Search

Your search keyword '"Bailey, Swneke"' showing total 230 results
Start Over Author "Bailey, Swneke"
230 results on '"Bailey, Swneke"'

1. ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip.

Author

Lee, John, Tao, Ran, You, Zhen, Haldipur, Parthiv, Erickson, Anders, Farooq, Hamza, Hendriske, Liam, Abeysundara, Namal, Richman, Cory, Wang, Evan, Das Gupta, Neha, Hadley, Jennifer, Batts, Melissa, Mount, Christopher, Wu, Xiaochong, Rasnitsyn, Alex, Bailey, Swneke, Cavalli, Florence, Morrissy, Sorana, Garzia, Livia, Michealraj, Kulandaimanuvel, Visvanathan, Abhi, Fong, Vernon, Palotta, Jonelle, Suarez, Raul, Livingston, Bryn, Liu, Miao, Luu, Betty, Daniels, Craig, Loukides, James, Bendel, Anne, French, Pim, Kros, Johan, Korshunov, Andrey, Kool, Marcel, Chico Ponce de León, Fernando, Perezpeña-Diazconti, Mario, Lach, Boleslaw, Singh, Sheila, Leary, Sarah, Cho, Byung-Kyu, Kim, Seung-Ki, Wang, Kyu-Chang, Lee, Ji-Yeoun, Tominaga, Teiji, Weiss, William, Phillips, Joanna, Dai, Shizhong, Zadeh, Gelareh, Saad, Ali, Bognár, László, Klekner, Almos, Pollack, Ian, Hamilton, Ronald, Ra, Young-Shin, Grajkowska, Wieslawa, Perek-Polnik, Marta, Thompson, Reid, Kenney, Anna, Cooper, Michael, Mack, Stephen, Jabado, Nada, Lupien, Mathieu, Gallo, Marco, Ramaswamy, Vijay, Suva, Mario, Suzuki, Hiromichi, Millen, Kathleen, Huang, L, Northcott, Paul, and Taylor, Michael

Abstract

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma ZIC1 mutants exhibit LOF phenotypes. Distinct ZIC1 mutations affect cells of the rhombic lip in diametrically opposed ways, suggesting that ZIC1 is a critical developmental transcriptional regulator in both the normal and transformed rhombic lip and identifying ZIC1 as an exquisitely context-dependent driver gene in medulloblastoma.

Published
2025

2. ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip

Author

Lee, John J. Y., Tao, Ran, You, Zhen, Haldipur, Parthiv, Erickson, Anders W., Farooq, Hamza, Hendriske, Liam D., Abeysundara, Namal, Richman, Cory M., Wang, Evan Y., Das Gupta, Neha, Hadley, Jennifer, Batts, Melissa, Mount, Christopher W., Wu, Xiaochong, Rasnitsyn, Alex, Bailey, Swneke, Cavalli, Florence M. G., Morrissy, Sorana, Garzia, Livia, Michealraj, Kulandaimanuvel Antony, Visvanathan, Abhi, Fong, Vernon, Palotta, Jonelle, Suarez, Raul, Livingston, Bryn G., Liu, Miao, Luu, Betty, Daniels, Craig, Loukides, James, Bendel, Anne, French, Pim J., Kros, Johan M., Korshunov, Andrey, Kool, Marcel, Chico Ponce de León, Fernando, Perezpeña-Diazconti, Mario, Lach, Boleslaw, Singh, Sheila K., Leary, Sarah E. S., Cho, Byung-Kyu, Kim, Seung-Ki, Wang, Kyu-Chang, Lee, Ji-Yeoun, Tominaga, Teiji, Weiss, William A., Phillips, Joanna J., Dai, Shizhong, Zadeh, Gelareh, Saad, Ali G., Bognár, László, Klekner, Almos, Pollack, Ian F., Hamilton, Ronald L., Ra, Young-shin, Grajkowska, Wieslawa A., Perek-Polnik, Marta, Thompson, Reid C., Kenney, Anna M., Cooper, Michael K., Mack, Stephen C., Jabado, Nada, Lupien, Mathieu, Gallo, Marco, Ramaswamy, Vijay, Suva, Mario L., Suzuki, Hiromichi, Millen, Kathleen J., Huang, L. Frank, Northcott, Paul A., and Taylor, Michael D.

