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24 results on '"Sui, Shannan Ho"'

3. A cell atlas of the adult Drosophila midgut

Author

Hung, Ruei-Jiun, Hu, Yanhui, Kirchner, Rory, Liu, Yifang, Xu, Chiwei, Comjean, Aram, Tattikota, Sudhir Gopal, Li, Fangge, Song, Wei, Sui, Shannan Ho, and Perrimon, Norbert

Published
2020

5. NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression

Author

Takashima, Ken, Lee, Dian-Jang, Trovero, María Fernanda, Rothi, M. Hafiz, Mistry, Meeta, Zhang, Ying, Li, Zhouyihan, Davis, Christopher P., Li, Zilan, Natale, Julia, Schmid, Ernst, Al Haddad, Joseph, Hoffmann, Gabriela Brunsting, Dietmann, Sabine, Sui, Shannan Ho, Oshiumi, Hiroyuki, Lieberman, Judy, and Greer, Eric Lieberman

Subjects
Article
Abstract

Post-translational modifications of histone tails alter chromatin accessibility to regulate gene expression. Some viruses exploit the importance of histone modifications by expressing histone mimetic proteins that contain histone-like sequences to sequester complexes that recognize modified histones. Here we identify an evolutionarily conserved and ubiquitously expressed, endogenous mammalian protein Nucleolar protein 16 (NOP16) that functions as a H3K27 mimic. NOP16 binds to EED in the H3K27 trimethylation PRC2 complex and to the H3K27 demethylase JMJD3. NOP16 knockout selectively globally increases H3K27me3, a heterochromatin mark, without altering methylation of H3K4, H3K9, or H3K36 or acetylation of H3K27. NOP16 is overexpressed and linked to poor prognosis in breast cancer. Depletion of NOP16 in breast cancer cell lines causes cell cycle arrest, decreases cell proliferation and selectively decreases expression of E2F target genes and of genes involved in cell cycle, growth and apoptosis. Conversely, ectopic NOP16 expression in triple negative breast cancer cell lines increases cell proliferation, cell migration and invasivity in vitro and tumor growth in vivo , while NOP16 knockout or knockdown has the opposite effect. Thus, NOP16 is a histone mimic that competes with Histone H3 for H3K27 methylation and demethylation. When it is overexpressed in cancer, it derepresses genes that promote cell cycle progression to augment breast cancer growth.

Published
2023

6. Abstract 5755: TP63 fusions drive enhancer rewiring, lymphomagenesis, and dependence on EZH2

Author

Wu, Gongwei, primary, Yoshida, Noriaki, additional, Liu, Jihe, additional, Zhang, Xiaoyang, additional, Xiong, Yuan, additional, Heavican-Foral, Tayla, additional, Liu, Huiyun, additional, Nelson, Geoffrey, additional, Yang, Lu, additional, Chen, Renee, additional, Donovan, Katherine, additional, Jones, Marcus, additional, Roshal, Mikhail, additional, Zhang, Yanming, additional, Xu, Ran, additional, Nirmal, Ajit, additional, Jain, Salvia, additional, Leahy, Catharine, additional, Jones, Kristen, additional, Stevenson, Kristen, additional, Galasso, Natasha, additional, Ganesan, Nivetha, additional, Chang, Tiffany, additional, Wu, Wen-Chao, additional, Louissaint, Abner, additional, Debaize, Lydie, additional, Yoon, Hojong, additional, Cin, Paola Dal, additional, Chan, Wing Chan, additional, Sui, Shannan Ho Sui Ho, additional, Ng, Samuel, additional, Feldman, Andrew, additional, Horwitz, Steven M., additional, Meyerson, Mathew, additional, Adelman, Karen, additional, Fischer, Eric, additional, Chen, Chun-Wei, additional, Weinstock, David, additional, and Brown, Myles, additional

Published
2023
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9. Immunoregulatory and lipid presentation pathways are upregulated in human face transplant rejection

Author

Win, Thet Su, Crisler, William J., Dyring-Andersen, Beatrice, Lopdrup, Rachel, Teague, Jessica E., Zhan, Qian, Barrera, Victor, Sui, Shannan Ho, Tasigiorgos, Sotirios, Murakami, Naoka, Chandraker, Anil, Tullius, Stefan G., Pomahac, Bohdan, Riella, Leonardo V., and Clark, Rachael A.

