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3. One-Way Matching of Datasets with Low Rank Signals

Author

Chen, Shuxiao, Jiang, Sizun, Ma, Zongming, Nolan, Garry P., and Zhu, Bokai

Subjects
Mathematics - Statistics Theory, Computer Science - Information Theory, Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods
Abstract

We study one-way matching of a pair of datasets with low rank signals. Under a stylized model, we first derive information-theoretic limits of matching under a mismatch proportion loss. We then show that linear assignment with projected data achieves fast rates of convergence and sometimes even minimax rate optimality for this task. The theoretical error bounds are corroborated by simulated examples. Furthermore, we illustrate practical use of the matching procedure on two single-cell data examples.

Published
2022

6. Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype

Author

Viswanathan, Vignesh, Cao, Hongbin, Saiki, Julie, Jiang, Dadi, Mattingly, Aaron, Nambiar, Dhanya, Bloomstein, Joshua, Li, Yang, Jiang, Sizun, Chamoli, Manish, Sirjani, Davud, Kaplan, Michael, Holsinger, F Christopher, Liang, Rachel, Von Eyben, Rie, Jiang, Haowen, Guan, Li, Lagory, Edward, Feng, Zhiping, Nolan, Garry, Ye, Jiangbin, Denko, Nicholas, Knox, Sarah, Rosen, Daria-Mochly, and Le, Quynh-Thu

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Stem Cell Research, Genetics, Stem Cell Research - Nonembryonic - Non-Human, Regenerative Medicine, Dental/Oral and Craniofacial Disease, Cancer, Digestive Diseases
Abstract

Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures postradiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from Aldh3a1 -/- mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels, depletes glutathione pool, and accumulates ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.

Published
2022

7. Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers

Author

Nakayama, Tsuguhisa, Lee, Ivan T, Jiang, Sizun, Matter, Matthias S, Yan, Carol H, Overdevest, Jonathan B, Wu, Chien-Ting, Goltsev, Yury, Shih, Liang-Chun, Liao, Chun-Kang, Zhu, Bokai, Bai, Yunhao, Lidsky, Peter, Xiao, Yinghong, Zarabanda, David, Yang, Angela, Easwaran, Meena, Schürch, Christian M, Chu, Pauline, Chen, Han, Stalder, Anna K, McIlwain, David R, Borchard, Nicole A, Gall, Phillip A, Dholakia, Sachi S, Le, Wei, Xu, Le, Tai, Chih-Jaan, Yeh, Te-Huei, Erickson-Direnzo, Elizabeth, Duran, Jason M, Mertz, Kirsten D, Hwang, Peter H, Haslbauer, Jasmin D, Jackson, Peter K, Menter, Thomas, Andino, Raul, Canoll, Peter D, DeConde, Adam S, Patel, Zara M, Tzankov, Alexandar, Nolan, Garry P, and Nayak, Jayakar V

Subjects
Dental/Oral and Craniofacial Disease, Tobacco, Prevention, Biodefense, Pneumonia & Influenza, Emerging Infectious Diseases, Infectious Diseases, Pneumonia, Tobacco Smoke and Health, Clinical Research, Vaccine Related, Lung, 2.1 Biological and endogenous factors, Aetiology, 2.2 Factors relating to the physical environment, Infection, Respiratory, Good Health and Well Being, Aged, Aged, 80 and over, Angiotensin-Converting Enzyme 2, COVID-19, Female, Gene Expression Regulation, Humans, Male, Middle Aged, Nasal Cavity, Respiratory Mucosa, SARS-CoV-2, Serine Endopeptidases, Smokers, Trachea, Viral Tropism, ACE2, IFN-β1, TMPRSS2, ciliated epithelial cell, nasal cavity, smoking, trachea, upper airway
Abstract

