Search

Your search keyword '"Mozsary, Christopher"' showing total 36 results
Start Over Author "Mozsary, Christopher"
36 results on '"Mozsary, Christopher"'

1. The Space Omics and Medical Atlas (SOMA) and international astronaut biobank

Author

Overbey, Eliah G., Kim, JangKeun, Tierney, Braden T., Park, Jiwoon, Houerbi, Nadia, Lucaci, Alexander G., Garcia Medina, Sebastian, Damle, Namita, Najjar, Deena, Grigorev, Kirill, Afshin, Evan E., Ryon, Krista A., Sienkiewicz, Karolina, Patras, Laura, Klotz, Remi, Ortiz, Veronica, MacKay, Matthew, Schweickart, Annalise, Chin, Christopher R., Sierra, Maria A., Valenzuela, Matias F., Dantas, Ezequiel, Nelson, Theodore M., Cekanaviciute, Egle, Deards, Gabriel, Foox, Jonathan, Narayanan, S. Anand, Schmidt, Caleb M., Schmidt, Michael A., Schmidt, Julian C., Mullane, Sean, Tigchelaar, Seth Stravers, Levitte, Steven, Westover, Craig, Bhattacharya, Chandrima, Lucotti, Serena, Wain Hirschberg, Jeremy, Proszynski, Jacqueline, Burke, Marissa, Kleinman, Ashley S., Butler, Daniel J., Loy, Conor, Mzava, Omary, Lenz, Joan, Paul, Doru, Mozsary, Christopher, Sanders, Lauren M., Taylor, Lynn E., Patel, Chintan O., Khan, Sharib A., Suhail Mohamad, Mir, Byhaqui, Syed Gufran Ahmad, Aslam, Burhan, Gajadhar, Aaron S., Williamson, Lucy, Tandel, Purvi, Yang, Qiu, Chu, Jessica, Benz, Ryan W., Siddiqui, Asim, Hornburg, Daniel, Blease, Kelly, Moreno, Juan, Boddicker, Andrew, Zhao, Junhua, Lajoie, Bryan, Scott, Ryan T., Gilbert, Rachel R., Lai Polo, San-huei, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Ariyapala, Ishara, Beer, Joanne, Zhang, Bingqing, Hudson, Briana M., Rininger, Aric, Church, Sarah E., Beheshti, Afshin, Church, George M., Smith, Scott M., Crucian, Brian E., Zwart, Sara R., Matei, Irina, Lyden, David C., Garrett-Bakelman, Francine, Krumsiek, Jan, Chen, Qiuying, Miller, Dawson, Shuga, Joe, Williams, Stephen, Nemec, Corey, Trudel, Guy, Pelchat, Martin, Laneuville, Odette, De Vlaminck, Iwijn, Gross, Steven, Bolton, Kelly L., Bailey, Susan M., Granstein, Richard, Furman, David, Melnick, Ari M., Costes, Sylvain V., Shirah, Bader, Yu, Min, Menon, Anil S., Mateus, Jaime, Meydan, Cem, and Mason, Christopher E.

Published
2024
Full Text
View/download PDF

2. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Author

Schoelmerich, Marie C., Ly, Lynn, West-Roberts, Jacob, Shi, Ling-Dong, Shen, Cong, Malvankar, Nikhil S., Taib, Najwa, Gribaldo, Simonetta, Woodcroft, Ben J., Schadt, Christopher W., Al-Shayeb, Basem, Dai, Xiaoguang, Mozsary, Christopher, Hickey, Scott, He, Christine, Beaulaurier, John, Juul, Sissel, Sachdeva, Rohan, and Banfield, Jillian F.

Published
2024
Full Text
View/download PDF

3. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Author

Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J, Ivanov, Nikolay A, Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T, Schenck, Edward J, Westover, Craig D, Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L, Granados, Andrea C, Santos, Yale A, Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M, Langhorst, Bradley W, Tanner, Nathan A, Kim, Youngmi, Reeves, Jason W, Hether, Tyler D, Warren, Sarah E, Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B, Rosenfeld, Jeffrey A, Chen, Ying, Steel, Peter AD, Shemesh, Amos J, Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R, Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M, Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F, Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E, Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, and Mason, Christopher E

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Vaccine Related, Biodefense, Rare Diseases, Emerging Infectious Diseases, Clinical Research, Prevention, Lung, Pneumonia & Influenza, Aetiology, Development of treatments and therapeutic interventions, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Adult, Aged, Angiotensin Receptor Antagonists, Angiotensin-Converting Enzyme Inhibitors, Antiviral Agents, COVID-19, COVID-19 Nucleic Acid Testing, Drug Interactions, Female, Gene Expression Profiling, Genome, Viral, HLA Antigens, Host Microbial Interactions, Humans, Male, Middle Aged, Molecular Diagnostic Techniques, New York City, Nucleic Acid Amplification Techniques, Pandemics, RNA-Seq, SARS-CoV-2, COVID-19 Drug Treatment
Abstract

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Published
2021

4. System-wide transcriptome damage and tissue identity loss in COVID-19 patients

Author

Park, Jiwoon, Foox, Jonathan, Hether, Tyler, Danko, David C., Warren, Sarah, Kim, Youngmi, Reeves, Jason, Butler, Daniel J., Mozsary, Christopher, Rosiene, Joel, Shaiber, Alon, Afshin, Evan E., MacKay, Matthew, Rendeiro, André F., Bram, Yaron, Chandar, Vasuretha, Geiger, Heather, Craney, Arryn, Velu, Priya, Melnick, Ari M., Hajirasouliha, Iman, Beheshti, Afshin, Taylor, Deanne, Saravia-Butler, Amanda, Singh, Urminder, Wurtele, Eve Syrkin, Schisler, Jonathan, Fennessey, Samantha, Corvelo, André, Zody, Michael C., Germer, Soren, Salvatore, Steven, Levy, Shawn, Wu, Shixiu, Tatonetti, Nicholas P., Shapira, Sagi, Salvatore, Mirella, Westblade, Lars F., Cushing, Melissa, Rennert, Hanna, Kriegel, Alison J., Elemento, Olivier, Imielinski, Marcin, Rice, Charles M., Borczuk, Alain C., Meydan, Cem, Schwartz, Robert E., and Mason, Christopher E.