Subjects
Medical research, Medicine, Experimental, Immune response -- Research, Graft rejection -- Risk factors, Facial transplantation -- Complications and side effects, Health care industry
Abstract

BACKGROUND. Rejection is the primary barrier to broader implementation of vascularized composite allografts (VCAs), including face and limb transplants. The immunologic pathways activated in face transplant rejection have not been fully characterized. METHODS. Using skin biopsies prospectively collected over 9 years from 7 face transplant patients, we studied rejection by gene expression profiling, histology, immunostaining, and T cell receptor sequencing. RESULTS. Grade 1 rejection did not differ significantly from nonrejection, suggesting that it does not represent a pathologic state. In grade 2, there was a balanced upregulation of both proinflammatory T cell activation pathways and antiinflammatory checkpoint and immunomodulatory pathways, with a net result of no tissue injury. In grade 3, IFN-[gamma]-driven inflammation, antigen-presenting cell activation, and infiltration of the skin by proliferative T cells bearing markers of antigen- specific activation and cytotoxicity tipped the balance toward tissue injury. Rejection of VCAs and solid organ transplants had both distinct and common features. VCA rejection was uniquely associated with upregulation of immunoregulatory genes, including SOCST, induction of lipid antigen-presenting CD1 proteins; and infiltration by T cells predicted to recognize CD1b and CD1c. CONCLUSION. Our findings suggest that the distinct features of VCA rejection reflect the unique immunobiology of skin and that enhancing cutaneous immunoregulatory networks may be a useful strategy in combatting rejection. TRIAL REGISTRATION. ClinicalTrials.gov NCT01281267. FUNDING. Assistant Secretary of Defense and Health Affairs, through Reconstructive Transplant Research (W81XWH-17-1-0278, W81XWH-16-1-0647, W81XWH-16-1-0689, W81XWH-18-1-0784, W81XWH-1-810798); American Society of Transplantation's Transplantation and Immunology Research Network Fellowship Research Grant; Plastic Surgery Foundation Fellowship from the American Society of Plastic Surgeons; Novo Nordisk Foundation (NNF150C0014092); Lundbeck Foundation; Aage Bangs Foundation; A.P. Moller Foundation for the Advancement of Medical Science; NIH UL1 RR025758., Introduction At least 40 human face transplants have been reported worldwide since the first procedure was performed in 2005. In the intervening years, face transplantation has proven to be an [...]

Published
2021
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11. Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells

Author

Morris, Vivian, primary, Wang, Dahai, additional, Li, Zhiheng, additional, Marion, William, additional, Hughes, Travis, additional, Sousa, Patricia, additional, Harada, Taku, additional, Sui, Shannan Ho, additional, Naumenko, Sergey, additional, Kalfon, Jérémie, additional, Sensharma, Prerana, additional, Falchetti, Marcelo, additional, Vinicius da Silva, Renan, additional, Candelli, Tito, additional, Schneider, Pauline, additional, Margaritis, Thanasis, additional, Holstege, Frank C.P., additional, Pikman, Yana, additional, Harris, Marian, additional, Stam, Ronald W., additional, Orkin, Stuart H., additional, Koehler, Angela N., additional, Shalek, Alex K., additional, North, Trista E., additional, Pimkin, Maxim, additional, Daley, George Q., additional, Lummertz da Rocha, Edroaldo, additional, and Rowe, R. Grant, additional

Published
2022
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13. 2001 – PLASTICITY OF B-LYMPHOBLASTIC LEUKEMIA STEM CELLS

Author

Rowe, Grant, primary, Morris, Vivian, additional, Wang, Dahai, additional, Marion, William, additional, Hughes, Travis, additional, Sousa, Patricia, additional, Harada, Taku, additional, Sui, Shannan Ho, additional, Naumenko, Sergey, additional, Kalfon, Jeremie, additional, Sensharma, Prerana, additional, da Silva, Renan Vinicius, additional, Pikman, Yana, additional, Harris, Marian, additional, Pimkin, Maxim, additional, Shalek, Alex, additional, North, Trista, additional, Daley, George, additional, and da Rocha, Edroaldo Lummertz, additional

Published
2021
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15. Supporting Single Cell RNA-seq Analysis at Harvard - A Community Approach

Author

Sui, Shannan Ho, Kirchner, Rory, Steinbaugh, Michael, Boswell, Sarah, Piper, Mary, Barrera, Victor, Pantano, Lorena, Khetani, Radhika, Mistry, Meeta, Rutherford, Kayleigh, and Hutchinson, John