Understanding viral tropism is an essential step toward reducing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, decreasing mortality from coronavirus disease 2019 (COVID-19) and limiting opportunities for mutant strains to arise. Currently, little is known about the extent to which distinct tissue sites in the human head and neck region and proximal respiratory tract selectively permit SARS-CoV-2 infection and replication. In this translational study, we discover key variabilities in expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2), essential SARS-CoV-2 entry factors, among the mucosal tissues of the human proximal airways. We show that SARS-CoV-2 infection is present in all examined head and neck tissues, with a notable tropism for the nasal cavity and tracheal mucosa. Finally, we uncover an association between smoking and higher SARS-CoV-2 viral infection in the human proximal airway, which may explain the increased susceptibility of smokers to developing severe COVID-19. This is at least partially explained by differences in interferon (IFN)-β1 levels between smokers and non-smokers.

Published
2021

9. SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment

Author

Wu, Chien-Ting, Lidsky, Peter V, Xiao, Yinghong, Lee, Ivan T, Cheng, Ran, Nakayama, Tsuguhisa, Jiang, Sizun, Demeter, Janos, Bevacqua, Romina J, Chang, Charles A, Whitener, Robert L, Stalder, Anna K, Zhu, Bokai, Chen, Han, Goltsev, Yury, Tzankov, Alexandar, Nayak, Jayakar V, Nolan, Garry P, Matter, Matthias S, Andino, Raul, and Jackson, Peter K

Subjects
Diabetes, Pneumonia & Influenza, Prevention, Lung, Autoimmune Disease, Pneumonia, Infectious Diseases, Emerging Infectious Diseases, Clinical Research, Aetiology, 2.1 Biological and endogenous factors, Metabolic and endocrine, Good Health and Well Being, A549 Cells, Adult, Aged, Aged, 80 and over, Angiotensin-Converting Enzyme 2, Antigens, CD, Apoptosis, Apoptosis Regulatory Proteins, COVID-19, Case-Control Studies, Diabetes Mellitus, Female, Host-Pathogen Interactions, Humans, Insulin, Insulin-Secreting Cells, Male, Middle Aged, Neuropilin-1, Receptors, Transferrin, Receptors, Virus, SARS-CoV-2, Serine Endopeptidases, Spike Glycoprotein, Coronavirus, Virus Internalization, ACE2, SARS-CoV-2 spike protein, apoptosis, insulin, neuropilin 1, pancreatic beta cell, phosphoproteomics, type 1 diabetes, Biochemistry and Cell Biology, Medical Biochemistry and Metabolomics, Endocrinology & Metabolism
Abstract

Emerging evidence points toward an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While preexisting diabetes is associated with severe COVID-19, it is unclear whether COVID-19 severity is a cause or consequence of diabetes. To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic β cells can be infected by SARS-CoV-2 and cause β cell depletion. We found that the SARS-CoV-2 receptor, ACE2, and related entry factors (TMPRSS2, NRP1, and TRFC) are expressed in β cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic β cells in patients who succumbed to COVID-19 and selectively infects human islet β cells in vitro. We demonstrated that SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion and induces β cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic β cell signaling, similar to that observed in type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce β cell killing.

Published
2021

10. Morphologic and molecular analysis of liver injury after SARS-CoV-2 vaccination reveals distinct characteristics

Author

Uzun, Sarp, Zinner, Carl P., Beenen, Amke C., Alborelli, Ilaria, Bartoszek, Ewelina M., Yeung, Jason, Calgua, Byron, Reinscheid, Matthias, Bronsert, Peter, Stalder, Anna K., Haslbauer, Jasmin D., Vosbeck, Juerg, Mazzucchelli, Luca, Hoffmann, Tobias, Terracciano, Luigi M., Hutter, Gregor, Manz, Michael, Panne, Isabelle, Boettler, Tobias, Hofmann, Maike, Bengsch, Bertram, Heim, Markus H., Bernsmeier, Christine, Jiang, Sizun, Tzankov, Alexandar, Terziroli Beretta-Piccoli, Benedetta, and Matter, Matthias S.

