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Bortul M, Giudici F, Tierno D, Generali D, Scomersi S, Grassi G, Bottin C, Cappelletti MR, Zanconati F, Scaggiante B. A Case-Control Study by ddPCR of ALU 260/111 and LINE-1 266/97 Copy Number Ratio in Circulating Cell-Free DNA in Plasma Revealed LINE-1 266/97 as a Potential Biomarker for Early Breast Cancer Detection. Int J Mol Sci 2023; 24:ijms24108520. [PMID: 37239866 DOI: 10.3390/ijms24108520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND In Western countries, breast cancer (BC) is the most common cancer in women. Early detection has a positive impact on survival, quality of life, and public health costs. Mammography screening programs have increased early detection rates, but new approaches to more personalized surveillance could further improve diagnosis. Circulating cell-free DNA (cfDNA) in blood could provide a potential tool for early diagnosis by analyzing cfDNA quantity, circulating tumor DNA mutations, or cfDNA integrity (cfDI). METHODS Plasma was obtained from the blood of 106 breast cancer patients (cases) and 103 healthy women (controls). Digital droplet PCR was used for the determination of ALU 260/111 bp and LINE-1 266/97 bp copy number ratio and cfDI. cfDNA abundance was calculated using copies of the EEF1A2 gene. The accuracy of biomarker discrimination was analyzed with receiver operating characteristic curve (ROC). Sensitivity analyses were performed to account for age as a potential confounder. RESULTS Cases had significantly lower ALU 260/111 or LINE-1 266/97 copy number ratios (median; ALU 260/111 = 0.08, LINE-1 266/97 = 0.20), compared with control (median; ALU 260/111 = 0.10, LINE-1 266/97 = 0.28) (p < 0.001). ROC analysis showed that copy number ratio discriminated cases from controls (area under the curve, AUC = 0.69, 95% CI: 0.62-0.76 for ALU and 0.80, 95% CI: 0.73-0.86 for LINE-1). ROC from cfDI confirmed the better diagnostic performance of LINE-1 compared with ALU. CONCLUSIONS Analysis of LINE-1 266/97 copy number ratio or cfDI by ddPCR appears to be a useful noninvasive test that could aid in early BC detection. Further studies in a large cohort are needed to validate the biomarker.
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Affiliation(s)
- Marina Bortul
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Breast Unit, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), 34149 Trieste, Italy
| | - Fabiola Giudici
- Cancer Epidemiologic Unit, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 33081 Aviano, Italy
| | - Domenico Tierno
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Daniele Generali
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Breast Cancer Unit and Translational Research Unit, Azienda Socio-Sanitaria Territoriale di Cremona-ASST, 26100 Cremona, Italy
| | - Serena Scomersi
- Breast Unit, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), 34149 Trieste, Italy
| | - Gabriele Grassi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Cristina Bottin
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Maria Rosa Cappelletti
- Breast Cancer Unit and Translational Research Unit, Azienda Socio-Sanitaria Territoriale di Cremona-ASST, 26100 Cremona, Italy
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Breast Unit, Azienda Sanitaria Universitaria Integrata Giuliano Isontina (ASUGI), 34149 Trieste, Italy
| | - Bruna Scaggiante
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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Munnia A, Bollati V, Russo V, Ferrari L, Ceppi M, Bruzzone M, Dugheri S, Arcangeli G, Merlo F, Peluso M. Traffic-Related Air Pollution and Ground-Level Ozone Associated Global DNA Hypomethylation and Bulky DNA Adduct Formation. Int J Mol Sci 2023; 24:ijms24032041. [PMID: 36768368 PMCID: PMC9916664 DOI: 10.3390/ijms24032041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Studies have indicated that air pollution, including surface-level ozone (O3), can significantly influence the risk of chronic diseases. To better understand the carcinogenic mechanisms of air pollutants and identify predictive disease biomarkers, we examined the association between traffic-related pollutants with DNA methylation alterations and bulky DNA adducts, two biomarkers of carcinogen exposure and cancer risk, in the peripheral blood of 140 volunteers-95 traffic police officers, and 45 unexposed subjects. The DNA methylation and adduct measurements were performed by bisulfite-PCR and pyrosequencing and 32P-postlabeling assay. Airborne levels of benzo(a)pyrene [B(a)P], carbon monoxide, and tropospheric O3 were determined by personal exposure biomonitoring or by fixed monitoring stations. Overall, air pollution exposure was associated with a significant reduction (1.41 units) in global DNA methylation (95% C.I. -2.65-0.04, p = 0.026). The decrement in ALU repetitive elements was greatest in the policemen working downtown (95% C.I. -3.23--0.49, p = 0.008). The DNA adducts were found to be significantly increased (0.45 units) in the municipal officers with respect to unexposed subjects (95% C.I. 0.02-0.88, p = 0.039), mainly in those who were controlling traffic in downtown areas (95% C.I. 0.39-1.29, p < 0.001). Regression models indicated an increment of ALU methylation at higher B(a)P concentrations (95% C.I. 0.03-0.60, p = 0.032). Moreover, statistical models showed a decrement in ALU methylation and an increment of DNA damage only above the cut-off value of 30 µg/m3 O3. A significant increment of 0.73 units of IL-6 gene methylation was also found in smokers with respect to non-smokers. Our results highlighted the role of air pollution on epigenetic alterations and genotoxic effects, especially above the target value of 30 µg/m3 surface-level O3, supporting the necessity for developing public health strategies aimed to reduce traffic-related air pollution molecular alterations.
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Affiliation(s)
- Armelle Munnia
- Research Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Valentina Bollati
- EPIGET Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, 20122 Milan, Italy
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Valentina Russo
- Research Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
| | - Luca Ferrari
- EPIGET Department of Clinical Sciences and Community Health, Università Degli Studi di Milano, 20122 Milan, Italy
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Marcello Ceppi
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Marco Bruzzone
- Clinical Epidemiology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Stefano Dugheri
- Laboratorio di Igiene e Tossicologia Industriale, Azienda Ospedaliero-Universitaria Careggi, 50134 Florence, Italy
| | - Giulio Arcangeli
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze, 50121 Florence, Italy
| | - Franco Merlo
- Research and Statistics Infrastructure, Azienda Unità Sanitaria Locale, IRCCS, 42121 Reggio Emilie, Italy
| | - Marco Peluso
- Research Branch, Regional Cancer Prevention Laboratory, ISPRO-Study, Prevention and Oncology Network Institute, 50139 Florence, Italy
- Correspondence:
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Muse ME, Bergman DT, Salas LA, Tom LN, Tan JM, Laino A, Lambie D, Sturm RA, Schaider H, Soyer HP, Christensen BC, Stark MS. Genome-scale DNA methylation analysis identifies repeat element alterations that modulate the genomic stability of melanocytic nevi. J Invest Dermatol 2021; 142:1893-1902.e7. [PMID: 34871578 DOI: 10.1016/j.jid.2021.11.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/31/2022]
Abstract
Acquired melanocytic nevi grow and persist in a stable form into adulthood. Using genome-wide methylation profiling, we evaluated 32 histopathologically and dermoscopically characterized nevi, to identify key epigenetic regulatory mechanisms involved in nevogenesis. Benign (69% globular and 31% non-specific dermoscopic pattern) and dysplastic (95% reticular/nonspecific dermoscopic pattern) nevi were dissimilar with only two shared differentially methylated (DM) loci. Benign nevi demonstrated an increase in both genome-scale methylation and methylation of Alu/LINE-1 retrotransposable elements, a marker of genomic stability, as well as global methylation. In contrast, dysplastic nevi showed evidence for genomic instability via hypomethylation of Alu/LINE-1 (Alu; P=0.00019 and LINE-1; P=0.000035). Using dermoscopic classifications, reticular/non-specific patterned nevi had 59,572 CpG DM loci (Q < 0.05), whereas globular nevi had no significant DM loci. In reticular/non-specific patterned nevi, the tumor suppressor PTEN had the greatest proportion of hypermethylated CpG loci in its promoter region compared to all other assayed gene promoters. The relative activity of reticular/non-specific nevi was evidenced by 50,720 hypomethylated loci being enriched for accessible chromatin, and 8,852 hypermethylated loci strongly enriched, for example, marks of active gene promoters, which suggests that gain of DNA methylation observed in these nevus types plays a role in gene regulation.