Subjects
Poster Abstracts
Abstract

Recent advances in single cell transcriptomics make it possible to examine the gene expression profiles of thousands of individual cells, providing unprecedented insights into tissue heterogeneity, development and pathogenesis. In 2015, the Harvard Chan Bioinformatics Core (http://bioinformatics.sph.harvard.edu) teamed up with the Harvard Medical School (HMS) Single Cell Core (https://iccb.med.harvard.edu/single-cell-core) to standardize data analysis for the InDrop droplet barcoding system and prepare for projected demand within the Harvard community. Here we describe our approach to building single cell analytical expertise and infrastructure through our partnership with the Single Cell Core and multiple research labs. We outline the challenges we faced and our current best practices for data analysis (quality assessment, quantitation, clustering, visualization, and differential expression). Our pipeline, implemented within the bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.io/), handles multiple UMI schemes to accommodate different single cell technologies (e.g. Drop-seq, Seq-well, Bio-Rad ddSeq, etc.). We also describe our approach to managing single cell projects, with their longer analysis times, increased complexity and need for rigorous experimental design, data management, computing infrastructure and methods evaluation. All of these require close collaboration and frequent communication with the bench biologists generating the data. Due to these factors, we have expanded our bioinformatics training program to include modules on single cell RNA-seq. With this program, we hope to develop analysis expertise within the community and an understanding of the methods and intricacies inherent in the technology - ultimately leading to better designed and more successful single cell RNA-seq experiments.

Published
2019

16. Integrated skin transcriptomics and serum multiplex assays reveal novel mechanisms of wound healing in diabetic foot ulcers

Author

Admin, Ada, primary, Theocharidis, Georgios, primary, Baltzis, Dimitrios, primary, Roustit, Matthieu, primary, Tellechea, Ana, primary, Dangwal, Seema, primary, Khetani, Radhika S., primary, Shu, Bin, primary, Zhao, Wanni, primary, Fu, Jianfang, primary, Bhasin, Swati, primary, Kafanas, Antonios, primary, Hui, Daniel, primary, Sui, Shannan Ho, primary, Patsopoulos, Nikolaos A., primary, Bhasin, Manoj, primary, and Veves, Aristidis, primary

Published
2020
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17. Integrated Skin Transcriptomics and Serum Multiplex Assays Reveal Novel Mechanisms of Wound Healing in Diabetic Foot Ulcers

Author

Theocharidis, Georgios, primary, Baltzis, Dimitrios, additional, Roustit, Matthieu, additional, Tellechea, Ana, additional, Dangwal, Seema, additional, Khetani, Radhika S., additional, Shu, Bin, additional, Zhao, Wanni, additional, Fu, Jianfang, additional, Bhasin, Swati, additional, Kafanas, Antonios, additional, Hui, Daniel, additional, Sui, Shannan Ho, additional, Patsopoulos, Nikolaos A., additional, Bhasin, Manoj, additional, and Veves, Aristidis, additional

Published
2020
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19. A single-cell survey ofDrosophilablood

Author

Tattikota, Sudhir Gopal, primary, Hu, Yanhui, additional, Liu, Yifang, additional, Cho, Bumsik, additional, Barrera, Victor, additional, Steinbaugh, Michael, additional, Yoon, Sang-Ho, additional, Comjean, Aram, additional, Li, Fangge, additional, Dervis, Franz, additional, Hung, Ruei-Jiun, additional, Nam, Jin-Wu, additional, Sui, Shannan Ho, additional, Shim, Jiwon, additional, and Perrimon, Norbert, additional

Published
2019
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20. A cell atlas of the adult Drosophila midgut

Author

Hung, Ruei-Jiun, primary, Hu, Yanhui, additional, Kirchner, Rory, additional, Li, Fangge, additional, Xu, Chiwei, additional, Comjean, Aram, additional, Tattikota, Sudhir Gopal, additional, Song, Wei Roc, additional, Sui, Shannan Ho, additional, and Perrimon, Norbert, additional

Published
2018
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21. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

