26 results on '"Sui, Shannan Ho"'
Search Results
2. Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
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Morris, Vivian, Wang, Dahai, Li, Zhiheng, Marion, William, Hughes, Travis, Sousa, Patricia, Harada, Taku, Sui, Shannan Ho, Naumenko, Sergey, Kalfon, Jérémie, Sensharma, Prerana, Falchetti, Marcelo, Vinicius da Silva, Renan, Candelli, Tito, Schneider, Pauline, Margaritis, Thanasis, Holstege, Frank C.P., Pikman, Yana, Harris, Marian, Stam, Ronald W., Orkin, Stuart H., Koehler, Angela N., Shalek, Alex K., North, Trista E., Pimkin, Maxim, Daley, George Q., Lummertz da Rocha, Edroaldo, and Rowe, R. Grant
- Published
- 2022
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3. Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin
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Byles, Vanessa, Cormerais, Yann, Kalafut, Krystle, Barrera, Victor, Hughes Hallett, James E., Sui, Shannan Ho, Asara, John M., Adams, Christopher M., Hoxhaj, Gerta, Ben-Sahra, Issam, and Manning, Brendan D.
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- 2021
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4. Exposure to benzyl butyl phthalate (BBP) leads to increased double-strand break formation and germline dysfunction in Caenorhabditis elegans.
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Henderson, Ayana L., Karthikraj, Rajendiran, Berdan, Emma L., Sui, Shannan Ho, Kannan, Kurunthachalam, and Colaiácovo, Monica P.
- Subjects
GAMETOGENESIS ,OVUM ,EXTRACELLULAR matrix ,SPERMATOZOA ,DOUBLE-strand DNA breaks - Abstract
Benzyl butyl phthalate (BBP), a plasticizer found in a wide range of consumer products including vinyl flooring, carpet backing, food packaging, personal care products, and children's toys, is an endocrine-disrupting chemical linked to impaired reproduction and development in humans. Despite evidence that BBP exposure perturbs the integrity of male and female gametes, its direct effect on early meiotic events is understudied. Here, using the nematode Caenorhabditis elegans, we show that BBP exposure elicits a non-monotonic dose response on the rate of X-chromosome nondisjunction measured using a high-throughput screening platform. From among the range of doses tested (1, 10, 100 and 500 μM BBP), we found that 10 μM BBP elicited the strongest effect on the germline, resulting in increased germ cell apoptosis and chromosome organization defects. Mass spectrometry analysis shows that C. elegans efficiently metabolizes BBP into its primary metabolites, monobutyl phthalate (MBP) and monobenzyl phthalate (MBzP), and that the levels of BBP, MBP, and MBzP detected in the worm are within the range detected in human biological samples. Exposure to 10 μM BBP leads to germlines with enlarged mitotic nuclei, altered meiotic progression, activation of a p53/CEP-1-dependent DNA damage checkpoint, increased double-strand break levels throughout the germline, chromosome morphology defects in oocytes at diakinesis, and increased oxidative stress. RNA sequencing analysis indicates that BBP exposure results in the altered expression of genes involved in xenobiotic metabolic processes, extracellular matrix organization, oocyte morphogenesis, meiotic cell cycle, and oxidoreduction. Taken together, we propose that C. elegans exposure to BBP leads to increased oxidative stress and double-strand break formation, thereby compromising germline genomic integrity and chromosome segregation. Author summary: Endocrine disrupting chemicals (EDCs) have been linked to various health problems including effects on reproductive health. Benzyl butyl phthalate (BBP) is a commonly used plasticizer found in many consumer products that has been shown to act as an EDC and affect human reproduction and development. However, how it might impact the germline and affect the specialized cell division program of meiosis, which results in the formation of haploid gametes (i.e. eggs and sperm), remained unclear. Here, using the nematode C. elegans, we show that BBP exposure at levels within the range of what is detected in humans impairs accurate chromosome segregation, which can result in aneuploidy. Similar to mammals, BBP exposure in C. elegans results in a non-monotonic dose response, whereby lower doses result in the strongest effects, and BBP is efficiently metabolized, underscoring the use of this model system for gaining mechanistic insights into how this EDC impacts the germline. BBP results in increased levels of DNA double-strand breaks (DSBs), activation of a DNA damage checkpoint, and altered chromosome morphology in exposed germlines. We propose that BBP exposure alters gene expression and results in increased oxidative stress, resulting in increased DSBs, thereby compromising chromosome morphology and accurate segregation. [ABSTRACT FROM AUTHOR]
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- 2024
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5. A cell atlas of the adult Drosophila midgut
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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
6. Altered gene expression linked to germline dysfunction following exposure to DEET
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Shin, Nara, Lascarez-Lagunas, Laura I., Henderson, Ayana L., Martínez-García, Marina, Karthikraj, Rajendiran, Barrera, Victor, Sui, Shannan Ho, Kannan, Kurunthachalam, and Colaiácovo, Mónica P.