Published
2022
Full Text
View/download PDF

5. LETHAL COVID-19 ASSOCIATES WITH RAAS-INDUCED INFLAMMATION FOR MULTIPLE ORGAN DAMAGE INCLUDING MEDIASTINAL LYMPH NODES

Author

Guarnieri, Joseph W, primary, Topper, Michael, additional, Beigel, Katherine, additional, Haltoom, Jeff A, additional, Chadburn, Amy, additional, Frere, Justin, additional, An, Julia, additional, Cope, Henry, additional, Borczuk, Alain, additional, Sinha, Saloni, additional, Lim, Christine, additional, Kim, JangKeun, additional, Park, Jiwoon, additional, Meydan, Cem, additional, Foox, Jonathan, additional, Mozsary, Christopher, additional, Bram, Yaron, additional, Richard, Stephanie, additional, Epsi, Nusrat, additional, Agan, Brian, additional, Chenoweth, Josh, additional, Simons, Mark, additional, Tribble, David, additional, Burgess, Timothy, additional, Dalgard, Clifton L., additional, Heise, Mark T., additional, Moorman, Nathaniel, additional, Baxter, Victoria, additional, Madden, Emily A., additional, Taft-Benz, Sharon, additional, Anderson, Elizabeth, additional, Sanders, Wes A., additional, Dickmander, Rebekah J., additional, Widjaja, Gabrielle A., additional, Janssen, Kevin, additional, Lie, Timothy, additional, Murdock, Deborah G, additional, Angelin, Alessia, additional, Albrecht, Yentli E. S., additional, Olali, Arnold, additional, Dybas, Joseph M., additional, Priebe, Waldemar, additional, Emmett, Mark R., additional, Best, Sonja, additional, Johnson, Maya Kelsey, additional, Trovao, Nidia S., additional, Clark, Kevin B., additional, Zaksiene, Viktoria, additional, Miller, Rob, additional, Grabhamr, Peter, additional, Schisler, Jonathan C, additional, Moraes-vieira, Pedro, additional, Pollett, Simon, additional, Mason, Christopher E., additional, Wurtele, Eve Syrkin, additional, Taylor, Deanne, additional, Schwartz, Robert E., additional, Beheshti, Afshin, additional, Wallace, Douglas C., additional, and Baylin, Stephen B., additional

Published
2023
Full Text
View/download PDF

6. Author Correction: The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, Łabaj, Paweł P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, de Caceres, Inmaculada Ibanez, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Published
2021
Full Text
View/download PDF

7. The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, Łabaj, Paweł P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, Ibanez de Caceres, Inmaculada, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Published
2021
Full Text
View/download PDF

8. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts

Author

Guarnieri, Joseph W., primary, Dybas, Joseph M., additional, Fazelinia, Hossein, additional, Kim, Man S., additional, Frere, Justin, additional, Zhang, Yuanchao, additional, Soto Albrecht, Yentli, additional, Murdock, Deborah G., additional, Angelin, Alessia, additional, Singh, Larry N., additional, Weiss, Scott L., additional, Best, Sonja M., additional, Lott, Marie T., additional, Zhang, Shiping, additional, Cope, Henry, additional, Zaksas, Victoria, additional, Saravia-Butler, Amanda, additional, Meydan, Cem, additional, Foox, Jonathan, additional, Mozsary, Christopher, additional, Bram, Yaron, additional, Kidane, Yared, additional, Priebe, Waldemar, additional, Emmett, Mark R., additional, Meller, Robert, additional, Demharter, Sam, additional, Stentoft-Hansen, Valdemar, additional, Salvatore, Marco, additional, Galeano, Diego, additional, Enguita, Francisco J., additional, Grabham, Peter, additional, Trovao, Nidia S., additional, Singh, Urminder, additional, Haltom, Jeffrey, additional, Heise, Mark T., additional, Moorman, Nathaniel J., additional, Baxter, Victoria K., additional, Madden, Emily A., additional, Taft-Benz, Sharon A., additional, Anderson, Elizabeth J., additional, Sanders, Wes A., additional, Dickmander, Rebekah J., additional, Baylin, Stephen B., additional, Wurtele, Eve Syrkin, additional, Moraes-Vieira, Pedro M., additional, Taylor, Deanne, additional, Mason, Christopher E., additional, Schisler, Jonathan C., additional, Schwartz, Robert E., additional, Beheshti, Afshin, additional, and Wallace, Douglas C., additional

Published
2023
Full Text
View/download PDF

9. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Author

Schoelmerich, Marie C, primary, Ly, Lynn, additional, West-Roberts, Jacob, additional, Shi, Ling-Dong, additional, Shen, Cong, additional, Malvankar, Nikhil, additional, Taib, Najwa, additional, Gribaldo, Simonetta, additional, Woodcroft, Ben J, additional, Al-Shayeb, Basem, additional, Dai, Xiaoguang, additional, Mozsary, Christopher, additional, Hickey, Scott, additional, He, Christine, additional, Beaulaurier, John A, additional, Juul, Sissel, additional, Sachdeva, Rohan, additional, and Banfield, Jill, additional

Published
2023
Full Text
View/download PDF

10. Geospatially-resolved public-health surveillance via wastewater sequencing

Author

Tierney, Braden T, Foox, Jonathan, Ryon, Krista A, Butler, Daniel, Damle, Namita, Young, Benjamin G, Mozsary, Christopher, Babler, Kristina M., Yin, Xue, Carattini, Yamina, Andrews, David, Solle, Natasha Schaefer, Kumar, Naresh, Shukla, Bhavarth, Vidovic, Dusica, Currall, Benjamin, Williams, Sion L., Schürer, Stephan C., Stevenson, Mario, Amirali, Ayaaz, Beaver, Cynthia C., Kobetz, Erin, Boone, Melinda M., Reding, Brian, Laine, Jennifer, Comerford, Samuel, Lamar, Walter E., Tallon, John J., Hirschberg, Jeremy Wain, Proszynski, Jacqueline, Sharkey, Mark E., Church, George M, Grills, George S, Solo-Gabriele, Helena M., and Mason, Christopher E

Subjects
Article
Abstract

Wastewater, which contains everything from pathogens to pollutants, is a geospatially-and temporally-linked microbial fingerprint of a given population. As a result, it can be leveraged for monitoring multiple dimensions of public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (n=1,419 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County from 2020-2022. First, we used targeted amplicon sequencing (n=966) to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with clinical caseloads from University students (N = 1,503) and Miami-Dade County hospital patients (N = 3,939 patients), as well as an 8-day earlier detection of the Delta variant in wastewater vs. in patients. Additionally, in 453 metatranscriptomic samples, we demonstrate that different wastewater sampling locations have clinically and public-health-relevant microbiota that vary as a function of the size of the human population they represent. Through assembly, alignment-based, and phylogenetic approaches, we also detect multiple clinically important viruses (e.g., norovirus ) and describe geospatial and temporal variation in microbial functional genes that indicate the presence of pollutants. Moreover, we found distinct profiles of antimicrobial resistance (AMR) genes and virulence factors across campus buildings, dorms, and hospitals, with hospital wastewater containing a significant increase in AMR abundance. Overall, this effort lays the groundwork for systematic characterization of wastewater to improve public health decision making and a broad platform to detect emerging pathogens.

Published
2023

11. Betacoronavirus-specific alternate splicing

Author

Karlebach, Guy, primary, Aronow, Bruce, additional, Baylin, Stephen B., additional, Butler, Daniel, additional, Foox, Jonathan, additional, Levy, Shawn, additional, Meydan, Cem, additional, Mozsary, Christopher, additional, Saravia-Butler, Amanda M., additional, Taylor, Deanne M., additional, Wurtele, Eve, additional, Mason, Christopher E., additional, Beheshti, Afshin, additional, and Robinson, Peter N., additional

