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2. Supplementary Table S3 from Molecular Analysis of Plasma DNA for the Early Detection of Lung Cancer by Quantitative Methylation-Specific PCR

Author

Ostrow, Kimberly Laskie, primary, Hoque, Mohammad O., primary, Loyo, Myriam, primary, Brait, Marianna, primary, Greenberg, Alissa, primary, Siegfried, Jill M., primary, Grandis, Jennifer R., primary, Gaither Davis, Autumn, primary, Bigbee, William L., primary, Rom, William, primary, and Sidransky, David, primary

Published
2023
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8. Data from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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9. Supplementary Table 6 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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10. Supplementary Table 8 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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11. Supplementary Table 3 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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12. Supplementary Table 5 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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13. Supplementary Table 7 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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14. Supplementary Table 4 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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15. Supplementary Table 1 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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16. Supplementary Table 2 from Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, primary, Ostrow, Kimberly Laskie, primary, Liu, Junwei, primary, Wisman, G. Bea A., primary, Park, Hannah Lui, primary, Poeta, Maria Luana, primary, Jeronimo, Carmen, primary, Henrique, Rui, primary, Lendvai, Ágnes, primary, Schuuring, Ed, primary, Begum, Shahnaz, primary, Rosenbaum, Eli, primary, Ongenaert, Maté, primary, Yamashita, Keishi, primary, Califano, Joseph, primary, Westra, William, primary, van der Zee, Ate G.J., primary, Criekinge, Wim Van, primary, and Sidransky, David, primary

Published
2023
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22. TIMP3 Promoter Methylation is an Independent Prognostic Factor for Bladder Cancer

Author

Hoque, Mohammad Obaidul, Begum, Shahnaz, Brait, Mariana, Jeronimo, Carmen, Zahurak, Marianna, Ostrow, Kimberly Laskie, Rosenbaum, Eli, Trock, Bruce, Westra, William H, Schoenberg, Mark, Goodman, Steven N., and Sidransky, David

Subjects
Male, Tissue Inhibitor of Metalloproteinase-3, Carcinoma, DNA Methylation, Middle Aged, Article, Cohort Studies, Survival Rate, Urinary Bladder Neoplasms, Humans, Female, Promoter Regions, Genetic, Aged, Neoplasm Staging
Abstract

TIMP-3 (tissue inhibitor of metalloproteinases-3) is 1 of 4 members of a family of proteins that were originally classified according to their ability to inhibit matrix metalloproteinases. We analyzed TIMP-3 methylation in 175 urine sediment DNA samples from patients with bladder cancer with well characterized clinicopathological parameters, including patient outcome.We examined urine sediment DNA for aberrant methylation of 9 genes, including TIMP-3, by quantitative fluorogenic real-time polymerase chain reaction.Using an optimal cutoff value by TaqMan(R) quantitation we found that the risk of death was statistically significantly higher in patients with higher TIMP-3 and ARF methylation (HR 1.99, 95% CI 1.12 to 3.27, p = 0.01 and HR 1.66, 95% CI 1.00 to 2.76, p = 0.05, respectively) than in patients without/lower TIMP3 and ARF methylation in urine. A significant correlation was also seen between the risk of death and stage 3 tumor (HR 2.73, 95% CI 1.58 to 4.72, p = 0.003) and metastasis (HR 3.32, 95% CI 1.98 to 5.57, p = 0.0001). Multivariate analysis subsequently revealed that TIMP-3 methylation was an independent prognostic factor for bladder cancer survival with stage and metastasis (p = 0.001 and 0.02, respectively).These results suggest that TIMP-3 promoter methylation could be a clinically applicable marker for bladder cancer progression.

Published
2007

23. Differential promoter methylation of kinesin family member 1a in plasma is associated with breast cancer and DNA repair capacity

Author

GUERRERO-PRESTON, RAFAEL, primary, HADAR, TAL, additional, OSTROW, KIMBERLY LASKIE, additional, SOUDRY, ETHAN, additional, ECHENIQUE, MIGUEL, additional, ILI-GANGAS, CARMEN, additional, PÉREZ, GABRIELA, additional, PEREZ, JIMENA, additional, BREBI-MIEVILLE, PRISCILLA, additional, DESCHAMPS, JOSÉ, additional, MORALES, LUISA, additional, BAYONA, MANUEL, additional, SIDRANSKY, DAVID, additional, and MATTA, JAIME, additional

Published
2014
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24. Molecular Analysis of Plasma DNA for the Early Detection of Lung Cancer by Quantitative Methylation-Specific PCR

Author

Ostrow, Kimberly Laskie, primary, Hoque, Mohammad O., additional, Loyo, Myriam, additional, Brait, Marianna, additional, Greenberg, Alissa, additional, Siegfried, Jill M., additional, Grandis, Jennifer R., additional, Gaither Davis, Autumn, additional, Bigbee, William L., additional, Rom, William, additional, and Sidransky, David, additional

Published
2010
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25. Promoter DNA Methylation of Oncostatin M receptor-β as a Novel Diagnostic and Therapeutic Marker in Colon Cancer

Author

Kim, Myoung Sook, primary, Louwagie, Joost, additional, Carvalho, Beatriz, additional, Terhaar sive Droste, Jochim S., additional, Park, Hannah Lui, additional, Chae, Young Kwang, additional, Yamashita, Keishi, additional, Liu, Junwei, additional, Ostrow, Kimberly Laskie, additional, Ling, Shizhang, additional, Guerrero-Preston, Rafael, additional, Demokan, Semra, additional, Yalniz, Zubeyde, additional, Dalay, Nejat, additional, Meijer, Gerrit A., additional, Van Criekinge, Wim, additional, and Sidransky, David, additional