Author

Mulder, Nicola J., Adebiyi, Ezekiel, Alami, Raouf, Benkahla, Alia, Brandful, James, Doumbia, Seydou, Everett, Dean, Fadlelmola, Faisal M., Gaboun, Fatima, Gaseitsiwe, Simani, Ghazal, Hassan, Hazelhurst, Scott, Hide, Winston, Ibrahimi, Azeddine, Jaufeerally Fakim, Yasmina, Jongeneel, C. Victor, Joubert, Fourie, Kassim, Samar, Kayondo, Jonathan, Kumuthini, Judit, Lyantagaye, Sylvester, Makani, Julie, Mansour Alzohairy, Ahmed, Masiga, Daniel, Moussa, Ahmed, Nash, Oyekanmi, Ouwe Missi Oukem-Boyer, Odile, Owusu-Dabo, Ellis, Panji, Sumir, Patterton, Hugh, Radouani, Fouzia, Sadki, Khalid, Seghrouchni, Fouad, Tastan Bishop, Ozlem, Tiffin, Nicki, Ulenga, Nzovu, Adebiyi, Marion, Ahmed, Azza E., Ahmed, Rehab I., Alearts, Maaike, Alibi, Mohamed, Aron, Shaun, Baichoo, Shakuntala, Bendou, Hocine, Botha, Gerrit, Brown, David, Chimusa, Emile, Christoffels, Alan, Cornick, Jennifer, Entfellner, Jean-Baka Domelevo, Fields, Chris, Fischer, Anne, Gamieldien, Junaid, Ghedira, Kais, Ghouila, Amel, Sui, Shannan Ho, Isewon, Itunuoluwa, Isokpehi, Raphael, Dashti, Mahjoubeh Jalali Sefid, Kamng'ona, Arox, Khetani, Radhika S., Kiran, Anmol, Kulohoma, Benard, Kumwenda, Benjamin, Lapine, Dan, Mainzer, Liudmila Sergeevna, Maslamoney, Suresh, Mbiyavanga, Mamana, Meintjes, Ayton, Mlyango, Flora Elias, Mmbando, Bruno, Mohammed, Somia A., Mpangase, Phelelani, Msefula, Chisomo, Mtatiro, Siana Nkya, Mugutso, Dunfunk, Mungloo-Dilmohammud, Zahra, Musicha, Patrick, Nembaware, Victoria, Osamor, Victor Chukwudi, Oyelade, Jelili, Rendon, Gloria, Salazar, Gustavo A., Salifu, Samson Pandam, Sangeda, Raphael, Souiai, Oussema, Van Heusden, Peter, and Wele, Mamadou

Abstract

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Published
2016
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22. The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework

Author

Sui, Shannan Ho, Merrill, Emily, Gehlenborg, Nils, Haseley, Psalm, Sytchev, Ilya, Park, Richard, Rocca-Serra, Philippe, Corlosquet, Stephane, Gonzalez-Beltran, Alejandra, Maguire, Eamonn, Hofmann, Oliver, Park, Peter, Das, Sudeshna, Sansone, Susanna-Assunta, and Hide, Winston

Abstract

Comparisons of stem cell experiments at both molecular and semantic levels remain challenging due to inconsistencies in results, data formats, and descriptions among biomedical research discoveries. The Harvard Stem Cell Institute (HSCI) has created the Stem Cell Commons (stemcellcommons.org), an open, community-based approach to data sharing. Experimental information is integrated using the Investigation-Study-Assay tabular format (ISA-Tab) used by over 30 organizations (ISA Commons, isacommons.org). The early adoption of this format permitted the novel integration of three independent systems to facilitate stem cell data storage, exchange and analysis: the Blood Genomics Repository, the Stem Cell Discovery Engine, and the new Refinery platform that links the Galaxy analytical engine to data repositories.

Published
2013

24. NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression.

Author

Takashima K, Lee DJ, Trovero MF, Rothi MH, Mistry M, Zhang Y, Li Z, Davis CP, Li Z, Natale J, Schmid E, Al Haddad J, Hoffmann GB, Dietmann S, Sui SH, Oshiumi H, Lieberman J, and Greer EL

Abstract

Post-translational modifications of histone tails alter chromatin accessibility to regulate gene expression. Some viruses exploit the importance of histone modifications by expressing histone mimetic proteins that contain histone-like sequences to sequester complexes that recognize modified histones. Here we identify an evolutionarily conserved and ubiquitously expressed, endogenous mammalian protein Nucleolar protein 16 (NOP16) that functions as a H3K27 mimic. NOP16 binds to EED in the H3K27 trimethylation PRC2 complex and to the H3K27 demethylase JMJD3. NOP16 knockout selectively globally increases H3K27me3, a heterochromatin mark, without altering methylation of H3K4, H3K9, or H3K36 or acetylation of H3K27. NOP16 is overexpressed and linked to poor prognosis in breast cancer. Depletion of NOP16 in breast cancer cell lines causes cell cycle arrest, decreases cell proliferation and selectively decreases expression of E2F target genes and of genes involved in cell cycle, growth and apoptosis. Conversely, ectopic NOP16 expression in triple negative breast cancer cell lines increases cell proliferation, cell migration and invasivity in vitro and tumor growth in vivo , while NOP16 knockout or knockdown has the opposite effect. Thus, NOP16 is a histone mimic that competes with Histone H3 for H3K27 methylation and demethylation. When it is overexpressed in cancer, it derepresses genes that promote cell cycle progression to augment breast cancer growth.

Published
2023
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