Published
2022
Full Text
View/download PDF

12. Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection

Author

Guarnieri, Joseph W., primary, Dybas, Joseph M., additional, Fazelinia, Hossein, additional, Kim, Man S., additional, Frere, Justin, additional, Zhang, Yuanchao, additional, Albrecht, Yentli Soto, additional, Murdock, Deborah G., additional, Angelin, Alessia, additional, Singh, Larry N., additional, Weiss, Scott L., additional, Best, Sonja M., additional, Lott, Marie T., additional, Cope, Henry, additional, Zaksas, Viktorija, additional, Saravia-Butler, Amanda, additional, Meydan, Cem, additional, Foox, Jonathan, additional, Mozsary, Christopher, additional, Kidane, Yared H., additional, Priebe, Waldemar, additional, Emmett, Mark R., additional, Meller, Robert, additional, Singh, Urminder, additional, Bram, Yaron, additional, tenOever, Benjamin R., additional, Heise, Mark T., additional, Moorman, Nathaniel J., additional, Madden, Emily A., additional, Taft-Benz, Sharon A., additional, Anderson, Elizabeth J., additional, Sanders, Wes A., additional, Dickmander, Rebekah J., additional, Baxter, Victoria K., additional, Baylin, Stephen B., additional, Wurtele, Eve Syrkin, additional, Moraes-Vieira, Pedro M., additional, Taylor, Deanne, additional, Mason, Christopher E., additional, Schisler, Jonathan C., additional, Schwartz, Robert E., additional, Beheshti, Afshin, additional, and Wallace, Douglas C., additional

Published
2022
Full Text
View/download PDF

13. Role of miR-2392 in driving SARS-CoV-2 infection

Author

McDonald, J. Tyson, primary, Enguita, Francisco J., additional, Taylor, Deanne, additional, Griffin, Robert J., additional, Priebe, Waldemar, additional, Emmett, Mark R., additional, Sajadi, Mohammad M., additional, Harris, Anthony D., additional, Clement, Jean, additional, Dybas, Joseph M., additional, Aykin-Burns, Nukhet, additional, Guarnieri, Joseph W., additional, Singh, Larry N., additional, Grabham, Peter, additional, Baylin, Stephen B., additional, Yousey, Aliza, additional, Pearson, Andrea N., additional, Corry, Peter M., additional, Saravia-Butler, Amanda, additional, Aunins, Thomas R., additional, Sharma, Sadhana, additional, Nagpal, Prashant, additional, Meydan, Cem, additional, Foox, Jonathan, additional, Mozsary, Christopher, additional, Cerqueira, Bianca, additional, Zaksas, Viktorija, additional, Singh, Urminder, additional, Wurtele, Eve Syrkin, additional, Costes, Sylvain V., additional, Davanzo, Gustavo Gastão, additional, Galeano, Diego, additional, Paccanaro, Alberto, additional, Meinig, Suzanne L., additional, Hagan, Robert S., additional, Bowman, Natalie M., additional, Wolfgang, Matthew C., additional, Altinok, Selin, additional, Sapoval, Nicolae, additional, Treangen, Todd J., additional, Moraes-Vieira, Pedro M., additional, Vanderburg, Charles, additional, Wallace, Douglas C., additional, Schisler, Jonathan C., additional, Mason, Christopher E., additional, Chatterjee, Anushree, additional, Meller, Robert, additional, Beheshti, Afshin, additional, Wallet, Shannon M., additional, Maile, Robert, additional, Mock, Jason R., additional, Torres-Castillo, Jose L., additional, Love, Miriya K., additional, Lovell, Will, additional, Rice, Colleen, additional, Mitchem, Olivia, additional, Burgess, Dominique, additional, Suggs, Jessica, additional, and Jacobs, Jordan, additional

Published
2021
Full Text
View/download PDF

14. A Rapid, Isothermal, and Point-of-Care System for COVID-19 Diagnostics

Author

Mozsary, Christopher, primary, McCloskey, Duncan, additional, Babler, Kristina M., additional, Boza, Juan, additional, Butler, Daniel, additional, Currall, Benjamin, additional, Williams, Sion, additional, Wiley, Anne, additional, Afshin, Evan E., additional, Grills, George S., additional, Sharkey, Mark E., additional, Premsrirut, Prem, additional, Solo-Gabriele, Helena, additional, Cardentey, Yoslayma, additional, Erickson, David, additional, and Mason, Christopher E., additional

Published
2021
Full Text
View/download PDF

15. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

Author

Moore, Keith J. M., primary, Cahill, Jeremy, additional, Aidelberg, Guy, additional, Aronoff, Rachel, additional, Bektaş, Ali, additional, Bezdan, Daniela, additional, Butler, Daniel J., additional, Chittur, Sridar V., additional, Codyre, Martin, additional, Federici, Fernan, additional, Tanner, Nathan A., additional, Tighe, Scott W., additional, True, Randy, additional, Ware, Sarah B., additional, Wyllie, Anne L., additional, Afshin, Evan E., additional, Bendesky, Andres, additional, Chang, Connie B., additional, Dela Rosa, Richard, additional, Elhaik, Eran, additional, Erickson, David, additional, Goldsborough, Andrew S., additional, Grills, George, additional, Hadasch, Kathrin, additional, Hayden, Andrew, additional, Her, Seong-Young, additional, Karl, Julie A., additional, Kim, Chang Hee, additional, Kriegel, Alison J., additional, Kunstman, Thomas, additional, Landau, Zeph, additional, Land, Kevin, additional, Langhorst, Bradley W., additional, Lindner, Ariel B., additional, Mayer, Benjamin E., additional, McLaughlin, Lee A., additional, McLaughlin, Matthew T., additional, Molloy, Jenny, additional, Mozsary, Christopher, additional, Nadler, Jerry L., additional, D'Silva, Melinee, additional, Ng, David, additional, O'Connor, David H., additional, Ongerth, Jerry E., additional, Osuolale, Olayinka, additional, Pinharanda, Ana, additional, Plenker, Dennis, additional, Ranjan, Ravi, additional, Rosbash, Michael, additional, Rotem, Assaf, additional, Segarra, Jacob, additional, Schürer, Stephan, additional, Sherrill-Mix, Scott, additional, Solo-Gabriele, Helena, additional, To, Shaina, additional, Vogt, Merly C., additional, Yu, Albert D., additional, and Mason, Christopher E., additional

Published
2021
Full Text
View/download PDF

16. Betacoronavirus-specific alternate splicing

Author

Karlebach, Guy, primary, Aronow, Bruce, additional, Baylin, Stephen B., additional, Butler, Daniel, additional, Foox, Jonathan, additional, Levy, Shawn, additional, Meydan, Cem, additional, Mozsary, Christopher, additional, Saravia-Butler, Amanda M, additional, Taylor, Deanne M, additional, Wurtele, Eve, additional, Mason, Christopher E, additional, Beheshti, Afshin, additional, and Robinson, Peter N, additional

Published
2021
Full Text
View/download PDF

17. The SEQC2 epigenomics quality control (EpiQC) study : comprehensive characterization of epigenetic methods, reproducibility, and quantification

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszyńska, Agata, Łabaj, Paweł, Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, Ibanez de Caceres, Inmaculada, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Abstract

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.