Published
2023
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13. Landscape of coordinated immune responses to H1N1 challenge in humans

Author

Rahil, Zainab, Leylek, Rebecca, Schürch, Christian M, Chen, Han, Bjornson-Hooper, Zach, Christensen, Shannon R, Gherardini, Pier Federico, Bhate, Salil S, Spitzer, Matthew H, Fragiadakis, Gabriela K, Mukherjee, Nilanjan, Kim, Nelson, Jiang, Sizun, Yo, Jennifer, Gaudilliere, Brice, Affrime, Melton, Bock, Bonnie, Hensley, Scott E, Idoyaga, Juliana, Aghaeepour, Nima, Kim, Kenneth, Nolan, Garry P, and McIlwain, David R

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Immunology, Pneumonia & Influenza, Emerging Infectious Diseases, Biodefense, Influenza, Infectious Diseases, 2.1 Biological and endogenous factors, Infection, Inflammatory and immune system, Good Health and Well Being, Female, Humans, Influenza A Virus, H1N1 Subtype, Influenza, Human, Killer Cells, Natural, Lymphocyte Activation, Male, T-Lymphocytes, Adaptive immunity, Infectious disease, Innate immunity, Medical and Health Sciences, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Influenza is a significant cause of morbidity and mortality worldwide. Here we show changes in the abundance and activation states of more than 50 immune cell subsets in 35 individuals over 11 time points during human A/California/2009 (H1N1) virus challenge monitored using mass cytometry along with other clinical assessments. Peak change in monocyte, B cell, and T cell subset frequencies coincided with peak virus shedding, followed by marked activation of T and NK cells. Results led to the identification of CD38 as a critical regulator of plasmacytoid dendritic cell function in response to influenza virus. Machine learning using study-derived clinical parameters and single-cell data effectively classified and predicted susceptibility to infection. The coordinated immune cell dynamics defined in this study provide a framework for identifying novel correlates of protection in the evaluation of future influenza therapeutics.

Published
2020

14. ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs.

Author

Lee, Ivan T, Nakayama, Tsuguhisa, Wu, Chien-Ting, Goltsev, Yury, Jiang, Sizun, Gall, Phillip A, Liao, Chun-Kang, Shih, Liang-Chun, Schürch, Christian M, McIlwain, David R, Chu, Pauline, Borchard, Nicole A, Zarabanda, David, Dholakia, Sachi S, Yang, Angela, Kim, Dayoung, Chen, Han, Kanie, Tomoharu, Lin, Chia-Der, Tsai, Ming-Hsui, Phillips, Katie M, Kim, Raymond, Overdevest, Jonathan B, Tyler, Matthew A, Yan, Carol H, Lin, Chih-Feng, Lin, Yi-Tsen, Bau, Da-Tian, Tsay, Gregory J, Patel, Zara M, Tsou, Yung-An, Tzankov, Alexandar, Matter, Matthias S, Tai, Chih-Jaan, Yeh, Te-Huei, Hwang, Peter H, Nolan, Garry P, Nayak, Jayakar V, and Jackson, Peter K

Subjects
Goblet Cells, Respiratory System, Lung, Cilia, Endothelial Cells, Humans, Pneumonia, Viral, Coronavirus Infections, Sinusitis, Peptidyl-Dipeptidase A, Angiotensin-Converting Enzyme Inhibitors, Smoking, Age Factors, Sex Factors, Gene Expression, Angiotensin Receptor Antagonists, Pandemics, COVID-19, Angiotensin-Converting Enzyme 2, Pneumonia, Viral
Abstract

The coronavirus SARS-CoV-2 is the causative agent of the ongoing severe acute respiratory disease pandemic COVID-19. Tissue and cellular tropism is one key to understanding the pathogenesis of SARS-CoV-2. We investigate the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of human donors using a diverse panel of banked tissues. Here, we report our discovery that the ACE2 receptor protein robustly localizes within the motile cilia of airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during host respiratory transmission. We further determine whether ciliary ACE2 expression in the upper airway is influenced by patient demographics, clinical characteristics, comorbidities, or medication use, and show the first mechanistic evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) does not increase susceptibility to SARS-CoV-2 infection through enhancing the expression of ciliary ACE2 receptor. These findings are crucial to our understanding of the transmission of SARS-CoV-2 for prevention and control of this virulent pathogen.