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Affiliation(s)
- Meghan E Muse
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Drew T Bergman
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Lisa N Tom
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Jean-Marie Tan
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Antonia Laino
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Duncan Lambie
- IQ Pathology, Brisbane, Australia; Pathology Queensland, Princess Alexandra Hospital, Brisbane, Australia
| | - Richard A Sturm
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Helmut Schaider
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia; Department of Dermatology, Sunshine Coast Hospital and Health Service, Birtinya, Australia
| | - H Peter Soyer
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia; Department of Dermatology, Princess Alexandra Hospital, Brisbane, Australia
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA; Department of Community & Family Medicine, Dartmouth Geisel School of Medicine, Hanover, New Hampshire, USA
| | - Mitchell S Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Australia.
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Abstract
ALUs contribute to genetic diversity by altering DNA's linear sequence through retrotransposition, recombination and repair. ALUs also have the potential to form alternative non-B-DNA conformations such as Z-DNA, triplexes and quadruplexes that alter the read-out of information from the genome. I suggest here these structures enable the rapid reprogramming of cellular pathways to offset DNA damage and regulate inflammation. The experimental data supporting this form of genetic encoding is presented. ALU sequence motifs that form non-B-DNA conformations under physiological conditions are called flipons. Flipons are binary switches. They are dissipative structures that trade energy for information. By efficiently targeting cellular machines to active genes, flipons expand the repertoire of RNAs compiled from a gene. Their action greatly increases the informational capacity of linearly encoded genomes. Flipons are programmable by epigenetic modification, synchronizing cellular events by altering both chromatin state and nucleosome phasing. Different classes of flipon exist. Z-flipons are based on Z-DNA and modify the transcripts compiled from a gene. T-flipons are based on triplexes and localize non-coding RNAs that direct the assembly of cellular machines. G-flipons are based on G-quadruplexes and sense DNA damage, then trigger the appropriate protective responses. Flipon conformation is dynamic, changing with context. When frozen in one state, flipons often cause disease. The propagation of flipons throughout the genome by ALU elements represents a novel evolutionary innovation that allows for rapid change. Each ALU insertion creates variability by extracting a different set of information from the neighbourhood in which it lands. By elaborating on already successful adaptations, the newly compiled transcripts work with the old to enhance survival. Systems that optimize flipon settings through learning can adapt faster than with other forms of evolution. They avoid the risk of relying on random and irreversible codon rewrites.
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Tuchalska-Czuroń J, Lenart J, Augustyniak J, Durlik M. Clinical v alue of tissue DNA integrity index in pancreatic cancer. Surgeon 2020; 18:269-279. [PMID: 32156475 DOI: 10.1016/j.surge.2019.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/08/2019] [Accepted: 10/28/2019] [Indexed: 10/24/2022]
Abstract
BACKGROUND DNA integrity index as a blood biomarker is associated with the prognosis of cancer patients. AIMS The primary goal of the study was to examine tissue DNA integrity index (DII) in a group of pancreatic cancer (PC) tumor tissues and control adjacent pancreatic tissues. We also aimed to test the relationship between the tumor tissue DII and the clinicopathological parameters and the overall survival. METHODS In the prospective study, DII was calculated using: the Alu 247/115 ratio, the LINE1 300/79 ratio and the average of the above values, based on the data obtained by real-time PCR. The tumors samples (n = 42) originated from the patients with pathologically confirmed pancreatic ductal adenocarcinoma and the control adjacent pancreatic tissue specimens (n = 32) were received from surgical margins. RESULTS Specimens from the tumors pathologically marked as R1 (microscopic residual tumor) had a significantly higher LINE1 300/79 ratio values than specimens from adjacent normal pancreatic tissue (P<0.05). ROC curve analysis revealed that LINE1 300/79 ratio is a good parameter to distinguish between R0 and R1 tumors (AUC = 0.703, P<0.05). CONCLUSIONS This is the first study exploring the tissue DNA integrity index (DII) in pancreatic cancer. LINE1 DII can be used as auxiliary parameter for objective evaluation of margin status.