Published
2025
Full Text
View/download PDF

4. Failure of human rhombic lip differentiation underlies medulloblastoma formation

Author

Hendrikse, Liam D, Haldipur, Parthiv, Saulnier, Olivier, Millman, Jake, Sjoboen, Alexandria H, Erickson, Anders W, Ong, Winnie, Gordon, Victor, Coudière-Morrison, Ludivine, Mercier, Audrey L, Shokouhian, Mohammad, Suárez, Raúl A, Ly, Michelle, Borlase, Stephanie, Scott, David S, Vladoiu, Maria C, Farooq, Hamza, Sirbu, Olga, Nakashima, Takuma, Nambu, Shohei, Funakoshi, Yusuke, Bahcheli, Alec, Diaz-Mejia, J Javier, Golser, Joseph, Bach, Kathleen, Phuong-Bao, Tram, Skowron, Patryk, Wang, Evan Y, Kumar, Sachin A, Balin, Polina, Visvanathan, Abhirami, Lee, John JY, Ayoub, Ramy, Chen, Xin, Chen, Xiaodi, Mungall, Karen L, Luu, Betty, Bérubé, Pierre, Wang, Yu C, Pfister, Stefan M, Kim, Seung-Ki, Delattre, Olivier, Bourdeaut, Franck, Doz, François, Masliah-Planchon, Julien, Grajkowska, Wieslawa A, Loukides, James, Dirks, Peter, Fèvre-Montange, Michelle, Jouvet, Anne, French, Pim J, Kros, Johan M, Zitterbart, Karel, Bailey, Swneke D, Eberhart, Charles G, Rao, Amulya AN, Giannini, Caterina, Olson, James M, Garami, Miklós, Hauser, Peter, Phillips, Joanna J, Ra, Young S, de Torres, Carmen, Mora, Jaume, Li, Kay KW, Ng, Ho-Keung, Poon, Wai S, Pollack, Ian F, López-Aguilar, Enrique, Gillespie, G Yancey, Van Meter, Timothy E, Shofuda, Tomoko, Vibhakar, Rajeev, Thompson, Reid C, Cooper, Michael K, Rubin, Joshua B, Kumabe, Toshihiro, Jung, Shin, Lach, Boleslaw, Iolascon, Achille, Ferrucci, Veronica, de Antonellis, Pasqualino, Zollo, Massimo, Cinalli, Giuseppe, Robinson, Shenandoah, Stearns, Duncan S, Van Meir, Erwin G, Porrati, Paola, Finocchiaro, Gaetano, Massimino, Maura, Carlotti, Carlos G, Faria, Claudia C, Roussel, Martine F, Boop, Frederick, Chan, Jennifer A, Aldinger, Kimberly A, Razavi, Ferechte, Silvestri, Evelina, McLendon, Roger E, and Thompson, Eric M

Subjects
Stem Cell Research, Brain Disorders, Neurosciences, Rare Diseases, Stem Cell Research - Nonembryonic - Non-Human, Aetiology, 1.1 Normal biological development and functioning, Underpinning research, 2.1 Biological and endogenous factors, Cell Differentiation, Cell Lineage, Cerebellar Neoplasms, Cerebellum, Core Binding Factor alpha Subunits, Hedgehog Proteins, Histone Demethylases, Humans, Ki-67 Antigen, Medulloblastoma, Metencephalon, Muscle Proteins, Mutation, Otx Transcription Factors, Repressor Proteins, T-Box Domain Proteins, Transcription Factors, General Science & Technology
Abstract

Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal neoplasms of the hindbrain with strong links to early development of the hindbrain1-4. Mutations that activate Sonic hedgehog signalling lead to Sonic hedgehog MB in the upper rhombic lip (RL) granule cell lineage5-8. By contrast, mutations that activate WNT signalling lead to WNT MB in the lower RL9,10. However, little is known about the more commonly occurring group 4 (G4) MB, which is thought to arise in the unipolar brush cell lineage3,4. Here we demonstrate that somatic mutations that cause G4 MB converge on the core binding factor alpha (CBFA) complex and mutually exclusive alterations that affect CBFA2T2, CBFA2T3, PRDM6, UTX and OTX2. CBFA2T2 is expressed early in the progenitor cells of the cerebellar RL subventricular zone in Homo sapiens, and G4 MB transcriptionally resembles these progenitors but are stalled in developmental time. Knockdown of OTX2 in model systems relieves this differentiation blockade, which allows MB cells to spontaneously proceed along normal developmental differentiation trajectories. The specific nature of the split human RL, which is destined to generate most of the neurons in the human brain, and its high level of susceptible EOMES+KI67+ unipolar brush cell progenitor cells probably predisposes our species to the development of G4 MB.

Published
2022

5. The transcriptional landscape of Shh medulloblastoma.

Author

Skowron, Patryk, Farooq, Hamza, Cavalli, Florence MG, Morrissy, A Sorana, Ly, Michelle, Hendrikse, Liam D, Wang, Evan Y, Djambazian, Haig, Zhu, Helen, Mungall, Karen L, Trinh, Quang M, Zheng, Tina, Dai, Shizhong, Stucklin, Ana S Guerreiro, Vladoiu, Maria C, Fong, Vernon, Holgado, Borja L, Nor, Carolina, Wu, Xiaochong, Abd-Rabbo, Diala, Bérubé, Pierre, Wang, Yu Chang, Luu, Betty, Suarez, Raul A, Rastan, Avesta, Gillmor, Aaron H, Lee, John JY, Zhang, Xiao Yun, Daniels, Craig, Dirks, Peter, Malkin, David, Bouffet, Eric, Tabori, Uri, Loukides, James, Doz, François P, Bourdeaut, Franck, Delattre, Olivier O, Masliah-Planchon, Julien, Ayrault, Olivier, Kim, Seung-Ki, Meyronet, David, Grajkowska, Wieslawa A, Carlotti, Carlos G, de Torres, Carmen, Mora, Jaume, Eberhart, Charles G, Van Meir, Erwin G, Kumabe, Toshihiro, French, Pim J, Kros, Johan M, Jabado, Nada, Lach, Boleslaw, Pollack, Ian F, Hamilton, Ronald L, Rao, Amulya A Nageswara, Giannini, Caterina, Olson, James M, Bognár, László, Klekner, Almos, Zitterbart, Karel, Phillips, Joanna J, Thompson, Reid C, Cooper, Michael K, Rubin, Joshua B, Liau, Linda M, Garami, Miklós, Hauser, Peter, Li, Kay Ka Wai, Ng, Ho-Keung, Poon, Wai Sang, Yancey Gillespie, G, Chan, Jennifer A, Jung, Shin, McLendon, Roger E, Thompson, Eric M, Zagzag, David, Vibhakar, Rajeev, Ra, Young Shin, Garre, Maria Luisa, Schüller, Ulrich, Shofuda, Tomoko, Faria, Claudia C, López-Aguilar, Enrique, Zadeh, Gelareh, Hui, Chi-Chung, Ramaswamy, Vijay, Bailey, Swneke D, Jones, Steven J, Mungall, Andrew J, Moore, Richard A, Calarco, John A, Stein, Lincoln D, Bader, Gary D, Reimand, Jüri, Ragoussis, Jiannis, Weiss, William A, Marra, Marco A, Suzuki, Hiromichi, and Taylor, Michael D

