identity. PLoS One 2012; 7:e52299. [PMID: 23284978 PMCID: PMC3527522 DOI: 10.1371/journal.pone.0052299] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/12/2012] [Indexed: 12/14/2022] Open
Abstract
DNA methylation plays a role in a variety of biological processes including embryonic development, imprinting, X-chromosome inactivation, and stem cell differentiation. Tissue specific differential methylation has also been well characterized. We sought to extend these studies to create a map of differential DNA methylation between different cell types derived from a single tissue. Using three pairs of isogenic human mammary epithelial and fibroblast cells, promoter region DNA methylation was characterized using MeDIP coupled to microarray analysis. Comparison of DNA methylation between these cell types revealed nearly three thousand cell-type specific differentially methylated regions (ctDMRs). MassARRAY was performed upon 87 ctDMRs to confirm and quantify differential DNA methylation. Each of the examined regions exhibited statistically significant differences ranging from 10-70%. Gene ontology analysis revealed the overrepresentation of many transcription factors involved in developmental processes. Additionally, we have shown that ctDMRs are associated with histone related epigenetic marks and are often aberrantly methylated in breast cancer. Overall, our data suggest that there are thousands of ctDMRs which consistently exhibit differential DNA methylation and may underlie cell type specificity in human breast tissue. In addition, we describe the pathways affected by these differences and provide insight into the molecular mechanisms and physiological overlap between normal cellular differentiation and breast carcinogenesis.
Collapse
Affiliation(s)
- Petr Novak
- Arizona Cancer Center, The University of Arizona, Tucson, Arizona, USA.
| | | | | | | | | | | | | |
Collapse
|
43
|
Pilato B, Pinto R, De Summa S, Lambo R, Paradiso A, Tommasi S. HOX gene methylation status analysis in patients with hereditary breast cancer. J Hum Genet 2012; 58:51-3. [PMID: 23051705 DOI: 10.1038/jhg.2012.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cancer development is related not only to genetic alterations but also to aberrant epigenetic changes that could lead to heritable gene patterns critical for neoplastic initiation and progression. Knowledge of epigenetic regulation in cancer cells is useful for both the understanding of carcinogenesis and for the possibility of using epigenetic drugs. HOX genes deregulation have a crucial role in oncogenesis process and tumor suppression. In this report, the methylation of HOXA1, HOXA9, HOXA10, HOXB13, HNF1B, OTX1, TLX1 genes have been analyzed in patients with hereditary breast cancer. This is the first study analyzing BRCA mutational status of patients with respect to methylation of HOX genes. HOXA10 has been found to be methylated in all patients analyzed but never in healthy subjects. With respect to clinical pathological information, hypermethylation of all studied genes, with the exception of OTX1, was significantly associated with absence of HER2 neu expression (P<0.05). Moreover, hypermethylation of HOXB13, HOXA10 and HOXA1 was associated with a high proliferation index (Mib1≥10%, P<0.05) and hypermethylation of HOXB13 and HOXA10 also with high expression of estrogen and progesterone receptors. These preliminary data suggest a possible involvement of HOX genes in familial breast cancer as marker helpful to identify high-risk patients.
Collapse
Affiliation(s)
- Brunella Pilato
- National Cancer Research Centre, Istituto Tumori Giovanni Paolo II, Bari, Italy
| | | | | | | | | | | |
Collapse
|
44
|
Severson PL, Tokar EJ, Vrba L, Waalkes MP, Futscher BW. Agglomerates of aberrant DNA methylation are associated with toxicant-induced malignant transformation. Epigenetics 2012; 7:1238-48. [PMID: 22976526 PMCID: PMC3499325 DOI: 10.4161/epi.22163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Epigenetic dysfunction is a known contributor in carcinogenesis, and is emerging as a mechanism involved in toxicant-induced malignant transformation for environmental carcinogens such as arsenicals or cadmium. In addition to aberrant DNA methylation of single genes, another manifestation of epigenetic dysfunction in cancer is agglomerative DNA methylation, which can participate in long-range epigenetic silencing that targets many neighboring genes and has been shown to occur in several types of clinical cancers. Using in vitro model systems of toxicant-induced malignant transformation, we found hundreds of aberrant DNA methylation events that emerge during malignant transformation, some of which occur in an agglomerative fashion. In an arsenite-transformed prostate epithelial cell line, the protocadherin (PCDH), HOXC and HOXD gene family clusters are targeted for agglomerative DNA methylation. The agglomerative DNA methylation changes induced by arsenicals appear to be common and clinically relevant events, since they occur in other human cancer cell lines and models of malignant transformation, as well as clinical cancer specimens. Aberrant DNA methylation in general occurred more often within histone H3 lysine-27 trimethylation stem cell domains. We found a striking association between enrichment of histone H3 lysine-9 trimethylation stem cell domains and toxicant-induced agglomerative DNA methylation, suggesting these epigenetic modifications may become aberrantly linked during malignant transformation. In summary, we found an association between toxicant-induced malignant transformation and agglomerative DNA methylation, which lends further support to the hypothesis that epigenetic dysfunction plays an important role in toxicant-induced malignant transformation.