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Affiliation(s)
- Julia Tuchalska-Czuroń
- Department of Surgical Research and Transplantology, Medical Research Centre Polish Academy of Sciences, Warsaw, Poland; Diagnostic Radiology Department, Central Clinical Hospital of the MSWiA in Warsaw, Poland.
| | - Jacek Lenart
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Justyna Augustyniak
- Department of Neurochemistry, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Durlik
- Department of Surgical Research and Transplantology, Medical Research Centre Polish Academy of Sciences, Warsaw, Poland; Department of Gastroenterological Surgery and Transplantation Medicine, Centre of Postgraduate Medical Education, Warsaw, Poland; Clinical Department of Gastroenterological Surgery and Transplantation Medicine, Central Clinical Hospital of the MSWiA in Warsaw, Poland
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Hernandez AJ, Zovoilis A, Cifuentes-Rojas C, Han L, Bujisic B, Lee JT. B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2. Proc Natl Acad Sci U S A 2020; 117:415-25. [PMID: 31871160 DOI: 10.1073/pnas.1917190117] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transposable elements make up half of the mammalian genome. One of the most abundant is the short interspersed nuclear element (SINE). Among their million copies, B2 accounts for ∼350,000 in the mouse genome and has garnered special interest because of emerging roles in epigenetic regulation. Our recent work demonstrated that B2 RNA binds stress genes to retard transcription elongation. Although epigenetically silenced, B2s become massively up-regulated during thermal and other types of stress. Specifically, an interaction between B2 RNA and the Polycomb protein, EZH2, results in cleavage of B2 RNA, release of B2 RNA from chromatin, and activation of thermal stress genes. Although an established RNA-binding protein and histone methyltransferase, EZH2 is not known to be a nuclease. Here, we provide evidence for the surprising conclusion that B2 is a self-cleaving ribozyme. Ribozyme activity depends on Mg+2 and monovalent cations but is resistant to protease treatment. However, contact with EZH2 accelerates cleavage rate by >100-fold, suggesting that EZH2 promotes a cleavage-competent RNA conformation. B2 modification-interference analysis demonstrates that phosphorothioate changes at A and C nucleotides can substitute for EZH2. B2 nucleotides 45 to 55 and 100 to 101 are essential for activity. Finally, another family of SINEs, the human ALU element, also produces a self-cleaving RNA and is cleaved during T-cell activation as well as thermal and endoplasmic reticulum (ER) stress. Thus, B2/ALU SINEs may be classified as "epigenetic ribozymes" that function as transcriptional switches during stress. Given their high copy numbers, B2 and ALU may represent the predominant ribozyme activity in mammalian cells.