Subjects
Humans, Medulloblastoma, Cerebellar Neoplasms, Signal Transduction, Gene Expression Regulation, Neoplastic, Adolescent, Adult, Middle Aged, Child, Child, Preschool, Infant, Female, Male, Hedgehog Proteins, Gene Regulatory Networks, Genetic Variation, Young Adult, Transcriptome, Pediatric Research Initiative, Brain Cancer, Pediatric, Rare Diseases, Genetics, Pediatric Cancer, Clinical Research, Brain Disorders, Neurosciences, Biotechnology, Human Genome, Cancer, 2.1 Biological and endogenous factors
Abstract

Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN. Furthermore, we discover an extensive network of fusions in focally amplified regions encompassing GLI2, and several loss-of-function fusions in tumor suppressor genes PTCH1, SUFU and NCOR1. Molecular convergence on a subset of genes by nucleotide variants, copy number aberrations, and gene fusions highlight the key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma and open up opportunities for therapeutic intervention.

Published
2021

8. Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities

Author

Casey, Alison E, Sinha, Ankit, Singhania, Rajat, Livingstone, Julie, Waterhouse, Paul, Tharmapalan, Pirashaanthy, Cruickshank, Jennifer, Shehata, Mona, Drysdale, Erik, Fang, Hui, Kim, Hyeyeon, Isserlin, Ruth, Bailey, Swneke, Medina, Tiago, Deblois, Genevieve, Shiah, Yu-Jia, Barsyte-Lovejoy, Dalia, Hofer, Stefan, Bader, Gary, Lupien, Mathieu, Arrowsmith, Cheryl, Knapp, Stefan, De Carvalho, Daniel, Berman, Hal, Boutros, Paul C, Kislinger, Thomas, and Khokha, Rama

Subjects
Prevention, Stem Cell Research - Nonembryonic - Non-Human, Cancer, Biotechnology, Human Genome, Stem Cell Research - Nonembryonic - Human, Breast Cancer, Stem Cell Research, Regenerative Medicine, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Breast Neoplasms, Cell Line, Tumor, Cell Lineage, DNA Methylation, DNA, Neoplasm, Epigenesis, Genetic, Epigenomics, Humans, Mice, Mice, Transgenic, Neoplastic Stem Cells, Progesterone, Proteome, RNA, Neoplasm, Risk Factors, Transcriptome, Tumor Suppressor Protein p53, Up-Regulation, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The mammary epithelium depends on specific lineages and their stem and progenitor function to accommodate hormone-triggered physiological demands in the adult female. Perturbations of these lineages underpin breast cancer risk, yet our understanding of normal mammary cell composition is incomplete. Here, we build a multimodal resource for the adult gland through comprehensive profiling of primary cell epigenomes, transcriptomes, and proteomes. We define systems-level relationships between chromatin-DNA-RNA-protein states, identify lineage-specific DNA methylation of transcription factor binding sites, and pinpoint proteins underlying progesterone responsiveness. Comparative proteomics of estrogen and progesterone receptor-positive and -negative cell populations, extensive target validation, and drug testing lead to discovery of stem and progenitor cell vulnerabilities. Top epigenetic drugs exert cytostatic effects; prevent adult mammary cell expansion, clonogenicity, and mammopoiesis; and deplete stem cell frequency. Select drugs also abrogate human breast progenitor cell activity in normal and high-risk patient samples. This integrative computational and functional study provides fundamental insight into mammary lineage and stem cell biology.

Published
2018

9. ZIC1is a context-dependent medulloblastoma driver in the rhombic lip

Author

Lee, John J. Y., Tao, Ran, You, Zhen, Haldipur, Parthiv, Erickson, Anders W., Farooq, Hamza, Hendriske, Liam D., Abeysundara, Namal, Richman, Cory M., Wang, Evan Y., Das Gupta, Neha, Hadley, Jennifer, Batts, Melissa, Mount, Christopher W., Wu, Xiaochong, Rasnitsyn, Alex, Bailey, Swneke, Cavalli, Florence M. G., Morrissy, Sorana, Garzia, Livia, Michealraj, Kulandaimanuvel Antony, Visvanathan, Abhi, Fong, Vernon, Palotta, Jonelle, Suarez, Raul, Livingston, Bryn G., Liu, Miao, Luu, Betty, Daniels, Craig, Loukides, James, Bendel, Anne, French, Pim J., Kros, Johan M., Korshunov, Andrey, Kool, Marcel, Chico Ponce de León, Fernando, Perezpeña-Diazconti, Mario, Lach, Boleslaw, Singh, Sheila K., Leary, Sarah E. S., Cho, Byung-Kyu, Kim, Seung-Ki, Wang, Kyu-Chang, Lee, Ji-Yeoun, Tominaga, Teiji, Weiss, William A., Phillips, Joanna J., Dai, Shizhong, Zadeh, Gelareh, Saad, Ali G., Bognár, László, Klekner, Almos, Pollack, Ian F., Hamilton, Ronald L., Ra, Young-shin, Grajkowska, Wieslawa A., Perek-Polnik, Marta, Thompson, Reid C., Kenney, Anna M., Cooper, Michael K., Mack, Stephen C., Jabado, Nada, Lupien, Mathieu, Gallo, Marco, Ramaswamy, Vijay, Suva, Mario L., Suzuki, Hiromichi, Millen, Kathleen J., Huang, L. Frank, Northcott, Paul A., and Taylor, Michael D.