Published
2020

15. Glucose dissociates DDX21 dimers to regulate mRNA splicing and tissue differentiation

Author

Miao, Weili, Porter, Douglas F., Lopez-Pajares, Vanessa, Siprashvili, Zurab, Meyers, Robin M., Bai, Yunhao, Nguyen, Duy T., Ko, Lisa A., Zarnegar, Brian J., Ferguson, Ian D., Mills, Matthew M., Jilly-Rehak, Christie E., Wu, Cheng-Guo, Yang, Yen-Yu, Meyers, Jordan M., Hong, Audrey W., Reynolds, David L., Ramanathan, Muthukumar, Tao, Shiying, Jiang, Sizun, Flynn, Ryan A., Wang, Yinsheng, Nolan, Garry P., and Khavari, Paul A.

Published
2023
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16. SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming

Author

Wu, Chien-Ting, Lidsky, Peter V., Xiao, Yinghong, Cheng, Ran, Lee, Ivan T., Nakayama, Tsuguhisa, Jiang, Sizun, He, Wei, Demeter, Janos, Knight, Miguel G., Turn, Rachel E., Rojas-Hernandez, Laura S., Ye, Chengjin, Chiem, Kevin, Shon, Judy, Martinez-Sobrido, Luis, Bertozzi, Carolyn R., Nolan, Garry P., Nayak, Jayakar V., Milla, Carlos, Andino, Raul, and Jackson, Peter K.

Published
2023
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17. Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19

Author

Feyaerts, Dorien, Hédou, Julien, Gillard, Joshua, Chen, Han, Tsai, Eileen S., Peterson, Laura S., Ando, Kazuo, Manohar, Monali, Do, Evan, Dhondalay, Gopal K.R., Fitzpatrick, Jessica, Artandi, Maja, Chang, Iris, Snow, Theo T., Chinthrajah, R. Sharon, Warren, Christopher M., Wittman, Richard, Meyerowitz, Justin G., Ganio, Edward A., Stelzer, Ina A., Han, Xiaoyuan, Verdonk, Franck, Gaudillière, Dyani K., Mukherjee, Nilanjan, Tsai, Amy S., Rumer, Kristen K., Jacobsen, Danielle R., Bjornson-Hooper, Zachary B., Jiang, Sizun, Saavedra, Sergio Fragoso, Valdés Ferrer, Sergio Iván, Kelly, J. Daniel, Furman, David, Aghaeepour, Nima, Angst, Martin S., Boyd, Scott D., Pinsky, Benjamin A., Nolan, Garry P., Nadeau, Kari C., Gaudillière, Brice, and McIlwain, David R.

Published
2022
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19. Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data

Author

Zhu, Bokai, primary, Gao, Sheng, additional, Chen, Shuxiao, additional, Yeung, Jason, additional, Bai, Yunhao, additional, Huang, Amy, additional, Yeo, Yao Yu, additional, Liao, Guanrui, additional, Mao, Shulian, additional, Jiang, Zhenghui, additional, Rodig, Scott, additional, Shalek, Alex K, additional, Nolan, Garry P, additional, Jiang, Sizun, additional, and Ma, Zongming, additional

Published
2024
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20. Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