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Luo Y, Liu S, Yao K. Transcriptome-wide Investigation of mRNA/circRNA in miR-184 and Its r.57c > u Mutant Type Treatment of Human Lens Epithelial Cells. Mol Ther Nucleic Acids 2017; 7:71-80. [PMID: 28624226 DOI: 10.1016/j.omtn.2017.02.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
m-miR-184 (mutant miR-184, r.57c > u) appears in familial hereditary ocular diseases, including keratoconus, cataracts, EDICT (endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning) syndrome, severe keratoconus, and non-ectatic corneal thinning. The biological function of m-miR-184 in these ocular diseases remains unclear. With the emergence of high-throughput sequencing, it is now possible to discover many different biological components simultaneously. Using two different RNA libraries, we sequenced the complete transcriptome of HLE cells treated with miR-184, m-miR-184, and a negative control. Data were integrated in an effort to identify any novel gene affected by m-miR-184. Notably, we concluded that ALDH5A1 and GABRA3 were disordered by m-miR-184, which might lead to ocular disease. Moreover, circRNA (circular RNA) expression was highy random across miR-184, m-miR-184, and negative control treatment groups. The sequences of the circRNAs did reveal a particularly high level of ALU sequences. In summary, we provide a new avenue for understanding the role of m-miR-184 in ocular diseases.
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Chen D, Zhang XR, Zhang Y, Zhang L, Ma JL, You WC, Pan KF. Hypomethylation of repetitive elements in blood leukocyte DNA and risk of gastric lesions in a Chinese population. Cancer Epidemiol 2016; 41:122-8. [PMID: 26943853 DOI: 10.1016/j.canep.2016.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/06/2016] [Accepted: 02/09/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND To explore the association between hypomethylation of repetitive elements (LINE-1, Sat2, and ALU) in blood leukocyte DNA and risks of gastric lesions, and development of gastric cancer (GC), a population-based study was conducted in a high-risk area of GC in China. MATERIALS Methylation levels were determined by MethyLight in 902 subjects with various gastric lesions from two cohort studies at baseline and 276 subjects with long-term follow-up data. RESULTS The frequency of LINE-1 or Sat2 hypomethylation was significantly increased in subjects with dysplasia (DYS) compared with superficial gastritis/chronic atrophic gastritis. The odds ratios (ORs) were 2.22 [95% confidence interval (CI): 1.45-3.40] for LINE-1 and 1.58 (95% CI: 1.14-2.21) for Sat2. A dose-response pattern was found for the risk of DYS and LINE-1 hypomethylation (P-trend<0.001). Further stratified analysis indicated that the frequency of LINE-1 or Sat2 hypomethylation was higher in subjects with Helicobacter pylori infection. The ORs were 1.83 (95% CI: 1.12-2.99) for LINE-1 and 1.44 (95% CI: 1.01-2.05) for Sat2. The follow-up data indicated that the risk of progression to GC was increased in intestinal metaplasia (IM) subjects with LINE-1 hypomethylation (OR=2.82; 95% CI: 1.17-6.77) or Sat2 hypomethylation (OR=2.78; 95% CI: 1.15-6.74). The risk of progression to GC was also increased in DYS subjects with Sat2 hypomethylation (OR=5.24; 95% CI: 2.00-13.74). CONCLUSIONS These findings suggest that hypomethylation of repetitive elements in blood leukocytes is associated with the risks of advanced gastric lesions and development of GC.
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Ladias P, Markopoulos G, Lazaros L, Markoula S, Tzavaras T, Georgiou I. Holliday Junctions Are Associated with Transposable Element Sequences in the Human Genome. J Mol Biol 2016; 428:658-67. [PMID: 26780549 DOI: 10.1016/j.jmb.2016.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Holliday junctions (HJs) constitute important intermediate structures for many cell functions such as DNA recombination and DNA repair. They derive from a 10-nt degenerate sequence, with a 3-nt core motif. In this study, we explored the human genome whether the HJ degenerate sequence associates with transposable elements (TEs) and mainly with those of the active and inactive ALU, LINE, SVA and HERV families. We identified six different forms of the HJ sequence motif, and we located the genomic coordinates of sequences containing both HJs and TEs. From 2982 total HJs, a significant number of 1319 TE-associated HJs were found, with a median distribution of 1 per 2.4 Mb. The HJs with higher GC content were observed more frequently at the genome. A high percentage of HJs were associated with all main TE families, with specificity for particular active or inactive elements: DNA elements and the retroelements ALUs, LINEs and HERVs up to 41.94%, 72.72%, 42.94% and 84.5%, respectively. Phylogenetic analysis revealed that HJs occur in both active and inactive TEs. Furthermore, the TE-associated HJs were almost exclusively found within a distance less than 1 Mb from human genes, while only 23 were not associated with any genes. This is the first report associating human HJs, with mobile elements. Our data pinpoint that particular HJ forms show preference for specific active retrotransposon families of ALUs and LINEs, suggesting that retrotransposon-incorporated HJs may relocate or replicate in the genome through retrotransposition, contributing to recombination, genome plasticity and DNA repair.