Abstract

Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma ZIC1 mutants exhibit LOF phenotypes. Distinct ZIC1mutations affect cells of the rhombic lip in diametrically opposed ways, suggesting that ZIC1is a critical developmental transcriptional regulator in both the normal and transformed rhombic lip and identifying ZIC1as an exquisitely context-dependent driver gene in medulloblastoma.

Published
2025
Full Text
View/download PDF

10. HiChIP-based Epigenomic Footprinting Identifies a Promoter Variant of UXS1 that Confers Genetic Susceptibility to Gastroesophageal Cancer.

Author

Gnanapragasam, Ansley, primary, Kirbizakis, Eftyhios, additional, Li, Anna, additional, White, Kyle H., additional, Mortenson, Katelyn L., additional, Cavalcante de Moura, Juliana, additional, Jawhar, Wajih, additional, Yan, Yifei, additional, Falter, Reilly, additional, Russett, Colleen, additional, Giannias, Betty, additional, Camilleri-Broët, Sophie, additional, Bertos, Nicholas, additional, Cools-Lartigue, Jonathan, additional, Garzia, Livia, additional, Sangwan, Veena, additional, Ferri, Lorenzo E., additional, Zhang, Xiaoyang, additional, and Bailey, Swneke D., additional

Published
2024
Full Text
View/download PDF

11. Author Correction: Failure of human rhombic lip differentiation underlies medulloblastoma formation

Author

Hendrikse, Liam D., Haldipur, Parthiv, Saulnier, Olivier, Millman, Jake, Sjoboen, Alexandria H., Erickson, Anders W., Ong, Winnie, Gordon, Victor, Coudière-Morrison, Ludivine, Mercier, Audrey L., Shokouhian, Mohammad, Suárez, Raúl A., Ly, Michelle, Borlase, Stephanie, Scott, David S., Vladoiu, Maria C., Farooq, Hamza, Sirbu, Olga, Nakashima, Takuma, Nambu, Shohei, Funakoshi, Yusuke, Bahcheli, Alec, Diaz-Mejia, J. Javier, Golser, Joseph, Bach, Kathleen, Phuong-Bao, Tram, Skowron, Patryk, Wang, Evan Y., Kumar, Sachin A., Balin, Polina, Visvanathan, Abhirami, Lee, John J. Y., Ayoub, Ramy, Chen, Xin, Chen, Xiaodi, Mungall, Karen L., Luu, Betty, Bérubé, Pierre, Wang, Yu C., Pfister, Stefan M., Kim, Seung-Ki, Delattre, Olivier, Bourdeaut, Franck, Doz, François, Masliah-Planchon, Julien, Grajkowska, Wieslawa A., Loukides, James, Dirks, Peter, Fèvre-Montange, Michelle, Jouvet, Anne, French, Pim J., Kros, Johan M., Zitterbart, Karel, Bailey, Swneke D., Eberhart, Charles G., Rao, Amulya A. N., Giannini, Caterina, Olson, James M., Garami, Miklós, Hauser, Peter, Phillips, Joanna J., Ra, Young S., de Torres, Carmen, Mora, Jaume, Li, Kay K. W., Ng, Ho-Keung, Poon, Wai S., Pollack, Ian F., López-Aguilar, Enrique, Gillespie, G. Yancey, Van Meter, Timothy E., Shofuda, Tomoko, Vibhakar, Rajeev, Thompson, Reid C., Cooper, Michael K., Rubin, Joshua B., Kumabe, Toshihiro, Jung, Shin, Lach, Boleslaw, Iolascon, Achille, Ferrucci, Veronica, de Antonellis, Pasqualino, Zollo, Massimo, Cinalli, Giuseppe, Robinson, Shenandoah, Stearns, Duncan S., Van Meir, Erwin G., Porrati, Paola, Finocchiaro, Gaetano, Massimino, Maura, Carlotti, Carlos G., Faria, Claudia C., Roussel, Martine F., Boop, Frederick, Chan, Jennifer A., Aldinger, Kimberly A., Razavi, Ferechte, Silvestri, Evelina, McLendon, Roger E., Thompson, Eric M., Ansari, Marc, Garre, Maria L., Chico, Fernando, Eguía, Pilar, Pérezpeña, Mario, Morrissy, A. Sorana, Cavalli, Florence M. G., Wu, Xiaochong, Daniels, Craig, Rich, Jeremy N., Jones, Steven J. M., Moore, Richard A., Marra, Marco A., Huang, Xi, Reimand, Jüri, Sorensen, Poul H., Wechsler-Reya, Robert J., Weiss, William A., Pugh, Trevor J., Garzia, Livia, Kleinman, Claudia L., Stein, Lincoln D., Jabado, Nada, Malkin, David, Ayrault, Olivier, Golden, Jeffrey A., Ellison, David W., Doble, Brad, Ramaswamy, Vijay, Werbowetski-Ogilvie, Tamra E., Suzuki, Hiromichi, Millen, Kathleen J., and Taylor, Michael D.