Published
2021

18. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Danko, David, primary, Bezdan, Daniela, additional, Afshin, Evan E., additional, Ahsanuddin, Sofia, additional, Bhattacharya, Chandrima, additional, Butler, Daniel J., additional, Chng, Kern Rei, additional, Donnellan, Daisy, additional, Hecht, Jochen, additional, Jackson, Katelyn, additional, Kuchin, Katerina, additional, Karasikov, Mikhail, additional, Lyons, Abigail, additional, Mak, Lauren, additional, Meleshko, Dmitry, additional, Mustafa, Harun, additional, Mutai, Beth, additional, Neches, Russell Y., additional, Ng, Amanda, additional, Nikolayeva, Olga, additional, Nikolayeva, Tatyana, additional, Png, Eileen, additional, Ryon, Krista A., additional, Sanchez, Jorge L., additional, Shaaban, Heba, additional, Sierra, Maria A., additional, Thomas, Dominique, additional, Young, Ben, additional, Abudayyeh, Omar O., additional, Alicea, Josue, additional, Bhattacharyya, Malay, additional, Blekhman, Ran, additional, Castro-Nallar, Eduardo, additional, Cañas, Ana M., additional, Chatziefthimiou, Aspassia D., additional, Crawford, Robert W., additional, De Filippis, Francesca, additional, Deng, Youping, additional, Desnues, Christelle, additional, Dias-Neto, Emmanuel, additional, Dybwad, Marius, additional, Elhaik, Eran, additional, Ercolini, Danilo, additional, Frolova, Alina, additional, Gankin, Dennis, additional, Gootenberg, Jonathan S., additional, Graf, Alexandra B., additional, Green, David C., additional, Hajirasouliha, Iman, additional, Hastings, Jaden J.A., additional, Hernandez, Mark, additional, Iraola, Gregorio, additional, Jang, Soojin, additional, Kahles, Andre, additional, Kelly, Frank J., additional, Knights, Kaymisha, additional, Kyrpides, Nikos C., additional, Łabaj, Paweł P., additional, Lee, Patrick K.H., additional, Leung, Marcus H.Y., additional, Ljungdahl, Per O., additional, Mason-Buck, Gabriella, additional, McGrath, Ken, additional, Meydan, Cem, additional, Mongodin, Emmanuel F., additional, Moraes, Milton Ozorio, additional, Nagarajan, Niranjan, additional, Nieto-Caballero, Marina, additional, Noushmehr, Houtan, additional, Oliveira, Manuela, additional, Ossowski, Stephan, additional, Osuolale, Olayinka O., additional, Özcan, Orhan, additional, Paez-Espino, David, additional, Rascovan, Nicolás, additional, Richard, Hugues, additional, Rätsch, Gunnar, additional, Schriml, Lynn M., additional, Semmler, Torsten, additional, Sezerman, Osman U., additional, Shi, Leming, additional, Shi, Tieliu, additional, Siam, Rania, additional, Song, Le Huu, additional, Suzuki, Haruo, additional, Court, Denise Syndercombe, additional, Tighe, Scott W., additional, Tong, Xinzhao, additional, Udekwu, Klas I., additional, Ugalde, Juan A., additional, Valentine, Brandon, additional, Vassilev, Dimitar I., additional, Vayndorf, Elena M., additional, Velavan, Thirumalaisamy P., additional, Wu, Jun, additional, Zambrano, María M., additional, Zhu, Jifeng, additional, Zhu, Sibo, additional, Mason, Christopher E., additional, Abdullah, Natasha, additional, Abraao, Marcos, additional, Adel, Ait-hamlat, additional, Afaq, Muhammad, additional, Al-Quaddoomi, Faisal S., additional, Alam, Ireen, additional, Albuquerque, Gabriela E., additional, Alexiev, Alex, additional, Ali, Kalyn, additional, Alvarado-Arnez, Lucia E., additional, Aly, Sarh, additional, Amachee, Jennifer, additional, Amorim, Maria G., additional, Ampadu, Majelia, additional, Amran, Muhammad Al-Fath, additional, An, Nala, additional, Andrew, Watson, additional, Andrianjakarivony, Harilanto, additional, Angelov, Michael, additional, Antelo, Verónica, additional, Aquino, Catharine, additional, Aranguren, Álvaro, additional, Araujo, Luiza F., additional, Vasquez Arevalo, Hitler Francois, additional, Arevalo, Jenny, additional, Arnan, Carme, additional, Alvarado Arnez, Lucia Elena, additional, Arredondo, Fernanda, additional, Arthur, Matthew, additional, Asenjo, Freddy, additional, Aung, Thomas Saw, additional, Auvinet, Juliette, additional, Aventin, Nuria, additional, Ayaz, Sadaf, additional, Baburyan, Silva, additional, Bakere, Abd-Manaaf, additional, Bakhl, Katrin, additional, Bartelli, Thais F., additional, Batdelger, Erdenetsetseg, additional, Baudon, François, additional, Becher, Kevin, additional, Bello, Carla, additional, Benchouaia, Médine, additional, Benisty, Hannah, additional, Benoiston, Anne-Sophie, additional, Benson, Joseph, additional, Benítez, Diego, additional, Bernardes, Juliana, additional, Bertrand, Denis, additional, Beurmann, Silvia, additional, Bitard-Feildel, Tristan, additional, Bittner, Lucie, additional, Black, Christina, additional, Blanc, Guillaume, additional, Blyther, Brittany, additional, Bode, Toni, additional, Boeri, Julia, additional, Boldgiv, Bazartseren, additional, Bolzli, Kevin, additional, Bordigoni, Alexia, additional, Borrelli, Ciro, additional, Bouchard, Sonia, additional, Bouly, Jean-Pierre, additional, Boyd, Alicia, additional, Branco, Gabriela P., additional, Breschi, Alessandra, additional, Brindefalk, Björn, additional, Brion, Christian, additional, Briones, Alan, additional, Buczansla, Paulina, additional, Burke, Catherine M., additional, Burrell, Aszia, additional, Butova, Alina, additional, Buttar, Irvind, additional, Bynoe, Jalia, additional, Bönigk, Sven, additional, Bøifot, Kari O., additional, Caballero, Hiram, additional, Cai, Xiao Wen, additional, Calderon, Dayana, additional, Cantillo, Angela, additional, Carbajo, Miguel, additional, Carbone, Alessandra, additional, Cardenas, Anais, additional, Carrillo, Katerine, additional, Casalot, Laurie, additional, Castro, Sofia, additional, Castro, Ana V., additional, Castro, Astred, additional, Castro, Ana Valeria B., additional, Cawthorne, Simone, additional, Cedillo, Jonathan, additional, Chaker, Salama, additional, Chalangal, Jasna, additional, Chan, Allison, additional, Chasapi, Anastasia I., additional, Chatziefthimiou, Starr, additional, Chaudhuri, Sreya Ray, additional, Chavan, Akash Keluth, additional, Chavez, Francisco, additional, Chem, Gregory, additional, Chen, Xiaoqing, additional, Chen, Michelle, additional, Chen, Jenn-Wei, additional, Chernomoretz, Ariel, additional, Chettouh, Allaeddine, additional, Cheung, Daisy, additional, Chicas, Diana, additional, Chiu, Shirley, additional, Choudhry, Hira, additional, Chrispin, Carl, additional, Ciaramella, Kianna, additional, Cifuentes, Erika, additional, Cohen, Jake, additional, Coil, David A., additional, Collin, Sylvie, additional, Conger, Colleen, additional, Conte, Romain, additional, Corsi, Flavia, additional, Cossio, Cecilia N., additional, Costa, Ana