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- 2024
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7. NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression
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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
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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.
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- 2023
8. Metastable Atrial State Underlies the Primary Genetic Substrate for MYL4 Mutation-Associated Atrial Fibrillation
- Author
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Ghazizadeh, Zaniar, Kiviniemi, Tuomas, Olafsson, Sigurast, Plotnick, David, Beerens, Manu E., Zhang, Kun, Gillon, Leah, Steinbaugh, Michael J., Barrera, Victor, Sui, Shannan Ho, Werdich, Andreas A., Kapur, Sunil, Eranti, Antti, Gunn, Jarmo, Jalkanen, Juho, Airaksinen, Juhani, Kleber, Andre G., Hollmén, Maija, and MacRae, Calum A.
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- 2020
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9. Immunoregulatory and lipid presentation pathways are upregulated in human face transplant rejection
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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.
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Complications and side effects ,Research ,Risk factors ,Facial transplantation -- Complications and side effects ,Medical research ,Immune response -- Research ,Graft rejection -- Risk factors ,Medicine, Experimental - Abstract
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 [...], 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.
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- 2021
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10. Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells
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Massachusetts Institute of Technology. Department of Biological Engineering, Morris, Vivian, Wang, Dahai, Li, Zhiheng, Marion, William, Hughes, Travis, Sousa, Patricia, Harada, Taku, Sui, Shannan Ho, Naumenko, Sergey, Kalfon, Jérémie, Sensharma, Prerana, Falchetti, Marcelo, Vinicius da Silva, Renan, Candelli, Tito, Schneider, Pauline, Margaritis, Thanasis, Holstege, Frank CP, Pikman, Yana, Harris, Marian, Stam, Ronald W, Orkin, Stuart H, Koehler, Angela N, Shalek, Alex K, North, Trista E, Pimkin, Maxim, Daley, George Q, Lummertz da Rocha, Edroaldo, Rowe, R Grant, Massachusetts Institute of Technology. Department of Biological Engineering, Morris, Vivian, Wang, Dahai, Li, Zhiheng, Marion, William, Hughes, Travis, Sousa, Patricia, Harada, Taku, Sui, Shannan Ho, Naumenko, Sergey, Kalfon, Jérémie, Sensharma, Prerana, Falchetti, Marcelo, Vinicius da Silva, Renan, Candelli, Tito, Schneider, Pauline, Margaritis, Thanasis, Holstege, Frank CP, Pikman, Yana, Harris, Marian, Stam, Ronald W, Orkin, Stuart H, Koehler, Angela N, Shalek, Alex K, North, Trista E, Pimkin, Maxim, Daley, George Q, Lummertz da Rocha, Edroaldo, and Rowe, R Grant
- Abstract
High-risk forms of B-acute lymphoblastic leukemia (B-ALL) remain a therapeutic challenge. Leukemia-initiating cells (LICs) self-renew and spark relapse and therefore have been the subject of intensive investigation; however, the properties of LICs in high-risk B-ALL are not well understood. Here, we use single-cell transcriptomics and quantitative xenotransplantation to understand LICs in MLL-rearranged (MLL-r) B-ALL. Compared with reported LIC frequencies in acute myeloid leukemia (AML), engraftable LICs in MLL-r B-ALL are abundant. Although we find that multipotent, self-renewing LICs are enriched among phenotypically undifferentiated B-ALL cells, LICs with the capacity to replenish the leukemic cellular diversity can emerge from more mature fractions. While inhibiting oxidative phosphorylation blunts blast proliferation, this intervention promotes LIC emergence. Conversely, inhibiting hypoxia and glycolysis impairs MLL-r B-ALL LICs, providing a therapeutic benefit in xenotransplantation systems. These findings provide insight into the aggressive nature of MLL-r B-ALL and provide a rationale for therapeutic targeting of hypoxia and glycolysis.
- Published
- 2023
11. Abstract 5755: TP63 fusions drive enhancer rewiring, lymphomagenesis, and dependence on EZH2
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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
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- 2023
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12. Organoid modeling reveals the tumorigenic potential of the alveolar progenitor cell state
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Kim, Carla, primary, Li, Jingyun, additional, Dang, Susanna, additional, Schurmann, Paul, additional, Dost, Antonella, additional, Moye, Aaron, additional, Paschini, Margherita, additional, Bhetariya, Preetida, additional, Bronson, Roderick, additional, and Sui, Shannan Ho, additional
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- 2023
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13. Prenatal Lead Levels, Plasma Amyloid β Levels, and Gene Expression in Young Adulthood
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Mazumdar, Maitreyi, Xia, Weiming, Hofmann, Oliver, Gregas, Matthew, Sui, Shannan Ho, Hide, Winston, Yang, Ting, Needleman, Herbert L., and Bellinger, David C.