Published
2022
Full Text
View/download PDF

14. Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma

Author

Suzuki, Hiromichi, Kumar, Sachin A., Shuai, Shimin, Diaz-Navarro, Ander, Gutierrez-Fernandez, Ana, De Antonellis, Pasqualino, Cavalli, Florence M. G., Juraschka, Kyle, Farooq, Hamza, Shibahara, Ichiyo, Vladoiu, Maria C., Zhang, Jiao, Abeysundara, Namal, Przelicki, David, Skowron, Patryk, Gauer, Nicole, Luu, Betty, Daniels, Craig, Wu, Xiaochong, Forget, Antoine, Momin, Ali, Wang, Jun, Dong, Weifan, Kim, Seung-Ki, Grajkowska, Wieslawa A., Jouvet, Anne, Fèvre-Montange, Michelle, Garrè, Maria Luisa, Nageswara Rao, Amulya A., Giannini, Caterina, Kros, Johan M., French, Pim J., Jabado, Nada, Ng, Ho-Keung, Poon, Wai Sang, Eberhart, Charles G., Pollack, Ian F., Olson, James M., Weiss, William A., Kumabe, Toshihiro, López-Aguilar, Enrique, Lach, Boleslaw, Massimino, Maura, Van Meir, Erwin G., Rubin, Joshua B., Vibhakar, Rajeev, Chambless, Lola B., Kijima, Noriyuki, Klekner, Almos, Bognár, László, Chan, Jennifer A., Faria, Claudia C., Ragoussis, Jiannis, Pfister, Stefan M., Goldenberg, Anna, Wechsler-Reya, Robert J., Bailey, Swneke D., Garzia, Livia, Morrissy, A. Sorana, Marra, Marco A., Huang, Xi, Malkin, David, Ayrault, Olivier, Ramaswamy, Vijay, Puente, Xose S., Calarco, John A., Stein, Lincoln, and Taylor, Michael D.

Published
2019
Full Text
View/download PDF

15. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height

Author

Lanktree, Matthew B, Guo, Yiran, Murtaza, Muhammed, Glessner, Joseph T, Bailey, Swneke D, Onland-Moret, N Charlotte, Lettre, Guillaume, Ongen, Halit, Rajagopalan, Ramakrishnan, Johnson, Toby, Shen, Haiqing, Nelson, Christopher P, Klopp, Norman, Baumert, Jens, Padmanabhan, Sandosh, Pankratz, Nathan, Pankow, James S, Shah, Sonia, Taylor, Kira, Barnard, John, Peters, Bas J, Maloney, Cliona M, Lobmeyer, Maximilian T, Stanton, Alice, Zafarmand, M Hadi, Romaine, Simon PR, Mehta, Amar, van Iperen, Erik PA, Gong, Yan, Price, Tom S, Smith, Erin N, Kim, Cecilia E, Li, Yun R, Asselbergs, Folkert W, Atwood, Larry D, Bailey, Kristian M, Bhatt, Deepak, Bauer, Florianne, Behr, Elijah R, Bhangale, Tushar, Boer, Jolanda MA, Boehm, Bernhard O, Bradfield, Jonathan P, Brown, Morris, Braund, Peter S, Burton, Paul R, Carty, Cara, Chandrupatla, Hareesh R, Chen, Wei, Connell, John, Dalgeorgou, Chrysoula, de Boer, Anthonius, Drenos, Fotios, Elbers, Clara C, Fang, James C, Fox, Caroline S, Frackelton, Edward C, Fuchs, Barry, Furlong, Clement E, Gibson, Quince, Gieger, Christian, Goel, Anuj, Grobbee, Diederik E, Hastie, Claire, Howard, Philip J, Huang, Guan-Hua, Johnson, W Craig, Li, Qing, Kleber, Marcus E, Klein, Barbara EK, Klein, Ronald, Kooperberg, Charles, Ky, Bonnie, LaCroix, Andrea, Lanken, Paul, Lathrop, Mark, Li, Mingyao, Marshall, Vanessa, Melander, Olle, Mentch, Frank D, Meyer, Nuala J, Monda, Keri L, Montpetit, Alexandre, Murugesan, Gurunathan, Nakayama, Karen, Nondahl, Dave, Onipinla, Abiodun, Rafelt, Suzanne, Newhouse, Stephen J, Otieno, F George, Patel, Sanjey R, Putt, Mary E, Rodriguez, Santiago, Safa, Radwan N, Sawyer, Douglas B, Schreiner, Pamela J, Simpson, Claire, Sivapalaratnam, Suthesh, Srinivasan, Sathanur R, and Suver, Christine

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Adult, Black or African American, Asian People, Body Height, Cardiovascular System, Female, Gene Frequency, Genetic Heterogeneity, Genetic Loci, Genome-Wide Association Study, Hispanic or Latino, Humans, Interleukin-11, Male, Polymorphism, Single Nucleotide, Smad3 Protein, White People, Hugh Watkins on behalf of PROCARDIS, Meena Kumari on behalf of the Whitehall II Study and the WHII 50K Group, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Height is a classic complex trait with common variants in a growing list of genes known to contribute to the phenotype. Using a genecentric genotyping array targeted toward cardiovascular-related loci, comprising 49,320 SNPs across approximately 2000 loci, we evaluated the association of common and uncommon SNPs with adult height in 114,223 individuals from 47 studies and six ethnicities. A total of 64 loci contained a SNP associated with height at array-wide significance (p < 2.4 × 10(-6)), with 42 loci surpassing the conventional genome-wide significance threshold (p < 5 × 10(-8)). Common variants with minor allele frequencies greater than 5% were observed to be associated with height in 37 previously reported loci. In individuals of European ancestry, uncommon SNPs in IL11 and SMAD3, which would not be genotyped with the use of standard genome-wide genotyping arrays, were strongly associated with height (p < 3 × 10(-11)). Conditional analysis within associated regions revealed five additional variants associated with height independent of lead SNPs within the locus, suggesting allelic heterogeneity. Although underpowered to replicate findings from individuals of European ancestry, the direction of effect of associated variants was largely consistent in African American, South Asian, and Hispanic populations. Overall, we show that dense coverage of genes for uncommon SNPs, coupled with large-scale meta-analysis, can successfully identify additional variants associated with a common complex trait.