Collapse
Affiliation(s)
- Paul L Severson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, USA
| | | | | | | | | |
Collapse
|
45
|
Cipriano R, Graham J, Miskimen KLS, Bryson BL, Bruntz RC, Scott SA, Brown HA, Stark GR, Jackson MW. FAM83B mediates EGFR- and RAS-driven oncogenic transformation. J Clin Invest 2012; 122:3197-210. [PMID: 22886302 DOI: 10.1172/jci60517] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 05/16/2012] [Indexed: 11/17/2022] Open
Abstract
Aberrant regulation of growth signaling is a hallmark of cancer development that often occurs through the constitutive activation of growth factor receptors or their downstream effectors. Using validation-based insertional mutagenesis (VBIM), we identified family with sequence similarity 83, member B (FAM83B), based on its ability to substitute for RAS in the transformation of immortalized human mammary epithelial cells (HMECs). We found that FAM83B coprecipitated with a downstream effector of RAS, CRAF. Binding of FAM83B with CRAF disrupted CRAF/14-3-3 interactions and increased CRAF membrane localization, resulting in elevated MAPK and mammalian target of rapamycin (mTOR) signaling. Ablation of FAM83B inhibited the proliferation and malignant phenotype of tumor-derived cells or RAS-transformed HMECs, implicating FAM83B as a key intermediary in EGFR/RAS/MAPK signaling. Analysis of human tumor specimens revealed that FAM83B expression was significantly elevated in cancer and was associated with specific cancer subtypes, increased tumor grade, and decreased overall survival. Cumulatively, these results suggest that FAM83B is an oncogene and potentially represents a new target for therapeutic intervention.
Collapse
Affiliation(s)
- Rocky Cipriano
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Bocker MT, Tuorto F, Raddatz G, Musch T, Yang FC, Xu M, Lyko F, Breiling A. Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster. Nat Commun 2012; 3:818. [PMID: 22569366 DOI: 10.1038/ncomms1826] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 04/05/2012] [Indexed: 12/22/2022] Open
Abstract
Differentiation is accompanied by extensive epigenomic reprogramming, leading to the repression of stemness factors and the transcriptional maintenance of activated lineage-specific genes. Here we use the mammalian Hoxa cluster of developmental genes as a model system to follow changes in DNA modification patterns during retinoic acid-induced differentiation. We find the inactive cluster to be marked by defined patterns of 5-methylcytosine (5mC). Upon the induction of differentiation, the active anterior part of the cluster becomes increasingly enriched in 5-hydroxymethylcytosine (5hmC), following closely the colinear activation pattern of the gene array, which is paralleled by the reduction of 5mC. Depletion of the 5hmC generating dioxygenase Tet2 impairs the maintenance of Hoxa activity and partially restores 5mC levels. Our results indicate that gene-specific 5mC-5hmC conversion by Tet2 is crucial for the maintenance of active chromatin states at lineage-specific loci.
Collapse
Affiliation(s)
- Michael T Bocker
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
47
|
da Costa Prando E, Cavalli LR, Rainho CA. Evidence of epigenetic regulation of the tumor suppressor gene cluster flanking RASSF1 in breast cancer cell lines. Epigenetics 2012; 6:1413-24. [PMID: 22139571 DOI: 10.4161/epi.6.12.18271] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Epigenetic mechanisms are frequently deregulated in cancer cells and can lead to the silencing of genes with tumor suppressor activities. The isoform A of the Ras-association domain family member 1 (RASSF1A) gene is one of the most frequently silenced transcripts in human tumors, however, few studies have simultaneously investigated epigenetic abnormalities associated with the 3p21.3 tumor suppressor gene cluster flanking RASSF1 (i.e., SEMA3B, HYAL3, HYAL2, HYAL1, TUSC2, RASSF1, ZMYND10, NPRL2, TMEM115, and CACNA2D2). This study aimed to investigate the role of epigenetic changes to these genes in seventeen breast cancer cell lines and in three non-tumorigenic epithelial breast cell lines (184A1, 184B5, and MCF 10A) and to evaluate the effect on gene expression of treatment with the demethylating agent 5-Aza-2'-deoxycytidine and/or Trichostatin A (TSA), a histone deacetylase inhibitor. We report that, although the RASSF1A isoform was determined to be epigenetically silenced in 15 of the 17 breast cancer cell lines, all the cell lines expressed the RASSF1C isoform. Five breast cancer cell lines overexpressed RASSF1C, when compared to the normal epithelial cell line 184A1. Furthermore, the genes HYAL1 and CACNA2D2 were significantly overexpressed after the treatments. After the combinated treatment, RASSF1A re-expression was accompanied by an increase in expression levels of the flanking genes. The Spearman's correlation coefficient indicated a positive co-regulation of the following gene pairs: RASSF1 and TUSC2 (r=0.64, p=0.002), RASSF1 and ZMYND10 (r=0.58, p=0.07), RASSF1 and NPRL2 (r=0.48, p=0.03), ZMYND10 and NPRL2 (r=0.71; p=0,0004), and NPRL2 and TMEM115 (r=0.66, p=0.001). Interestingly, the genes TUSC2, NPRL2 and TMEM115 were found to be unmethylated in each of the untreated cell lines. Chromatin immunoprecipitation using antibodies against the acetylated and trimethylated lysine 9 of histone H3 demonstrated low levels of histone methylation in these genes, which are located closest to RASSF1. These results provide evidence that epigenetic repression is involved in the down-regulation of multiple genes at 3p21.3 in breast cancer cells.