Published
2009
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27. Genome-Wide Promoter Analysis Uncovers Portions of the Cancer Methylome

Author

Hoque, Mohammad Obaidul, primary, Kim, Myoung Sook, additional, Ostrow, Kimberly Laskie, additional, Liu, Junwei, additional, Wisman, G. Bea A., additional, Park, Hannah Lui, additional, Poeta, Maria Luana, additional, Jeronimo, Carmen, additional, Henrique, Rui, additional, Lendvai, Ágnes, additional, Schuuring, Ed, additional, Begum, Shahnaz, additional, Rosenbaum, Eli, additional, Ongenaert, Maté, additional, Yamashita, Keishi, additional, Califano, Joseph, additional, Westra, William, additional, van der Zee, Ate G.J., additional, Criekinge, Wim Van, additional, and Sidransky, David, additional

Published
2008
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30. Promoter DNA Methylation of Oncostatin M receptor-β as a Novel Diagnostic and Therapeutic Marker in Colon Cancer.

Author

Myoung Sook Kim, Louwagie, Joost, Carvalho, Beatriz, sive Droste, Jochim S. Terhaar, Hannah Lui Park, Young Kwang Chae, Yamashita, Keishi, Junwei Liu, Ostrow, Kimberly Laskie, Shizhang Ling, Guerrero-Preston, Rafael, Demokan, Semra, Yalniz, Zubeyde, Dalay, Nejat, Meijer, Gerrit A, Van Criekinge, Wim, and Sidransky, David

Subjects
GENES, CANCER patients, TISSUES, ALKYLATION, DEOXYRIBOSE, DNA, TISSUE banks, HEREDITY, CRYOBIOLOGY
Abstract

In addition to genetic changes, the occurrence of epigenetic alterations is associated with accumulation of both genetic and epigenetic events that promote the development and progression of human cancer. Previously, we reported a set of candidate genes that comprise part of the emerging ''cancer methylome''. In the present study, we first tested 23 candidate genes for promoter methylation in a small number of primary colon tumor tissues and controls. Based on these results, we then examined the methylation frequency of Oncostatin M receptor-β (OSMR) in a larger number of tissue and stool DNA samples collected from colon cancer patients and controls. We found that OSMR was frequently methylated in primary colon cancer tissues (80%, 80/100), but not in normal tissues (4%, 4/100). Methylation of OSMR was also detected in stool DNA from colorectal cancer patients (38%, 26/69) (cut-off in TaqMan-MSP, 4). Detection of other methylated markers in stool DNA improved sensitivity with little effect on specificity. Promoter methylation mediated silencing of OSMR in cell lines, and CRC cells with low OSMR expression were resistant to growth inhibition by Oncostatin M. Our data provide a biologic rationale for silencing of OSMR in colon cancer progression and highlight a new therapeutic target in this disease. Moreover, detection and quantification of OSMR promoter methylation in fecal DNA is a highly specific diagnostic biomarker for CRC. [ABSTRACT FROM AUTHOR]

Published
2009
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31. Promoter DNA methylation of oncostatin m receptor-beta as a novel diagnostic and therapeutic marker in colon cancer.

Author

Kim MS, Louwagie J, Carvalho B, Terhaar Sive Droste JS, Park HL, Chae YK, Yamashita K, Liu J, Ostrow KL, Ling S, Guerrero-Preston R, Demokan S, Yalniz Z, Dalay N, Meijer GA, Van Criekinge W, and Sidransky D

Subjects
Cell Line, Tumor, Colorectal Neoplasms diagnosis, Colorectal Neoplasms pathology, Colorectal Neoplasms therapy, Epigenesis, Genetic, Gene Silencing, Humans, Immunohistochemistry, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity, Biomarkers, Tumor genetics, Colorectal Neoplasms genetics, DNA Methylation, Oncostatin M Receptor beta Subunit genetics, Promoter Regions, Genetic
Abstract

In addition to genetic changes, the occurrence of epigenetic alterations is associated with accumulation of both genetic and epigenetic events that promote the development and progression of human cancer. Previously, we reported a set of candidate genes that comprise part of the emerging "cancer methylome". In the present study, we first tested 23 candidate genes for promoter methylation in a small number of primary colon tumor tissues and controls. Based on these results, we then examined the methylation frequency of Oncostatin M receptor-beta (OSMR) in a larger number of tissue and stool DNA samples collected from colon cancer patients and controls. We found that OSMR was frequently methylated in primary colon cancer tissues (80%, 80/100), but not in normal tissues (4%, 4/100). Methylation of OSMR was also detected in stool DNA from colorectal cancer patients (38%, 26/69) (cut-off in TaqMan-MSP, 4). Detection of other methylated markers in stool DNA improved sensitivity with little effect on specificity. Promoter methylation mediated silencing of OSMR in cell lines, and CRC cells with low OSMR expression were resistant to growth inhibition by Oncostatin M. Our data provide a biologic rationale for silencing of OSMR in colon cancer progression and highlight a new therapeutic target in this disease. Moreover, detection and quantification of OSMR promoter methylation in fecal DNA is a highly specific diagnostic biomarker for CRC.

Published
2009
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