F., additional, Cuebas, Delisia, additional, D’Alessandro, Bruno, additional, Dahlhausen, Katherine E., additional, Darling, Aaron E., additional, Das, Pujita, additional, Davenport, Lucinda B., additional, David, Laurent, additional, Davidson, Natalie R., additional, Dayama, Gargi, additional, Delmas, Stéphane, additional, Deng, Chris K., additional, Dequeker, Chloé, additional, Desert, Alexandre, additional, Devi, Monika, additional, Dezem, Felipe S., additional, Dias, Clara N., additional, Donahoe, Timothy Ryan, additional, Dorado, Sonia, additional, Dorsey, LaShonda, additional, Dotsenko, Valeriia, additional, Du, Steven, additional, Dutan, Alexandra, additional, Eady, Naya, additional, Eisen, Jonathan A., additional, Elaskandrany, Miar, additional, Epping, Lennard, additional, Escalera-Antezana, Juan P., additional, Ettinger, Cassie L., additional, Faiz, Iqra, additional, Fan, Luice, additional, Farhat, Nadine, additional, Faure, Emile, additional, Fauzi, Fazlina, additional, Feigin, Charlie, additional, Felice, Skye, additional, Ferreira, Laís Pereira, additional, Figueroa, Gabriel, additional, Fleiss, Aubin, additional, Flores, Denisse, additional, Velasco Flores, Jhovana L., additional, Fonseca, Marcos A.S., additional, Foox, Jonathan, additional, Forero, Juan Carlos, additional, Francis, Aaishah, additional, French, Kelly, additional, Fresia, Pablo, additional, Friedman, Jacob, additional, Fuentes, Jaime J., additional, Galipon, Josephine, additional, Garcia, Mathilde, additional, Garcia, Laura, additional, García, Catalina, additional, Geiger, Annie, additional, Gerner, Samuel M., additional, Ghose, Sonia L., additional, Giang, Dao Phuong, additional, Giménez, Matías, additional, Giovannelli, Donato, additional, Githae, Dedan, additional, Gkotzis, Spyridon, additional, Godoy, Liliana, additional, Goldman, Samantha, additional, Gonnet, Gaston H., additional, Gonzalez, Juana, additional, Gonzalez, Andrea, additional, Gonzalez-Poblete, Camila, additional, Gray, Andrew, additional, Gregory, Tranette, additional, Greselle, Charlotte, additional, Guasco, Sophie, additional, Guerra, Juan, additional, Gurianova, Nika, additional, Haehr, Wolfgang, additional, Halary, Sebastien, additional, Hartkopf, Felix, additional, Hawkins-Zafarnia, Arya, additional, Hazrin-Chong, Nur Hazlin, additional, Helfrich, Eric, additional, Hell, Eva, additional, Henry, Tamera, additional, Hernandez, Samuel, additional, Hernandez, Pilar Lopez, additional, Hess-Homeier, David, additional, Hittle, Lauren E., additional, Hoan, Nghiem Xuan, additional, Holik, Aliaksei, additional, Homma, Chiaki, additional, Hoxie, Irene, additional, Huber, Michael, additional, Humphries, Elizabeth, additional, Hyland, Stephanie, additional, Hässig, Andrea, additional, Häusler, Roland, additional, Hüsser, Nathalie, additional, Petit, Robert A., additional, Iderzorig, Badamnyambuu, additional, Igarashi, Mizuki, additional, Iqbal, Shaikh B., additional, Ishikawa, Shino, additional, Ishizuka, Sakura, additional, Islam, Sharah, additional, Islam, Riham, additional, Ito, Kohei, additional, Ito, Sota, additional, Ito, Takayuki, additional, Ivankovic, Tomislav, additional, Iwashiro, Tomoki, additional, Jackson, Sarah, additional, Jacobs, JoAnn, additional, James, Marisano, additional, Jaubert, Marianne, additional, Jerier, Marie-Laure, additional, Jiminez, Esmeralda, additional, Jinfessa, Ayantu, additional, De Jong, Ymke, additional, Joo, Hyun Woo, additional, Jospin, Guilllaume, additional, Kajita, Takema, additional, Ahmad Kassim, Affifah Saadah, additional, Kato, Nao, additional, Kaur, Amrit, additional, Kaur, Inderjit, additional, de Souza Gomes Kehdy, Fernanda, additional, Khadka, Vedbar S., additional, Khan, Shaira, additional, Khavari, Mahshid, additional, Ki, Michelle, additional, Kim, Gina, additional, Kim, Hyung Jun, additional, Kim, Sangwan, additional, King, Ryan J., additional, KoLoMonaco, Giuseppe, additional, Koag, Ellen, additional, Kobko-Litskevitch, Nadezhda, additional, Korshevniuk, Maryna, additional, Kozhar, Michael, additional, Krebs, Jonas, additional, Kubota, Nanami, additional, Kuklin, Andrii, additional, Kumar, Sheelta S., additional, Kwong, Rachel, additional, Kwong, Lawrence, additional, Lafontaine, Ingrid, additional, Lago, Juliana, additional, Lai, Tsoi Ying, additional, Laine, Elodie, additional, Laiola, Manolo, additional, Lakhneko, Olha, additional, Lamba, Isha, additional, de Lamotte, Gerardo, additional, Lannes, Romain, additional, De Lazzari, Eleonora, additional, Leahy, Madeline, additional, Lee, Hyunjung, additional, Lee, Yunmi, additional, Lee, Lucy, additional, Lemaire, Vincent, additional, Leong, Emily, additional, Lewandowska, Dagmara, additional, Li, Chenhao, additional, Liang, Weijun, additional, Lin, Moses, additional, Lisboa, Priscilla, additional, Litskevitch, Anna, additional, Liu, Eric Minwei, additional, Liu, Tracy, additional, Livia, Mayra Arauco, additional, Lo, Yui Him, additional, Losim, Sonia, additional, Loubens, Manon, additional, Lu, Jennifer, additional, Lykhenko, Olexandr, additional, Lysakova, Simona, additional, Mahmoud, Salah, additional, Majid, Sara Abdul, additional, Makogon, Natalka, additional, Maldonado, Denisse, additional, Mallari, Krizzy, additional, Malta, Tathiane M., additional, Mamun, Maliha, additional, Manoir, Dimitri, additional, Marchandon, German, additional, Marciniak, Natalia, additional, Marinovic, Sonia, additional, Marques, Brunna, additional, Mathews, Nicole, additional, Matsuzaki, Yuri, additional, Matthys, Vincent, additional, May, Madelyn, additional, McComb, Elias, additional, Meagher, Annabelle, additional, Melamed, Adiell, additional, Menary, Wayne, additional, Mendez, Katterinne N., additional, Mendez, Ambar, additional, Mendy, Irène Mauricette, additional, Meng, Irene, additional, Menon, Ajay, additional, Menor, Mark, additional, Meoded, Roy, additional, Merino, Nancy, additional, Miah, Karishma, additional, Mignotte, Mathilde, additional, Miketic, Tanja, additional, Miranda, Wilson, additional, Mitsios, Athena, additional, Miura, Ryusei, additional, Miyake, Kunihiko, additional, Moccia, Maria D., additional, Mohan, Natasha, additional, Mohsin, Mohammed, additional, Moitra, Karobi, additional, Moldes, Mauricio, additional, Molina, Laura, additional, Molinet, Jennifer, additional, Molomjamts, Orgil-Erdene, additional, Moniruzzaman, Eftar, additional, Moon, Sookwon, additional, de Oliveira Moraes, Isabelle, additional, Moreno, Mario, additional, Mosella, Maritza S., additional, Moser, Josef W., additional, Mozsary, Christopher, additional, Muehlbauer, Amanda