Published
2011

16. 380. INTEGRATIVE TRANSCRIPTOMIC AND FUNCTIONAL ANALYSIS OF CHEMOTHERAPY RESISTANCE IN ESOPHAGEAL ADENOCARCINOMA

Author

Kong, Mingyang (Iris), primary, Pal, Sanjima, additional, Qian, Qiu, additional, Tai, Kulsum, additional, Osman, Nathan, additional, Berube, Julie, additional, Bourdeau, France, additional, Zeng, Wotan, additional, Giannias, Betty, additional, Huang, Sui, additional, Bailey, Swneke, additional, Sangwan, Veena, additional, Bertos, Nick, additional, and Ferri, Lorenzo, additional

Published
2023
Full Text
View/download PDF

17. Tumour extracellular vesicles induce neutrophil extracellular traps to promote lymph node metastasis

Author

Su, Xin, primary, Brassard, Ariane, additional, Bartolomucci, Alexandra, additional, Dhoparee‐Doomah, Iqraa, additional, Qiu, Qian, additional, Tsering, Thupten, additional, Rohanizadeh, Ramin, additional, Koufos, Olivia, additional, Giannias, Betty, additional, Bourdeau, France, additional, Feng, Lixuan, additional, Messina‐Pacheco, Julia, additional, Leo, Sabrina, additional, Sangwan, Veena, additional, Quail, Daniela, additional, Tankel, James, additional, Spicer, Jonathan, additional, Burnier, Julia Valdemarin, additional, Bailey, Swneke Donovan, additional, Ferri, Lorenzo, additional, and Cools‐Lartigue, Jonathan, additional

Published
2023
Full Text
View/download PDF

18. Abstract 5959: Dissecting the stromal drivers of gastroesophageal adenocarcinoma chemoresistance

Author

Tai, Kulsum, primary, Pal, Sanjima, additional, Bérubé, Julie, additional, Kong, Iris, additional, Hoffman, Adam, additional, Bailey, Swneke, additional, Kirbizakis, Aki, additional, Huang, Sui, additional, Strasser, Michael, additional, Gibbs, David, additional, Bertos, Nicholas, additional, Sangwan, Veena, additional, and Ferri, Lorenzo, additional

Published
2023
Full Text
View/download PDF

24. Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation

Author

Marcon, Edyta, Ni, Zuyao, Pu, Shuye, Turinsky, Andrei L., Trimble, Sandra Smiley, Olsen, Jonathan B., Silverman-Gavrila, Rosalind, Silverman-Gavrila, Lorelei, Phanse, Sadhna, Guo, Hongbo, Zhong, Guoqing, Guo, Xinghua, Young, Peter, Bailey, Swneke, Roudeva, Denitza, Zhao, Dorothy, Hewel, Johannes, Li, Joyce, Gräslund, Susanne, Paduch, Marcin, Kossiakoff, Anthony A., Lupien, Mathieu, Emili, Andrew, Wodak, Shoshana J., and Greenblatt, Jack

Published
2014
Full Text
View/download PDF

26. Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer

Author

Song, Yueqiang, Li, Fuyuan, Wang, Shangzi, Wang, Yuntong, Lai, Cong, Chen, Lian, Jiang, Ning, Li, Jin, Chen, Xingdong, Bailey, Swneke D., and Zhang, Xiaoyang

Abstract

As a major type of structural variants, tandem duplication plays a critical role in tumorigenesis by increasing oncogene dosage. Recent work has revealed that noncoding enhancers are also affected by duplications leading to the activation of oncogenes that are inside or outside of the duplicated regions. However, the prevalence of enhancer duplication and the identity of their target genes remains largely unknown in the cancer genome. Here, by analyzing whole-genome sequencing data in a non-gene-centric manner, we identify 881 duplication hotspots in 13 major cancer types, most of which do not contain protein-coding genes. We show that the hotspots are enriched with distal enhancer elements and are highly lineage-specific. We develop a HiChIP-based methodology that navigates enhancer–promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63, and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1. In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1gene to promote migration of gastric cancer cells. Focusing on tandem duplications, our study substantially extends the catalog of noncoding driver alterations in multiple cancer types, revealing attractive targets for functional characterization and therapeutic intervention.

Published
2024
Full Text
View/download PDF

28. Soluble factors in malignant ascites promote the metastatic adhesion of gastric adenocarcinoma cells

Author

Al-Marzouki, Luai, primary, Stavrakos, Vivian S., additional, Pal, Sanjima, additional, Giannias, Betty, additional, Bourdeau, France, additional, Rayes, Roni, additional, Bertos, Nicholas, additional, Najmeh, Sara, additional, Spicer, Jonathan D., additional, Cools-Lartigue, Jonathan, additional, Bailey, Swneke D., additional, Ferri, Lorenzo, additional, and Sangwan, Veena, additional

Published
2022
Full Text
View/download PDF

31. Human somatic cell mutagenesis creates genetically tractable sarcomas

Author

Molyneux, Sam D, Waterhouse, Paul D, Shelton, Dawne, Shao, Yang W, Watling, Christopher M, Tang, Qing-Lian, Harris, Isaac S, Dickson, Brendan C, Tharmapalan, Pirashaanthy, Sandve, Geir K, Zhang, Xiaoyang, Bailey, Swneke D, Berman, Hal, Wunder, Jay S, Izsvák, Zsuzsanna, Lupien, Mathieu, Mak, Tak W, and Khokha, Rama