Author

Yeo, Yao Yu, primary, Qiu, Huaying, additional, Bai, Yunhao, additional, Zhu, Bokai, additional, Chang, Yuzhou, additional, Yeung, Jason, additional, Michel, Hendrik A., additional, Wright, Kyle, additional, Shaban, Muhammad, additional, Sadigh, Sam, additional, Nkosi, Dingani, additional, Shanmugam, Vignesh, additional, Rock, Philip, additional, Tung Yiu, Stephanie Pei, additional, Cramer, Precious, additional, Paczkowska, Julia, additional, Stephan, Pierre, additional, Liao, Guanrui, additional, Huang, Amy Y., additional, Wang, Hongbo, additional, Chen, Han, additional, Frauenfeld, Leonie, additional, Mitra, Bidisha, additional, Gewurz, Benjamin E., additional, Schürch, Christian M., additional, Zhao, Bo, additional, Nolan, Garry P., additional, Zhang, Baochun, additional, Shalek, Alex K., additional, Angelo, Michael, additional, Mahmood, Faisal, additional, Ma, Qin, additional, Burack, W. Richard, additional, Shipp, Margaret A., additional, Rodig, Scott J., additional, and Jiang, Sizun, additional

Published
2024
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22. Innovative Technologies for Advancement of WHO Risk Group 4 Pathogens Research

Author

Logue, James, Solomon, Jeffrey, Niemeyer, Brian F., Benam, Kambez H., Lin, Aaron E., Bjornson, Zach, Jiang, Sizun, McIlwain, David R., Nolan, Garry P., Palacios, Gustavo, Kuhn, Jens H., Shapshak, Paul, editor, Balaji, Seetharaman, editor, Kangueane, Pandjassarame, editor, Chiappelli, Francesco, editor, Somboonwit, Charurut, editor, Menezes, Lynette J., editor, and Sinnott, John T., editor

Published
2019
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23. Graph Fourier transform for spatial omics representation and analyses of complex organs

Author

Ma, Qin, primary, Chang, Yuzhou, additional, Liu, Jixin, additional, Jiang, Yi, additional, Ma, Anjun, additional, Yeo, Yao Yu, additional, Guo, Qi, additional, McNutt, Megan, additional, Krull, Jodran, additional, Rodig, Scott, additional, Barouch, Dan, additional, Nolan, Garry, additional, Xu, Dong, additional, Jiang, Sizun, additional, Li, Zihai, additional, and Liu, Bingqiang, additional

Published
2024
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24. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

Author

Patel, Anand G., primary, Ashenberg, Orr, additional, Collins, Natalie B., additional, Segerstolpe, Åsa, additional, Jiang, Sizun, additional, Slyper, Michal, additional, Huang, Xin, additional, Caraccio, Chiara, additional, Jin, Hongjian, additional, Sheppard, Heather, additional, Xu, Ke, additional, Chang, Ti-Cheng, additional, Orr, Brent A., additional, Shirinifard, Abbas, additional, Chapple, Richard H., additional, Shen, Amber, additional, Clay, Michael R., additional, Tatevossian, Ruth G., additional, Reilly, Colleen, additional, Patel, Jaimin, additional, Lupo, Marybeth, additional, Cline, Cynthia, additional, Dionne, Danielle, additional, Porter, Caroline B.M., additional, Waldman, Julia, additional, Bai, Yunhao, additional, Zhu, Bokai, additional, Barrera, Irving, additional, Murray, Evan, additional, Vigneau, Sébastien, additional, Napolitano, Sara, additional, Wakiro, Isaac, additional, Wu, Jingyi, additional, Grimaldi, Grace, additional, Dellostritto, Laura, additional, Helvie, Karla, additional, Rotem, Asaf, additional, Lako, Ana, additional, Cullen, Nicole, additional, Pfaff, Kathleen L., additional, Karlström, Åsa, additional, Jané-Valbuena, Judit, additional, Todres, Ellen, additional, Thorner, Aaron, additional, Geeleher, Paul, additional, Rodig, Scott J., additional, Zhou, Xin, additional, Stewart, Elizabeth, additional, Johnson, Bruce E., additional, Wu, Gang, additional, Chen, Fei, additional, Yu, Jiyang, additional, Goltsev, Yury, additional, Nolan, Garry P., additional, Rozenblatt-Rosen, Orit, additional, Regev, Aviv, additional, and Dyer, Michael A., additional

Published
2024
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25. mRNA vaccines against SARS-CoV-2 induce divergent antigen-specific T-cell responses in patients with lung cancer