L., additional, Muner, Oasima, additional, Munia, Muntaha, additional, Munim, Naimah, additional, Muscat, Maureen, additional, Mustac, Tatjana, additional, Muñoz, Cristina, additional, Nadalin, Francesca, additional, Naeem, Areeg, additional, Nagy-Szakal, Dorottya, additional, Nakagawa, Mayuko, additional, Narce, Ashanti, additional, Nasu, Masaki, additional, Navarrete, Irene González, additional, Naveed, Hiba, additional, Nazario, Bryan, additional, Nedunuri, Narasimha Rao, additional, Neff, Thomas, additional, Nesimi, Aida, additional, Ng, Wan Chiew, additional, Ng, Synti, additional, Nguyen, Gloria, additional, Ngwa, Elsy, additional, Nicolas, Agier, additional, Nicolas, Pierre, additional, Nika, Abdollahi, additional, Noorzi, Hosna, additional, Nosrati, Avigdor, additional, Nunes, Diana N., additional, O’Brien, Kathryn, additional, O’Hara, Niamh B., additional, Oken, Gabriella, additional, Olawoyin, Rantimi A., additional, Oliete, Javier Quilez, additional, Olmeda, Kiara, additional, Oluwadare, Tolulope, additional, Oluwadare, Itunu A., additional, Ordioni, Nils, additional, Orpilla, Jenessa, additional, Orrego, Jacqueline, additional, Ortega, Melissa, additional, Osma, Princess, additional, Osuolale, Israel O., additional, Osuolale, Oluwatosin M., additional, Ota, Mitsuki, additional, Oteri, Francesco, additional, Oto, Yuya, additional, Ounit, Rachid, additional, Ouzounis, Christos A., additional, Pakrashi, Subhamitra, additional, Paras, Rachel, additional, Pardo-Este, Coral, additional, Park, Young-Ja, additional, Pastuszek, Paulina, additional, Patel, Suraj, additional, Pathmanathan, Jananan, additional, Patrignani, Andrea, additional, Perez, Manuel, additional, Peros, Ante, additional, Persaud, Sabrina, additional, Peters, Anisia, additional, Phillips, Adam, additional, Pineda, Lisbeth, additional, Pizzi, Melissa P., additional, Plaku, Alma, additional, Plaku, Alketa, additional, Pompa-Hogan, Brianna, additional, Portilla, María Gabriela, additional, Posada, Leonardo, additional, Priestman, Max, additional, Prithiviraj, Bharath, additional, Priya, Sambhawa, additional, Pugdeethosal, Phanthira, additional, Pugh, Catherine E., additional, Pulatov, Benjamin, additional, Pupiec, Angelika, additional, Pyrshev, Kyrylo, additional, Qing, Tao, additional, Rahiel, Saher, additional, Rahmatulloev, Savlatjon, additional, Rajendran, Kannan, additional, Ramcharan, Aneisa, additional, Ramirez-Rojas, Adan, additional, Rana, Shahryar, additional, Ratnanandan, Prashanthi, additional, Read, Timothy D., additional, Rehrauer, Hubert, additional, Richer, Renee, additional, Rivera, Alexis, additional, Rivera, Michelle, additional, Robertiello, Alessandro, additional, Robinson, Courtney, additional, Rodríguez, Paula, additional, Rojas, Nayra Aguilar, additional, Roldán, Paul, additional, Rosario, Anyelic, additional, Roth, Sandra, additional, Ruiz, Maria, additional, Boja Ruiz, Stephen Eduard, additional, Russell, Kaitlan, additional, Rybak, Mariia, additional, Sabedot, Thais S., additional, Sabina, Mahfuza, additional, Saito, Ikuto, additional, Saito, Yoshitaka, additional, Malca Salas, Gustavo Adolfo, additional, Salazar, Cecilia, additional, San, Kaung Myat, additional, Sanchez, Jorge, additional, Sanchir, Khaliun, additional, Sankar, Ryan, additional, de Souza Santos, Paulo Thiago, additional, Saravi, Zulena, additional, Sasaki, Kai, additional, Sato, Yuma, additional, Sato, Masaki, additional, Sato, Seisuke, additional, Sato, Ryo, additional, Sato, Kaisei, additional, Sayara, Nowshin, additional, Schaaf, Steffen, additional, Schacher, Oli, additional, Schinke, Anna-Lena M., additional, Schlapbach, Ralph, additional, Schori, Christian, additional, Schriml, Jason R., additional, Segato, Felipe, additional, Sepulveda, Felipe, additional, Serpa, Marianna S., additional, De Sessions, Paola F., additional, Severyn, Juan C., additional, Shakil, Maheen, additional, Shalaby, Sarah, additional, Shari, Aliyah, additional, Shim, Hyenah, additional, Shirahata, Hikaru, additional, Shiwa, Yuh, additional, Da Silva, Ophélie, additional, Silva, Jordana M., additional, Simon, Gwenola, additional, Singh, Shaleni K., additional, Sluzek, Kasia, additional, Smith, Rebecca, additional, So, Eunice, additional, Andreu Somavilla, Núria, additional, Sonohara, Yuya, additional, Rufino de Sousa, Nuno, additional, Souza, Camila, additional, Sperry, Jason, additional, Sprinsky, Nicolas, additional, Stark, Stefan G., additional, La Storia, Antonietta, additional, Suganuma, Kiyoshi, additional, Suliman, Hamood, additional, Sullivan, Jill, additional, Supie, Arif Asyraf Md, additional, Suzuki, Chisato, additional, Takagi, Sora, additional, Takahara, Fumie, additional, Takahashi, Naoya, additional, Takahashi, Kou, additional, Takeda, Tomoki, additional, Takenaka, Isabella K., additional, Tanaka, Soma, additional, Tang, Anyi, additional, Man Tang, Yuk, additional, Tarcitano, Emilio, additional, Tassinari, Andrea, additional, Taye, Mahdi, additional, Terrero, Alexis, additional, Thambiraja, Eunice, additional, Thiébaut, Antonin, additional, Thomas, Sade, additional, Thomas, Andrew M., additional, Togashi, Yuto, additional, Togashi, Takumi, additional, Tomaselli, Anna, additional, Tomita, Masaru, additional, Tomita, Itsuki, additional, Toth, Oliver, additional, Toussaint, Nora C., additional, Tran, Jennifer M., additional, Truong, Catalina, additional, Tsonev, Stefan I., additional, Tsuda, Kazutoshi, additional, Tsurumaki, Takafumi, additional, Tuz, Michelle, additional, Tymoshenko, Yelyzaveta, additional, Urgiles, Carmen, additional, Usui, Mariko, additional, Vacant, Sophie, additional, Vann, Laura E., additional, Velter, Fabienne, additional, Ventorino, Valeria, additional, Vera-Wolf, Patricia, additional, Vicedomini, Riccardo, additional, Suarez-Villamil, Michael A., additional, Vincent, Sierra, additional, Vivancos-Koopman, Renee, additional, Wan, Andrew, additional, Wang, Cindy, additional, Warashina, Tomoro, additional, Watanabe, Ayuki, additional, Weekes, Samuel, additional, Werner, Johannes, additional, Westfall, David, additional, Wieler, Lothar H., additional, Williams, Michelle, additional, Wolf, Silver A., additional, Wong, Brian, additional, Wong, Yan Ling, additional, Wong, Tyler, additional, Wright, Rasheena, additional, Wunderlin, Tina, additional, Yamanaka, Ryota, additional, Yang, Jingcheng, additional, Yano, Hirokazu, additional, Yeh, George C., additional, Yemets, Olena, additional, Yeskova, Tetiana, additional, Yoshikawa, Shusei, additional, Zafar, Laraib, additional, Zhang, Yang, additional, Zhang, Shu, additional, Zhang, Amy, additional, Zheng, Yuanting, additional, and Zubenko, Stas, additional