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Lee WP, Wu J, Marth GT. Toolbox for mobile-element insertion detection on cancer genomes. Cancer Inform 2015; 14:37-44. [PMID: 25931804 PMCID: PMC4338948 DOI: 10.4137/cin.s24657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 11/05/2022] Open
Abstract
Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram.
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Affiliation(s)
- Wan-Ping Lee
- Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at Seven Bridges Genomics, Cambridge, MA, USA
| | - Jiantao Wu
- Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at Yelp, Inc. San Francisco, CA, USA
| | - Gabor T Marth
- Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at the Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
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Than NG, Romero R, Xu Y, Erez O, Xu Z, Bhatti G, Leavitt R, Chung TH, El-Azzamy H, LaJeunesse C, Wang B, Balogh A, Szalai G, Land S, Dong Z, Hassan SS, Chaiworapongsa T, Krispin M, Kim CJ, Tarca AL, Papp Z, Bohn H. Evolutionary origins of the placental expression of chromosome 19 cluster galectins and their complex dysregulation in preeclampsia. Placenta 2014; 35:855-65. [PMID: 25266889 PMCID: PMC4203431 DOI: 10.1016/j.placenta.2014.07.015] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/04/2014] [Accepted: 07/28/2014] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The dysregulation of maternal-fetal immune tolerance is one of the proposed mechanisms leading to preeclampsia. Galectins are key regulator proteins of the immune response in vertebrates and maternal-fetal immune tolerance in eutherian mammals. Previously we found that three genes in a Chr19 cluster encoding for human placental galectin-13 (PP13), galectin-14 and galectin-16 emerged during primate evolution and may confer immune tolerance to the semi-allogeneic fetus. MATERIALS AND METHODS This study involved various methodologies for gene and protein expression profiling, genomic DNA methylation analyses, functional assays on differentiating trophoblasts including gene silencing, luciferase reporter and methylation assays. These methods were applied on placental specimens, umbilical cord blood cells, primary trophoblasts and BeWo cells. Genomic DNA sequences were analyzed for transposable elements, transcription factor binding sites and evolutionary conservation. RESULTS AND DISCUSSION The villous trophoblastic expression of Chr19 cluster galectin genes is developmentally regulated by DNA methylation and induced by key transcription factors of villous placental development during trophoblast fusion and differentiation. This latter mechanism arose via the co-option of binding sites for these transcription factors through promoter evolution and the insertion of an anthropoid-specific L1PREC2 transposable element into the 5' untranslated region of an ancestral gene followed by gene duplication events. Among placental Chr19 cluster galectin genes, the expression of LGALS13 and LGALS14 is down-regulated in preterm severe preeclampsia associated with SGA. We reveal that this phenomenon is partly originated from the dysregulated expression of key transcription factors controlling trophoblastic functions and galectin gene expression. In addition, the differential DNA methylation of these genes was also observed in preterm preeclampsia irrespective of SGA. CONCLUSIONS These findings reveal the evolutionary origins of the placental expression of Chr19 cluster galectins. The complex dysregulation of these genes in preeclampsia may alter immune tolerance mechanisms at the maternal-fetal interface.