Author

Song, No-Joon, primary, Chakravarthy, Karthik B, additional, Jeon, Hyeongseon, additional, Bolyard, Chelsea, additional, Reynolds, Kelsi, additional, Weller, Kevin P, additional, Reisinger, Sarah, additional, Wang, Yi, additional, Li, Anqi, additional, Jiang, Sizun, additional, Ma, Qin, additional, Barouch, Dan H, additional, Rubinstein, Mark P, additional, Shields, Peter G, additional, Oltz, Eugene M, additional, Chung, Dongjun, additional, and Li, Zihai, additional

Published
2024
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29. Deep Learning Model Imputes Missing Stains in Multiplex Images

Author

Shaban, Muhammad, primary, Lassoued, Wiem, additional, Canubas, Kenneth, additional, Bailey, Shania, additional, Liu, Yanling, additional, Allen, Clint, additional, Strauss, Julius, additional, Gulley, James L, additional, Jiang, Sizun, additional, Mahmood, Faisal, additional, Zaki, George, additional, and Sater, Houssein A, additional

Published
2023
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31. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology

Author

Bai, Yunhao, primary, Zhu, Bokai, additional, Oliveria, John-Paul, additional, Cannon, Bryan J., additional, Feyaerts, Dorien, additional, Bosse, Marc, additional, Vijayaragavan, Kausalia, additional, Greenwald, Noah F., additional, Phillips, Darci, additional, Schürch, Christian M., additional, Naik, Samuel M., additional, Ganio, Edward A., additional, Gaudilliere, Brice, additional, Rodig, Scott J., additional, Miller, Michael B., additional, Angelo, Michael, additional, Bendall, Sean C., additional, Rovira-Clavé, Xavier, additional, Nolan, Garry P., additional, and Jiang, Sizun, additional

Published
2023
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32. MAPS: Pathologist-level cell type annotation from tissue images through machine learning

Author

Shaban, Muhammad, primary, Bai, Yunhao, additional, Qiu, Huaying, additional, Mao, Shulin, additional, Yeung, Jason, additional, Yeo, Yao Yu, additional, Shanmugam, Vignesh, additional, Chen, Han, additional, Zhu, Bokai, additional, Nolan, Garry P., additional, Shipp, Margaret A., additional, Rodig, Scott J., additional, Jiang, Sizun, additional, and Mahmood, Faisal, additional

Published
2023
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34. MIBI dataset for Expanded Vacuum-Stable Gels for Multiplexed High Resolution Spatial Histopathology

Author

Bai, Yunhao, Zhu, Bokai, Oliveria, John-Paul, Cannon, Bryan J., Feyaerts, Dorien, Bosse, Marc, Vijayaragavan, Kausalia, Greenwald, Noah F., Phillips, Darci, Schürch, Christian M., Naik, Samuel M., Ganio, Edward A., Gaudilliere, Brice, Rodig, Scott J., Miller, Michael B., Angelo, Michael, Bendall, Sean C., Rovira-Clavé, Xavier, Nolan, Garry P., and Jiang, Sizun

Subjects
Mass spectrometry-based imaging, Multiplexed imaging, Spatial proteomics, Expansion microscopy, Brain, Immunostaining
Abstract

Multiplexed MIBI images used in Figures for manuscript "Expanded Vacuum-Stable Gels for Multiplexed High Resolution Spatial Histopathology", a manuscript described a method permitting the accomendation of expansion microscopy (ExM) hydrogel in high vacuum chamber or desiccated environment, and allows for interrogation of archival tissue sections by multiplexed imaging mass spectroscopy (IMS) methodologies.