Published
2021
Full Text
View/download PDF

19. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps

Author

Park, Jiwoon, primary, Foox, Jonathan, additional, Hether, Tyler, additional, Danko, David, additional, Warren, Sarah, additional, Kim, Youngmi, additional, Reeves, Jason, additional, Butler, Daniel J., additional, Mozsary, Christopher, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshinnekoo, Ebrahim, additional, MacKay, Matthew, additional, Bram, Yaron, additional, Chandar, Vasuretha, additional, Geiger, Heather, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Beheshti, Afshin, additional, Taylor, Deanne, additional, Saravia-Butler, Amanda, additional, Singh, Urminder, additional, Wurtele, Eve Syrkin, additional, Schisler, Jonathan, additional, Fennessey, Samantha, additional, Corvelo, André, additional, Zody, Michael C., additional, Germer, Soren, additional, Salvatore, Steven, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas, additional, Shapira, Sagi, additional, Salvatore, Mirella, additional, Loda, Massimo, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Rennert, Hanna, additional, Kriegel, Alison J., additional, Elemento, Olivier, additional, Imielinski, Marcin, additional, Borczuk, Alain C., additional, Meydan, Cem, additional, Schwartz, Robert E., additional, and Mason, Christopher E., additional

Published
2021
Full Text
View/download PDF

20. Clonal hematopoiesis before, during, and after human spaceflight

Author

Mencia-Trinchant, Nuria, primary, MacKay, Matthew J., additional, Chin, Christopher, additional, Afshinnekoo, Ebrahim, additional, Foox, Jonathan, additional, Meydan, Cem, additional, Butler, Daniel, additional, Mozsary, Christopher, additional, Vernice, Nicholas A., additional, Darby, Charlotte, additional, Schatz, Michael C., additional, Bailey, Susan M., additional, Melnick, Ari M., additional, Guzman, Monica L., additional, Bolton, Kelly, additional, Braunstein, Lior Z., additional, Garrett-Bakelman, Francine, additional, Levine, Ross L., additional, Hassane, Duane C., additional, and Mason, Christopher E., additional

Published
2021
Full Text
View/download PDF

21. The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

Author

Foox, Jonathan, primary, Nordlund, Jessica, additional, Lalancette, Claudia, additional, Gong, Ting, additional, Lacey, Michelle, additional, Lent, Samantha, additional, Langhorst, Bradley W, additional, Ponnaluri, V K Chaithanya, additional, Williams, Louise, additional, Padmamabhan, Karthik Ramaswamy, additional, Cavalcante, Raymond G, additional, Lundmark, Anders, additional, Butler, Daniel, additional, Mozsary, Christopher, additional, Gurvitch, Justin M, additional, Greally, John M, additional, Suzuki, Masako, additional, Menor, Mark, additional, Nasu, Masaki, additional, Alonso, Alicia, additional, Sheridan, Caroline, additional, Scherer, Andreas, additional, Bruinsma, Stephen, additional, Golda, Gosia, additional, Muszynska, Agata, additional, Łabaj, Paweł Piotr, additional, Campbell, Matthew A, additional, Wos, Frank, additional, Raine, Amanda, additional, Liljedahl, Ulrika, additional, Axelsson, Tomas, additional, Wang, Charles, additional, Chen, Zhong, additional, Yang, Zhaowei, additional, Li, Jing, additional, Yang, Xiaopeng, additional, Wang, Hongwei, additional, Melnick, Ari, additional, Guo, Shang, additional, Blume, Alexander, additional, Franke, Vedran, additional, Ibanez de Caceres, Inmaculada, additional, Rodriguez-Antolin, Carlos, additional, Rosas, Rocio, additional, Davis, Justin Wade, additional, Ishii, Jennifer, additional, Megherbi, Dalila B, additional, Xiao, Wenming, additional, Liao, Will, additional, Xu, Joshua, additional, Hong, Huixiao, additional, Ning, Baitang, additional, Tong, Weida, additional, Akalin, Altuna, additional, Wang, Yunliang, additional, Deng, Youping, additional, and Mason, Christopher, additional

Published
2020
Full Text
View/download PDF

22. Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity

Author

Gertz, Monica L., primary, Chin, Christopher R., additional, Tomoiaga, Delia, additional, MacKay, Matthew, additional, Chang, Christina, additional, Butler, Daniel, additional, Afshinnekoo, Ebrahim, additional, Bezdan, Daniela, additional, Schmidt, Michael A., additional, Mozsary, Christopher, additional, Melnick, Ari, additional, Garrett-Bakelman, Francine, additional, Crucian, Brian, additional, Lee, Stuart M.C., additional, Zwart, Sara R., additional, Smith, Scott M., additional, Meydan, Cem, additional, and Mason, Christopher E., additional

Published
2020
Full Text
View/download PDF

23. Telomere Length Dynamics and DNA Damage Responses Associated with Long-Duration Spaceflight

Author

Luxton, Jared J., primary, McKenna, Miles J., additional, Lewis, Aidan, additional, Taylor, Lynn E., additional, George, Kerry A., additional, Dixit, Sameer M., additional, Moniz, Matthew, additional, Benegas, Willie, additional, Mackay, Matthew J., additional, Mozsary, Christopher, additional, Butler, Daniel, additional, Bezdan, Daniela, additional, Meydan, Cem, additional, Crucian, Brian E., additional, Zwart, Sara R., additional, Smith, Scott M., additional, Mason, Christopher E., additional, and Bailey, Susan M., additional

Published
2020
Full Text
View/download PDF

24. Clonal Hematopoiesis Before, During, and After Human Spaceflight

Author

Mencia-Trinchant, Nuria, primary, MacKay, Matthew J., additional, Chin, Christopher, additional, Afshinnekoo, Ebrahim, additional, Foox, Jonathan, additional, Meydan, Cem, additional, Butler, Daniel, additional, Mozsary, Christopher, additional, Vernice, Nicholas A., additional, Darby, Charlotte, additional, Schatz, Michael C., additional, Bailey, Susan M., additional, Melnick, Ari M., additional, Guzman, Monica L., additional, Bolton, Kelly, additional, Braunstein, Lior Z., additional, Garrett-Bakelman, Francine, additional, Levine, Ross L., additional, Hassane, Duane C., additional, and Mason, Christopher E., additional

Published
2020
Full Text
View/download PDF

25. Genetic and Immunological Evidence for Microbial Transfer Between the International Space Station and an Astronaut

Author

Danko, David C., primary, Singh, Nitin, additional, Butler, Daniel J., additional, Mozsary, Christopher, additional, Jiang, Peng, additional, Keshavarzian, Ali, additional, Maienschein-Cline, Mark, additional, Chlipala, George, additional, Afshinnekoo, Ebrahim, additional, Bezdan, Daniela, additional, Garrett-Bakelman, Francine, additional, Green, Stefan J., additional, Turek, Fred W., additional, Vitaterna, Martha Hotz, additional, Venkateswaran, Kasthuri, additional, and Mason, Christopher E., additional