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- 2012
14. SOX15 regulates stem cell pluripotency and promotes neural fate during differentiation by activating Hes5
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Choi, Eun-Bee, primary, Vodnala, Munender, additional, Saini, Prince, additional, Zerbato, Madeleine, additional, Ho, Jaclyn J., additional, Anugula, Sharath, additional, Wang, Jianing, additional, Sui, Shannan Ho, additional, Yoon, Joon, additional, Inouye, Carla, additional, and Fong, Yick W, additional
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- 2022
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15. 2001 – PLASTICITY OF B-LYMPHOBLASTIC LEUKEMIA STEM CELLS
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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
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- 2021
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16. Hepatic mTORC1 signaling activates ATF4 as part of its metabolic response to feeding and insulin
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Byles, Vanessa, primary, Cormerais, Yann, additional, Kalafut, Krystle, additional, Barrera, Victor, additional, Hughes Hallett, James E., additional, Sui, Shannan Ho, additional, Asara, John M., additional, Adams, Christopher M., additional, Hoxhaj, Gerta, additional, Ben-Sahra, Issam, additional, and Manning, Brendan D., additional
- Published
- 2021
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17. Integrated skin transcriptomics and serum multiplex assays reveal novel mechanisms of wound healing in diabetic foot ulcers
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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
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- 2020
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18. Integrated Skin Transcriptomics and Serum Multiplex Assays Reveal Novel Mechanisms of Wound Healing in Diabetic Foot Ulcers
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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
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- 2020
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19. Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities
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Dragon, Julie A., primary, Gates, Chris, additional, Sui, Shannan Ho, additional, Hutchinson, John N., additional, Karuturi, R. Krishna Murthy, additional, Kucukural, Alper, additional, Polson, Shawn, additional, Riva, Alberto, additional, Settles, Matthew Lee, additional, Thimmapuram, Jyothi, additional, and Levine, Stuart S., additional
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- 2020
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20. Supporting Single Cell RNA-seq Analysis at Harvard - A Community Approach
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Sui, Shannan Ho, Kirchner, Rory, Steinbaugh, Michael, Boswell, Sarah, Piper, Mary, Barrera, Victor, Pantano, Lorena, Khetani, Radhika, Mistry, Meeta, Rutherford, Kayleigh, and Hutchinson, John
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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.
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- 2019
21. A single-cell survey ofDrosophilablood
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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
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- 2019
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22. A cell atlas of the adult Drosophila midgut
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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
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- 2018
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23. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa
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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.
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- 2016
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24. The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework
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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
25. An aging-sensitive compensatory secretory phospholipase that confers neuroprotection and cognitive resilience.
- Author
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Vicidomini C, Goode TD, McAvoy KM, Yu R, Beveridge CH, Iyer SN, Victor MB, Leary N, Evans L, Steinbaugh MJ, Lai ZW, Lyon MC, Silvestre MRFS, Bonilla G, Sadreyev RI, Walther TC, Sui SH, Saido T, Yamamoto K, Murakami M, Tsai LH, Chopra G, and Sahay A
- Abstract
Breakdown of lipid homeostasis is thought to contribute to pathological aging, the largest risk factor for neurodegenerative disorders such as Alzheimer's Disease (AD). Cognitive reserve theory posits a role for compensatory mechanisms in the aging brain in preserving neuronal circuit functions, staving off cognitive decline, and mitigating risk for AD. However, the identities of such mechanisms have remained elusive. A screen for hippocampal dentate granule cell (DGC) synapse loss-induced factors identified a secreted phospholipase , Pla2g2f , whose expression increases in DGCs during aging. Pla2g2f deletion in DGCs exacerbates aging-associated pathophysiological changes including synapse loss, inflammatory microglia, reactive astrogliosis, impaired neurogenesis, lipid dysregulation and hippocampal-dependent memory loss. Conversely, boosting Pla2g2f in DGCs during aging is sufficient to preserve synapses, reduce inflammatory microglia and reactive gliosis, prevent hippocampal-dependent memory impairment and modify trajectory of cognitive decline. Ex vivo, neuronal-PLA2G2F mediates intercellular signaling to decrease lipid droplet burden in microglia. Boosting Pla2g2f expression in DGCs of an aging-sensitive AD model reduces amyloid load and improves memory. Our findings implicate PLA2G2F as a compensatory neuroprotective factor that maintains lipid homeostasis to counteract aging-associated cognitive decline.
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- 2024
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26. NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression.
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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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- View/download PDF
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