Published
2014
Full Text
View/download PDF

33. Inhibition of LPS-mediated TLR4 activation abrogates gastric adenocarcinoma-associated peritoneal metastasis

Author

Sangwan, Veena, primary, Al-Marzouki, Luai, additional, Pal, Sanjima, additional, Stavrakos, Vivian, additional, Alzahrani, Malak, additional, Antonatos, Dorothy, additional, Nevo, Yehonatan, additional, Camilleri-Broët, Sophie, additional, Rayes, Roni, additional, Bourdeau, France, additional, Giannias, Betty, additional, Bertos, Nicholas, additional, Bailey, Swneke, additional, Rousseau, Simon, additional, Cools-Lartigue, Jonathan, additional, Spicer, Jonathan D., additional, and Ferri, Lorenzo, additional

Published
2021
Full Text
View/download PDF

35. Abstract 1767: Peripheral blood neutrophil-to-lymphocyte ratio (NLR), a predictor of poor survival in cancer patients, was positively associated with the percentage of circulating low-density neutrophil fraction

Author

Rohanizadeh, Ramin, primary, Koufos, Olivia, additional, Su, Xin, additional, Brassard, Ariane, additional, Giannias, Betty, additional, Bourdeau, France, additional, Rayes, Roni, additional, Spicer, Jonathan, additional, Sangwan, Veena, additional, Bailey, Swneke, additional, Ferri, Lorenzo, additional, and Cools-Lartigue, Jonathan, additional

Published
2021
Full Text
View/download PDF

36. Genetic Information and the Prediction of Incident Type 2 Diabetes in a High-Risk Multiethnic Population: The EpiDREAM genetic study

Author

Anand, Sonia S., Meyre, David, Pare, Guillaume, Bailey, Swneke D., Xie, Changchun, Zhang, Xiaohe, Montpetit, Alexandre, Desai, Dipika, Bosch, Jackie, Mohan, Viswanathan, Diaz, Rafael, McQueen, Matthew J., Cordell, Heather J., Keavney, Bernard, Yusuf, Salim, Gaudet, Daniel, Gerstein, Hertzel, and Engert, James C.

Published
2013
Full Text
View/download PDF

42. Common polymorphisms in the promoter of the visfatin gene (PBEF1) influence plasma insulin levels in a French Canadian population

Author

Bailey, Swneke D., Bouchard, Claude, Loredo-Osti, J. Concepci­ón, Pérusse, Louis, Lepage, Pierre, Gaudet, Daniel, Faith, Janet, Vohl, Marie-Claude, Fontaine, Joelle, Desbiens, Katia, Hudson, Thomas J., Engert, James, Bailey, Swneke D., Bouchard, Claude, Loredo-Osti, J. Concepci­ón, Pérusse, Louis, Lepage, Pierre, Gaudet, Daniel, Faith, Janet, Vohl, Marie-Claude, Fontaine, Joelle, Desbiens, Katia, Hudson, Thomas J., and Engert, James

Abstract

The adipokine visfatin (PBEF1) exhibits insulin-mimetic effects and correlates strongly with visceral adiposity. We sequenced visfatin gene exons and 1,480 bp of the promoter in 23 individuals, including 18 individuals from the Quebec Family Study (QFS) with varying degrees of abdominal visceral fat, assessed by computed tomography, and 5 individuals from the Saguenay-Lac-Saint-Jean region of Québec. We identified a synonymous polymorphism in exon 7 (SER301SER) but no nonsynonymous mutations. We observed an additional 10 polymorphisms, including 5 intronic, 4 within the promoter, and 1 within the 3' untranslated region. Further promoter sequencing (816 bp) identified five additional single nucleotide polymorphisms (SNPs) in the QFS population. To investigate the role of visfatin gene variants in obesity-related phenotypes, we genotyped a total of 13 SNPs in the promoter region of the gene. From these, we analyzed the seven common SNPs in the QFS sample (918 participants from 208 families). A significant association was found between two SNPs (rs9770242 and rs1319501), in perfect linkage disequilibrium, and fasting insulin levels (P = 0.002). These SNPs were also associated with fasting glucose (P

Published
2020

43. Genetic variants of FTO influence adiposity, insulin sensitivity, leptin levels, and resting metabolic rate in the Quebec family study

Author

Do, Ron, Bouchard, Claude, Bailey, Swneke D., Pérusse, Louis, Desbiens, Katia, Vohl, Marie-Claude, Belisle, Alexandre, Montpetit, Alexandre, Engert, James, Do, Ron, Bouchard, Claude, Bailey, Swneke D., Pérusse, Louis, Desbiens, Katia, Vohl, Marie-Claude, Belisle, Alexandre, Montpetit, Alexandre, and Engert, James

Abstract

Objective: A genome-wide association study conducted by the Wellcome Trust Case Control Consortium recently associated single nucleotide polymorphisms (SNPs) in the FTO (fatso/fat mass and obesity associated) gene with type 2 diabetes. These associations were shown to be mediated by obesity. Other research groups found similar results in Europeans and Hispanics but not African Americans. The mechanism by which FTO influences obesity and type 2 diabetes is currently unknown. The present study investigated the role of two FTO SNPs (rs17817449 and rs1421085) in adiposity, insulin sensitivity, and body weight regulation, including energy intake and expenditure. Research design and methods: We genotyped 908 individuals from the Quebec City metropolitan area that participated in the Quebec Family Study, a long-term study of extensively phenotyped individuals designed to investigate factors involved in adiposity. Results: We found significant associations for both SNPs with several obesity-related phenotypes. In particular, rs17817449 was associated with BMI (P = 0.0014), weight (P = 0.0059), and waist circumference (P = 0.0021) under an additive model. In addition, this FTO SNP influenced fasting insulin (P = 0.011), homeostasis model assessment of insulin resistance (P = 0.038), and an insulin sensitivity index derived from an oral glucose tolerance test (P = 0.0091). Associations were also found with resting metabolic rate (RMR) (P = 0.042) and plasma leptin levels (P = 0.036). Adjustment for BMI abolished the associations with insulin sensitivity, RMR, and plasma leptin levels. Conclusions: These results confirm that genetic variation at the FTO locus contributes to the etiology of obesity, insulin resistance, and increased plasma leptin levels.