Published
2020
Full Text
View/download PDF

26. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

Author

Butler, Daniel J., primary, Mozsary, Christopher, additional, Meydan, Cem, additional, Danko, David, additional, Foox, Jonathan, additional, Rosiene, Joel, additional, Shaiber, Alon, additional, Afshinnekoo, Ebrahim, additional, MacKay, Matthew, additional, Sedlazeck, Fritz J., additional, Ivanov, Nikolay A., additional, Sierra, Maria, additional, Pohle, Diana, additional, Zietz, Michael, additional, Gisladottir, Undina, additional, Ramlall, Vijendra, additional, Westover, Craig D., additional, Ryon, Krista, additional, Young, Benjamin, additional, Bhattacharya, Chandrima, additional, Ruggiero, Phyllis, additional, Langhorst, Bradley W., additional, Tanner, Nathan, additional, Gawrys, Justyna, additional, Meleshko, Dmitry, additional, Xu, Dong, additional, Steel, Peter A. D., additional, Shemesh, Amos J., additional, Xiang, Jenny, additional, Thierry-Mieg, Jean, additional, Thierry-Mieg, Danielle, additional, Schwartz, Robert E., additional, Iftner, Angelika, additional, Bezdan, Daniela, additional, Sipley, John, additional, Cong, Lin, additional, Craney, Arryn, additional, Velu, Priya, additional, Melnick, Ari M., additional, Hajirasouliha, Iman, additional, Horner, Stacy M., additional, Iftner, Thomas, additional, Salvatore, Mirella, additional, Loda, Massimo, additional, Westblade, Lars F., additional, Cushing, Melissa, additional, Levy, Shawn, additional, Wu, Shixiu, additional, Tatonetti, Nicholas, additional, Imielinski, Marcin, additional, Rennert, Hanna, additional, and Mason, Christopher E., additional

Published
2020
Full Text
View/download PDF

27. Clonal Hematopoiesis Before, During, and After Human Spaceflight.

Author

Trinchant, Nuria Mencia, MacKay, Matthew J., Chin, Christopher, Afshinnekoo, Ebrahim, Foox, Jonathan, Meydan, Cem, Butler, Daniel, Mozsary, Christopher, Vernice, Nicholas A., Darby, Charlotte, Schatz, Michael C., Bailey, Susan M., Melnick, Ari M., Guzman, Monica, Bolton, Kelly, Braunstein, Lior Z., Garrett-Bakelman, Francine, Levine, Ross L., Hassane, Duane, and Mason, Christopher E.

Abstract

Clonal hematopoiesis (CH) occurs when blood cells harboring an advantageous mutation propagate faster than others. These mutations confer a risk for hematological cancers and cardiovascular disease. Here, we analyze CH in blood samples from a pair of twin astronauts over 4 years in bulk and fractionated cell populations using a targeted CH panel, linked-read whole-genome sequencing, and deep RNA sequencing. We show CH with distinct mutational profiles and increasing allelic fraction that includes a high-risk, TET2 clone in one subject and two DNMT3A mutations on distinct alleles in the other twin. These astronauts exhibit CH almost two decades prior to the mean age at which it is typically detected and show larger shifts in clone size than age-matched controls or radiotherapy patients, based on a longitudinal cohort of 157 cancer patients. As such, longitudinal monitoring of CH may serve as an important metric for overall cancer and cardiovascular risk in astronauts. • Blood samples from twin astronauts were studied for clonal hematopoiesis (CH) • Distinct CH mutations and RNA variant trajectories were found across 4 years • CH was found almost two decades prior to the mean age at which it is typically detected • Longitudinal monitoring of CH is an important disease risk metric for astronauts. Trinchant et al. examined twin astronauts for clonal hematopoiesis (CH). Some high-risk CH clones (TET2 and DNMT3A) were observed two decades before expected, with TET2 decreasing in spaceflight and elevating later post flight. Thus, CH is an important metric for overall cancer and cardiovascular risk in astronauts. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

28. Additional file 2 of The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, ��abaj, Pawe�� P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, Ibanez de Caceres, Inmaculada, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Subjects
3. Good health
Abstract

Additional file 2. contains the supplementary tables (Supplementary Table 1���6).

29. Additional file 1 of The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, ��abaj, Pawe�� P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, Ibanez de Caceres, Inmaculada, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Subjects
3. Good health
Abstract

Additional file 1. contains the supplementary figures (Supplementary Figure 1���14).

30. Additional file 1 of The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, ��abaj, Pawe�� P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, Ibanez de Caceres, Inmaculada, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Subjects
3. Good health
Abstract

Additional file 1. contains the supplementary figures (Supplementary Figure 1���14).

31. Geospatially-resolved public-health surveillance via wastewater sequencing.

Author

Tierney BT, Foox J, Ryon KA, Butler D, Damle N, Young BG, Mozsary C, Babler KM, Yin X, Carattini Y, Andrews D, Solle NS, Kumar N, Shukla B, Vidovic D, Currall B, Williams SL, Schürer SC, Stevenson M, Amirali A, Beaver CC, Kobetz E, Boone MM, Reding B, Laine J, Comerford S, Lamar WE, Tallon JJ, Hirschberg JW, Proszynski J, Sharkey ME, Church GM, Grills GS, Solo-Gabriele HM, and Mason CE

Abstract

Wastewater, which contains everything from pathogens to pollutants, is a geospatially-and temporally-linked microbial fingerprint of a given population. As a result, it can be leveraged for monitoring multiple dimensions of public health across locales and time. Here, we integrate targeted and bulk RNA sequencing (n=1,419 samples) to track the viral, bacterial, and functional content over geospatially distinct areas within Miami Dade County from 2020-2022. First, we used targeted amplicon sequencing (n=966) to track diverse SARS-CoV-2 variants across space and time, and we found a tight correspondence with clinical caseloads from University students (N = 1,503) and Miami-Dade County hospital patients (N = 3,939 patients), as well as an 8-day earlier detection of the Delta variant in wastewater vs. in patients. Additionally, in 453 metatranscriptomic samples, we demonstrate that different wastewater sampling locations have clinically and public-health-relevant microbiota that vary as a function of the size of the human population they represent. Through assembly, alignment-based, and phylogenetic approaches, we also detect multiple clinically important viruses (e.g., norovirus ) and describe geospatial and temporal variation in microbial functional genes that indicate the presence of pollutants. Moreover, we found distinct profiles of antimicrobial resistance (AMR) genes and virulence factors across campus buildings, dorms, and hospitals, with hospital wastewater containing a significant increase in AMR abundance. Overall, this effort lays the groundwork for systematic characterization of wastewater to improve public health decision making and a broad platform to detect emerging pathogens.

Published
2023
Full Text
View/download PDF

32. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION.

Author

Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, and Wallace DC

Abstract

Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.

Published
2022
Full Text
View/download PDF

33. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection.

Author

McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler J, Mason CE, Chatterjee A, Meller R, and Beheshti A

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.

Published
2021
Full Text
View/download PDF

34. Betacoronavirus-specific alternate splicing.

Author

Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, and Robinson PN

Abstract

Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.

Published
2021
Full Text
View/download PDF

35. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps.

Author

Park J, Foox J, Hether T, Danko D, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti N, Shapira S, Salvatore M, Loda M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Borczuk AC, Meydan C, Schwartz RE, and Mason CE

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.

Published
2021
Full Text
View/download PDF

36. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.

Author

Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, and Mason CE

Abstract

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets., Competing Interests: Conflicts of Interest Nathan Tanner and Bradley W. Langhorst are employees at New England Biolabs.

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results