Collapse
Affiliation(s)
- Erika da Costa Prando
- Department of Genetics, Biosciences Institute, Sao Paulo State University, Sao Paulo, Brazil
| | | | | |
Collapse
|
48
|
Quantitative methylation analysis of HOXA3, 7, 9, and 10 genes in glioma: association with tumor WHO grade and clinical outcome. J Cancer Res Clin Oncol 2011; 138:35-47. [DOI: 10.1007/s00432-011-1070-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 09/13/2011] [Indexed: 01/29/2023]
|
49
|
Yamamoto M, Cid E, Bru S, Yamamoto F. Rare and frequent promoter methylation, respectively, of TSHZ2 and 3 genes that are both downregulated in expression in breast and prostate cancers. PLoS One 2011; 6:e17149. [PMID: 21423795 PMCID: PMC3056709 DOI: 10.1371/journal.pone.0017149] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 01/20/2011] [Indexed: 01/28/2023] Open
Abstract
Background Neoplastic cells harbor both hypomethylated and hypermethylated regions of
DNA. Whereas hypomethylation is found mainly in repeat sequences, regional
hypermethylation has been linked to the transcriptional silencing of certain
tumor suppressor genes. We attempted to search for candidate genes involved
in breast/prostate carcinogenesis, using the criteria that they should be
expressed in primary cultures of normal breast/prostate epithelial cells but
are frequently downregulated in breast/prostate cancer cell lines and that
their promoters are hypermethylated. Methodology/Principal Findings We identified several dozens of candidates among 194 homeobox and related
genes using Systematic Multiplex RT-PCR and among 23,000 known genes and
23,000 other expressed sequences in the human genome by DNA microarray
hybridization. An additional examination, by real-time
qRT-PCR of clinical specimens of breast cancer, further narrowed the list of
the candidates. Among them, the most frequently downregulated genes in
tumors were NP_775756 and ZNF537, from the homeobox gene search and the
genome-wide search, respectively. To our surprise, we later discovered that
these genes belong to the same gene family, the 3-member Teashirt family,
bearing the new names of TSHZ2 and TSHZ3. We subsequently determined the
methylation status of their gene promoters. The TSHZ3 gene promoter was
found to be methylated in all the breast/prostate cancer cell lines and some
of the breast cancer clinical specimens analyzed. The TSHZ2 gene promoter,
on the other hand, was unmethylated except for the MDA-MB-231 breast cancer
cell line. The TSHZ1 gene was always expressed, and its promoter was
unmethylated in all cases. Conclusions/Significance TSHZ2 and TSHZ3 genes turned out to be the most interesting candidates for
novel tumor suppressor genes. Expression of both genes is downregulated.
However, differential promoter methylation suggests the existence of
distinctive mechanisms of transcriptional inactivation for these genes.
Collapse
Affiliation(s)
- Miyako Yamamoto
- Burnham Institute for Medical Research, La Jolla, California, United States of America.
| | | | | | | |
Collapse
|
50
|
DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesis. Mamm Genome 2011; 22:249-59. [PMID: 21373886 DOI: 10.1007/s00335-011-9318-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 02/08/2011] [Indexed: 10/18/2022]
Abstract
Epigenetic inactivation due to aberrant promoter methylation is a key process in breast tumorigenesis. Murine models for human breast cancer have been established for nearly every important human oncogene or tumor suppressor gene. Mouse-to-human comparative gene expression and cytogenetic profiling have been widely investigated for these models; however, little is known about the conservation of epigenetic alterations during tumorigenesis. To determine if this key process in human breast tumorigenesis is also mirrored in a murine breast cancer model, we mapped cytosine methylation changes in primary adenocarcinomas and paired lung metastases derived from the polyomavirus middle T antigen mouse model. Global changes in methylcytosine levels were observed in all tumors when compared to the normal mammary gland. Aberrant methylation and associated gene silencing was observed for Hoxa7, a gene that is differentially methylated in human breast tumors, and Gata2, a novel candidate gene. Analysis of HOXA7 and GATA2 expression in a bank of human primary tumors confirms that the expression of these genes is also reduced in human breast cancer. In addition, HOXA7 hypermethylation is observed in breast cancer tissues when compared to adjacent tumor-free tissue. Based on these studies, we present a model in which comparative epigenetic techniques can be used to identify novel candidate genes important for human breast tumorigenesis, in both primary and metastatic tumors.
Collapse
|