Published
2023
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35. SARS-CoV-2 infection drives an inflammatory response in human adipose tissue through infection of adipocytes and macrophages

Author

Martínez-Colón, Giovanny J., primary, Ratnasiri, Kalani, additional, Chen, Heping, additional, Jiang, Sizun, additional, Zanley, Elizabeth, additional, Rustagi, Arjun, additional, Verma, Renu, additional, Chen, Han, additional, Andrews, Jason R., additional, Mertz, Kirsten D., additional, Tzankov, Alexandar, additional, Azagury, Dan, additional, Boyd, Jack, additional, Nolan, Garry P., additional, Schürch, Christian M., additional, Matter, Matthias S., additional, Blish, Catherine A., additional, and McLaughlin, Tracey L., additional

Published
2022
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37. Spatial epitope barcoding reveals clonal tumor patch behaviors

Author

Rovira-Clavé, Xavier, primary, Drainas, Alexandros P., additional, Jiang, Sizun, additional, Bai, Yunhao, additional, Baron, Maya, additional, Zhu, Bokai, additional, Dallas, Alec E., additional, Lee, Myung Chang, additional, Chu, Theresa P., additional, Holzem, Alessandra, additional, Ayyagari, Ramya, additional, Bhattacharya, Debadrita, additional, McCaffrey, Erin F., additional, Greenwald, Noah F., additional, Markovic, Maxim, additional, Coles, Garry L., additional, Angelo, Michael, additional, Bassik, Michael C., additional, Sage, Julien, additional, and Nolan, Garry P., additional

Published
2022
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41. Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments

Author

Jiang, Sizun, primary, Chan, Chi Ngai, additional, Rovira-Clavé, Xavier, additional, Chen, Han, additional, Bai, Yunhao, additional, Zhu, Bokai, additional, McCaffrey, Erin, additional, Greenwald, Noah F., additional, Liu, Candace, additional, Barlow, Graham L., additional, Weirather, Jason L., additional, Oliveria, John Paul, additional, Nakayama, Tsuguhisa, additional, Lee, Ivan T., additional, Matter, Matthias S., additional, Carlisle, Anne E., additional, Philips, Darci, additional, Vazquez, Gustavo, additional, Mukherjee, Nilanjan, additional, Busman-Sahay, Kathleen, additional, Nekorchuk, Michael, additional, Terry, Margaret, additional, Younger, Skyler, additional, Bosse, Marc, additional, Demeter, Janos, additional, Rodig, Scott J., additional, Tzankov, Alexandar, additional, Goltsev, Yury, additional, McIlwain, David Robert, additional, Angelo, Michael, additional, Estes, Jacob D., additional, and Nolan, Garry P., additional

Published
2022
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43. Inflammatory molecular endotypes of nasal polyps derived from White and Japanese populations

Author

Nakayama, Tsuguhisa, primary, Lee, Ivan T., additional, Le, Wei, additional, Tsunemi, Yasuhiro, additional, Borchard, Nicole A., additional, Zarabanda, David, additional, Dholakia, Sachi S., additional, Gall, Philip A., additional, Yang, Angela, additional, Kim, Dayoung, additional, Akutsu, Makoto, additional, Kashiwagi, Takashi, additional, Patel, Zara M., additional, Hwang, Peter H., additional, Frank, Daniel N., additional, Haruna, Shin-ichi, additional, Ramakrishnan, Vijay R., additional, Nolan, Garry P., additional, Jiang, Sizun, additional, and Nayak, Jayakar V., additional

Published
2022
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44. Abstract PD6-03: Spatio-molecular dissection of the breast cancer metastatic microenvironment

