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2. An atlas of healthy and injured cell states and niches in the human kidney.

Author

Lake, Blue, Menon, Rajasree, Winfree, Seth, Hu, Qiwen, Ferreira, Ricardo, Kalhor, Kian, Barwinska, Daria, Otto, Edgar, Ferkowicz, Michael, Diep, Dinh, Plongthongkum, Nongluk, Knoten, Amanda, Urata, Sarah, Mariani, Laura, Naik, Abhijit, Eddy, Sean, Zhang, Bo, Wu, Yan, Salamon, Diane, Williams, James, Wang, Xin, Balderrama, Karol, Hoover, Paul, Murray, Evan, Marshall, Jamie, Noel, Teia, Vijayan, Anitha, Hartman, Austin, Chen, Fei, Waikar, Sushrut, Rosas, Sylvia, Wilson, Francis, Palevsky, Paul, Kiryluk, Krzysztof, Sedor, John, Toto, Robert, Parikh, Chirag, Kim, Eric, Satija, Rahul, Greka, Anna, Macosko, Evan, Kharchenko, Peter, Gaut, Joseph, Hodgin, Jeffrey, Eadon, Michael, Dagher, Pierre, El-Achkar, Tarek, Kretzler, Matthias, Jain, Sanjay, and Zhang, Kun

Subjects
Humans, Cell Nucleus, Gene Expression Profiling, Kidney, Kidney Diseases, Transcriptome, Single-Cell Analysis, Case-Control Studies, Imaging, Three-Dimensional
Abstract

Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.

Published
2023

6. The association of low birthweight and prematurity on outcomes in children and adults with nephrotic syndrome-a NEPTUNE cohort study

Author

Hingorani, Sangeeta, Gibson, Keisha L., Xie, Yuping, Wang, Yujie, Eddy, Sean, Hartman, John, and Sampson, Matthew

Subjects
Birth weight, Low -- Health aspects, Nephrotic syndrome -- Care and treatment -- Patient outcomes, Infants (Premature) -- Health aspects, Health
Abstract

Background In single-center studies, both preterm birth and low birth weight (LBW) are associated with worse outcomes in childhood nephrotic syndrome. Using the Nephrotic Syndrome Study Network (NEPTUNE) observational cohort, we tested the hypothesis that in patients with nephrotic syndrome, hypertension, proteinuria status, and disease progression would be more prevalent and more severe in subjects with LBW and prematurity singly or in combination (LBW/prematurity). Methods Three hundred fifty-nine adults and children with focal segmental glomerulosclerosis (FSGS) or minimal change disease (MCD) and available birth history were included. Estimated glomerular filtration rate (eGFR) decline and remission status were primary outcomes, and secondary outcomes were kidney histopathology, kidney gene expression, and urinary biomarkers. Logistic regression was used to identify associations with LBW/prematurity and these outcomes. Results We did not find an association between LBW/prematurity and remission of proteinuria. However, LBW/prematurity was associated with greater decline in eGFR. This decline in eGFR was partially explained by the association of LBW/prematurity with APOL1 high-risk alleles, but the association remained after adjustment. There were no differences in kidney histopathology or gene expression in the LBW/prematurity group compared to normal birth weight/term birth. Conclusion LBW and premature babies who develop nephrotic syndrome have a more rapid decline in kidney function. We did not identify clinical or laboratory features that distinguished the groups. Additional studies in larger groups are needed to fully ascertain the effects of (LBW) and prematurity alone or in combination on kidney function in the setting of nephrotic syndrome., Author(s): Sangeeta Hingorani [sup.1] , Keisha L. Gibson [sup.2] , Yuping Xie [sup.3] , Yujie Wang [sup.4] , Sean Eddy [sup.4] , John Hartman [sup.4] , Matthew Sampson [sup.5] [sup.6] [...]

Published
2023
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8. Unbiased kidney-centric molecular categorization of chronic kidney disease as a step towards precision medicine

Author

Reznichenko, Anna, Nair, Viji, Eddy, Sean, Fermin, Damian, Tomilo, Mark, Slidel, Timothy, Ju, Wenjun, Henry, Ian, Badal, Shawn S., Wesley, Johnna D., Liles, John T., Moosmang, Sven, Williams, Julie M., Quinn, Carol Moreno, Bitzer, Markus, Hodgin, Jeffrey B., Barisoni, Laura, Karihaloo, Anil, Breyer, Matthew D., Duffin, Kevin L., Patel, Uptal D., Magnone, Maria Chiara, Bhat, Ratan, and Kretzler, Matthias

Published
2024
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9. Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project