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Affiliation(s)
- N G Than
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Maternity Private Department, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
| | - R Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA.
| | - Y Xu
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - O Erez
- Department of Obstetrics and Gynecology, Ben-Gurion University, Beer-Sheva, Israel
| | - Z Xu
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - G Bhatti
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - R Leavitt
- Zymo Research Corporation, Irvine, CA, USA
| | - T H Chung
- Zymo Research Corporation, Irvine, CA, USA
| | - H El-Azzamy
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - C LaJeunesse
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - B Wang
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - A Balogh
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA; Department of Immunology, Eotvos Lorand University, Budapest, Hungary
| | - G Szalai
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - S Land
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Z Dong
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA
| | - S S Hassan
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - T Chaiworapongsa
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - M Krispin
- Zymo Research Corporation, Irvine, CA, USA
| | - C J Kim
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - A L Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD, and Detroit, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Z Papp
- Maternity Private Department, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary
| | - H Bohn
- Behringwerke AG, Marburg/Lahn, Germany
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12
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Lee WP, Wu J, Marth GT. Toolbox for mobile-element insertion detection on cancer genomes. Cancer Inform 2014; 13:45-52. [PMID: 25452688 PMCID: PMC4218655 DOI: 10.4137/cin.s13979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 11/05/2022] Open
Abstract
Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram.
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Affiliation(s)
- Wan-Ping Lee
- Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at Seven Bridges Genomics, Cambridge, MA, USA
| | - Jiantao Wu
- Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at Yelp, Inc. San Francisco, CA, USA
| | - Gabor T Marth
- Department of Biology, Boston College, Chestnut Hill, MA, USA. ; Currently at the Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
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13
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Islam MM, Hassan MM, Lee GW, Huh EN. A survey on virtualization of Wireless Sensor Networks. Sensors (Basel) 2012; 12:2175-207. [PMID: 22438759 PMCID: PMC3304161 DOI: 10.3390/s120202175] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 02/10/2012] [Accepted: 02/14/2012] [Indexed: 11/16/2022]
Abstract
Wireless Sensor Networks (WSNs) are gaining tremendous importance thanks to their broad range of commercial applications such as in smart home automation, health-care and industrial automation. In these applications multi-vendor and heterogeneous sensor nodes are deployed. Due to strict administrative control over the specific WSN domains, communication barriers, conflicting goals and the economic interests of different WSN sensor node vendors, it is difficult to introduce a large scale federated WSN. By allowing heterogeneous sensor nodes in WSNs to coexist on a shared physical sensor substrate, virtualization in sensor network may provide flexibility, cost effective solutions, promote diversity, ensure security and increase manageability. This paper surveys the novel approach of using the large scale federated WSN resources in a sensor virtualization environment. Our focus in this paper is to introduce a few design goals, the challenges and opportunities of research in the field of sensor network virtualization as well as to illustrate a current status of research in this field. This paper also presents a wide array of state-of-the art projects related to sensor network virtualization.
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Affiliation(s)
- Md. Motaharul Islam
- Internet Computing and Network Security (ICNS) Laboratory, Department of Computer Engineering, College of Electronics and Information, Kyung Hee University, Yongin-si 446-701, Korea; E-Mails: (M.M.I.); (G.-W.L.)
| | - Mohammad Mehedi Hassan
- Research Chair of Pervasive and Mobile Computing, College of Computer and Information Sciences, King Saud University, P.O. Box 51178, Riyadh 11543, Saudi Arabia; E-Mail:
| | - Ga-Won Lee
- Internet Computing and Network Security (ICNS) Laboratory, Department of Computer Engineering, College of Electronics and Information, Kyung Hee University, Yongin-si 446-701, Korea; E-Mails: (M.M.I.); (G.-W.L.)
| | - Eui-Nam Huh
- Internet Computing and Network Security (ICNS) Laboratory, Department of Computer Engineering, College of Electronics and Information, Kyung Hee University, Yongin-si 446-701, Korea; E-Mails: (M.M.I.); (G.-W.L.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +82-31-201-2454; Fax: +82-31-204-3778
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