Author

Abravanel, Daniel L, primary, Klughammer, Johanna, additional, Blosser, Timothy, additional, Goltsev, Yury, additional, Jiang, Sizun, additional, Bai, Yunjao, additional, Murray, Evan, additional, Alon, Shahar, additional, Cui, Yi, additional, Goodwin, Daniel R, additional, Sinha, Anubhav, additional, Cohen, Ofir, additional, Slyper, Michal, additional, Ashenberg, Orr, additional, Dionne, Danielle, additional, Jané-Valbuena, Judit, additional, Porter, Caroline BM, additional, Segerstolpe, Asa, additional, Waldman, Julia, additional, Vigneau, Sébastien, additional, Helvie, Karla, additional, Frangieh, Allison, additional, DelloStritto, Laura, additional, Patel, Miraj, additional, We, Jingyi, additional, Pfaff, Kathleen, additional, Cullen, Nicole, additional, Lako, Ana, additional, Turner, Madison, additional, Wakiro, Isaac, additional, Napolitano, Sara, additional, Kanodia, Abhay, additional, Ortiz, Rebecca, additional, MacKichan, Colin, additional, Inga, Stephanie, additional, Chen, Judy, additional, Thorner, Aaron R, additional, Rotem, Asaf, additional, Rodig, Scott, additional, Chen, Fei, additional, Boyden, Edward S, additional, Nolan, Garry P, additional, Zhuang, Xiaowei, additional, Rozenblatt-Rosen, Orit, additional, Johnson, Bruce E, additional, Regev, Aviv, additional, and Wagle, Nikhil, additional

Published
2022
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47. SARS-CoV-2 Replication in Airway Epithelia Requires Motile Cilia and Microvillar Reprogramming

Author

Wu, Chien-Ting, primary, Lidsky, Peter V., additional, Xiao, Yinghong, additional, Cheng, Ran, additional, Lee, Ivan T., additional, Nakayama, Tsuguhisa, additional, Jiang, Sizun, additional, He, Wei, additional, Demeter, Janos, additional, Knight, Miguel G., additional, Turn, Rachel E., additional, Rojas-Hernandez, Laura S., additional, Nolan, Garry, additional, Milla, Carlos, additional, Nayak, Jayakar V., additional, Andino, Raul, additional, and Jackson, Peter K., additional

Published
2022
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48. Rhesus Macaque CODEX Multiplexed Immunohistochemistry Panel for Studying Immune Responses During Ebola Infection

Author

Jiang, Sizun, primary, Mukherjee, Nilanjan, additional, Bennett, Richard S., additional, Chen, Han, additional, Logue, James, additional, Dighero-Kemp, Bonnie, additional, Kurtz, Jonathan R., additional, Adams, Ricky, additional, Phillips, Darci, additional, Schürch, Christian M., additional, Goltsev, Yury, additional, Hickey, John W., additional, McCaffrey, Erin F., additional, Delmastro, Alea, additional, Chu, Pauline, additional, Reader, J. Rachel, additional, Keesler, Rebekah I., additional, Galván, José A., additional, Zlobec, Inti, additional, Van Rompay, Koen K. A., additional, Liu, David X., additional, Hensley, Lisa E., additional, Nolan, Garry P., additional, and McIlwain, David R., additional

Published
2021
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49. Robust Single-cell Matching and Multi-modal Analysis Using Shared and Distinct Features Reveals Orchestrated Immune Responses

Author

Zhu, Bokai, primary, Chen, Shuxiao, additional, Bai, Yunhao, additional, Chen, Han, additional, Mukherjee, Nilanjan, additional, Vazquez, Gustavo, additional, McIlwain, David R, additional, Tzankov, Alexandar, additional, Lee, Ivan T, additional, Matter, Matthias S, additional, Golstev, Yury, additional, Ma, Zongming, additional, Nolan, Garry P, additional, and Jiang, Sizun, additional

Published
2021
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50. Human influenza virus challenge identifies cellular correlates of protection for oral vaccination

Author

McIlwain, David R., primary, Chen, Han, additional, Rahil, Zainab, additional, Bidoki, Neda Hajiakhoond, additional, Jiang, Sizun, additional, Bjornson, Zach, additional, Kolhatkar, Nikita S., additional, Martinez, C. Josefina, additional, Gaudillière, Brice, additional, Hedou, Julien, additional, Mukherjee, Nilanjan, additional, Schürch, Christian M., additional, Trejo, Angelica, additional, Affrime, Melton, additional, Bock, Bonnie, additional, Kim, Kenneth, additional, Liebowitz, David, additional, Aghaeepour, Nima, additional, Tucker, Sean N., additional, and Nolan, Garry P., additional

Published
2021
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