Published
2020

46. The effect of chromosome 9p21 variants on cardiovascular disease may be modified by dietary intake: evidence from a case/control and a prospective study

Author

Do, Ron, Xie, Changchun, Zhang, Xiaohe, Mannisto, Satu, Harald, Kennet, Islam, Shofiqul, Bailey, Swneke D., Rangarajan, Sumathy, McQueen, Matthew J., Diaz, Rafael, Lisheng, Liu, Wang, Xingyu, Silander, Kaisa, Peltonen, Leena, Yusuf, Salim, Salomaa, Veikko, Engert, James C., and Anand, Sonia S.

Subjects
Genetic aspects, Research, Risk factors, Genetic variation -- Research, Cardiovascular diseases -- Risk factors -- Genetic aspects -- Research
Abstract

Introduction Cardiovascular disease (CVD), including myocardial infarction (MI), is one of the leading causes of death and disability worldwide [1]. The etiology of the disease is well characterized and includes [...], Background: One of the most robust genetic associations for cardiovascular disease (CVD) is the Chromosome 9p21 region. However, the interaction of this locus with environmental factors has not been extensively explored. We investigated the association of 9p21 with myocardial infarction (MI) in individuals of different ethnicities, and tested for an interaction with environmental factors. Methods and Findings: We genotyped four 9p21 SNPs in 8,114 individuals from the global INTERHEART study. All four variants were associated with MI, with odds ratios (ORs) of 1.18 to 1.20 (1.85 x [10.sup.-8] [less than or equal to] p [less than or equal to] 5.21 x [10.sup.-7]). A significant interaction (p = 4.0 x [10.sup.-4]) was observed between rs2383206 and a factor-analysis-derived "prudent" diet pattern score, for which a major component was raw vegetables. An effect of 9p21 on MI was observed in the group with a low prudent diet score (OR = 1.32, p = 6.82 x [10.sup.-7]), but the effect was diminished in a step-wise fashion in the medium (OR = 1.17, p = 4.9 x [10.sup.-3]) and high prudent diet scoring groups (OR = 1.02, p = 0.68) (p = 0.014 for difference). We also analyzed data from 19,129 individuals (including 1,014 incident cases of CVD) from the prospective FINRISK study, which used a closely related dietary variable. In this analysis, the 9p21 risk allele demonstrated a larger effect on CVD risk in the groups with diets low or average for fresh vegetables, fruits, and berries (hazard ratio [HR]=1.22, p = 3.0 x [10.sup.-4], and HR=1.35, p = 4.1 x [10.sup.-3], respectively) compared to the group with high consumption of these foods (HR = 0.96, p = 0.73) (p = 0.0011 for difference). The combination of the least prudent diet and two copies of the risk allele was associated with a 2-fold increase in risk for MI (OR = 1.98, p = 2.11 x [10.sup.-9]) in the INTERHEART study and a 1.66-fold increase in risk for CVD in the FINRISK study (HR=1.66, p = 0.0026). Conclusions: The risk of MI and CVD conferred by Chromosome 9p21 SNPs appears to be modified by a prudent diet high in raw vegetables and fruits.

Published
2011
Full Text
View/download PDF

48. Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer

Author

Bailey, Swneke D, primary, Desai, Kinjal, additional, Kron, Ken J, additional, Mazrooei, Parisa, additional, Sinnott-Armstrong, Nicholas A, additional, Treloar, Aislinn E, additional, Dowar, Mark, additional, Thu, Kelsie L, additional, Cescon, David W, additional, Silvester, Jennifer, additional, Yang, S Y Cindy, additional, Wu, Xue, additional, Pezo, Rossanna C, additional, Haibe-Kains, Benjamin, additional, Mak, Tak W, additional, Bedard, Philippe L, additional, Pugh, Trevor J, additional, Sallari, Richard C, additional, and Lupien, Mathieu, additional

Published
2016
Full Text
View/download PDF

49. Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer

Author

Guo, Haiyang, primary, Ahmed, Musaddeque, additional, Zhang, Fan, additional, Yao, Cindy Q, additional, Li, SiDe, additional, Liang, Yi, additional, Hua, Junjie, additional, Soares, Fraser, additional, Sun, Yifei, additional, Langstein, Jens, additional, Li, Yuchen, additional, Poon, Christine, additional, Bailey, Swneke D, additional, Desai, Kinjal, additional, Fei, Teng, additional, Li, Qiyuan, additional, Sendorek, Dorota H, additional, Fraser, Michael, additional, Prensner, John R, additional, Pugh, Trevor J, additional, Pomerantz, Mark, additional, Bristow, Robert G, additional, Lupien, Mathieu, additional, Feng, Felix Y, additional, Boutros, Paul C, additional, Freedman, Matthew L, additional, Walsh, Martin J, additional, and He, Housheng Hansen, additional

Published
2016
Full Text
View/download PDF

50. The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence

Author

Boukhaled, Giselle M., primary, Cordeiro, Brendan, additional, Deblois, Genevieve, additional, Dimitrov, Vassil, additional, Bailey, Swneke D., additional, Holowka, Thomas, additional, Domi, Anisa, additional, Guak, Hannah, additional, Chiu, Huai-Hsuan Clare, additional, Everts, Bart, additional, Pearce, Edward J., additional, Lupien, Mathieu, additional, White, John H., additional, and Krawczyk, Connie M., additional

Published
2016
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results