Author

Lake, Blue, Zhang, Kun, Lecker, Stewart, Morales, Alexander, Bogen, Steve, Amodu, Afolarin A., Beck, Laurence, Henderson, Joel, Ilori, Titlayo, Maikhor, Shana, Onul, Ingrid, Schmidt, Insa, Verma, Ashish, Waikar, Sushrut, Yadati, Pranav, Yu, Guanghao, Colona, Mia R., McMahon, Gearoid, Hacohen, Nir, Greka, Anna, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Bush, William, Chen, Yijiang, Crawford, Dana, Madabhushi, Anant, Viswanathan, Vidya S., Bush, Lakeshia, Cooperman, Leslie, Gadegbeku, Crystal, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’Malley, Charles, O’Toole, John, Palmer, Ellen, Poggio, Emilio, Spates-Harden, Kassandra, Sedor, John, Sendrey, Dianna, Taliercio, Jonathan, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan, Berroue, Cecilia, Bomback, Andrew, Canetta, Pietro A., D’Agati, Vivette, Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Sabatello, Maya, Shang, Ning, de Pinho Gonçalves, Joana, Lardenoije, Roy, Migas, Lukasz, Van de Plas, Raf, Rennke, Helmut, Azeloglu, Evren, Campbell, Kirk, Coca, Steven, He, Cijang, He, John, Iyengar, Srinivas Ravi, Lefferts, Seanee, Nadkarni, Girish, Patel, Marissa, Tokita, Joji, Ward, Stephen, Xiong, Yuguang, Verdoes, Abraham, Sabo, Angela, Barwinska, Daria, Gisch, Debora Lidia, Williams, James, Kelly, Katherine, Dunn, Kenneth, Asghari, Mahla, Eadon, Michael, Ferkowicz, Michael, Dagher, Pierre, Ferreira, Ricardo Melo, Winfree, Seth, Bledsoe, Sharon, Wofford, Stephanie, El-Achkar, Tarek, Sutton, Timothy, Bowen, William, Cheng, Ying-Hua, Slade, Austen, Record, Elizabeth, Cheng, Yinghua, Borner, Katy, Herr, Bruce, Jain, Yashvardhan, Quardokus, Ellen, Atta, Mohamed, Bernard, Lauren, Menez, Steven, Parikh, Chirag, Corona Villalobos, Celia Pamela, Wang, Ashley, Wen, Yumeng, Xu, Alan, Chen, Sarah, Donohoe, Isabel, Johansen, Camille, Rosas, Sylvia, Sun, Jennifer, Ardayfio, Joseph, Bebiak, Jack, Campbell, Taneisha, Fox, Monica, Knight, Richard, Koewler, Robert, Pinkeney, Roy, Saul, John, Shpigel, Anna, Prasad, Pottumarthi, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher, Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George, Mao, Weiguang, Sealfon, Rachel, Troyanskaya, Olga, Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Anjani, Kavya, Laszik, Zoltan G., Mukatash, Tariq, Nolan, Garry, Beyda, David, Bracamonte, Erika, Brosius, Frank, Campos, Baltazar, Marquez, Nicole, Mendoza, Katherine, Scott, Raymond, Thajudeen, Bijin, Tsosie, Rebecca, Woodhead, Gregory, Saunders, Milda, Alloway, Rita R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Bjornstad, Petter, Hsieh, Elena, Kendrick, Jessica, Pyle, Laura, Thurman, Joshua, Vinovskis, Carissa, Wrobel, Julia, Lucarelli, Nicholas, Sarder, Pinaki, Bui, James, Carmona-Powell; Ron Gaba, Eunice, Kelly, Tanika, Lash, James, Meza, Natalie, Redmond, Devona, Renteria, Amada, Ricardo, Ana, Setty, Suman, Srivastava, Anand, Alakwaa, Fadhl, Ascani, Heather, Balis, Ul, Bitzer, Markus, Blanc, Victoria, Bonevich, Nikki, Conser, Ninive, Demeke, Dawit, Dull, Rachel, Eddy, Sean, Frey, Renee, Hartman, John, He, Yongqun Oliver, Hodgin, Jeffrey, Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura, McCown, Phillip, Menon, Rajasree, Nair, Viji, Otto, Edgar, Reamy, Rebecca, Rose, Michael, Schaub, Jennifer, Steck, Becky, Wright, Zachary, Coleman, Alyson, Henderson-Brown; Jerica Berge, Dorisann, Caramori, Maria Luiza, Adeyi, Oyedele, Nachman, Patrick, Safadi, Sami, Flanagan, Siobhan, Ma, Sisi, Klett, Susan, Wolf, Susan, Harindhanavudhi, Tasma, Rao, Via, Bream, Peter, Froment, Anne, Kelley, Sara, Mottl, Amy, Chaudhury; Evan Zeitler, Prabir Roy, Bender, Filitsa, Elder, Michele, Gilliam, Matthew, Hall, Daniel E., Kellum, John A., Murugan, Raghavan, Palevsky, Paul, Rosengart, Matthew, Tan, Roderick, Tublin, Mitchell, Winters, James, Bansal, Shweta, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Cai, Qi, Hendricks, Allen, Hedayati, Susan, Kermani, Asra, Lee, Simon C., Ma, Shihong, Miller, Richard Tyler, Moe, Orson W., Park, Harold, Patel, Jiten, Pillai, Anil, Sambandam, Kamalanathan, Torrealba, Jose, Toto, Robert D., Vazquez, Miguel, Wang, Nancy, Wen, Natasha, Zhang, Dianbo, Alpers, Charles, Berglund, Ashley, Berry, Brooke, Blank, Kristina, Brown, Keith, Carson, Jonas, Daniel, Stephen, de Boer, Ian H., Dighe, Ashveena L., Dowd, Frederick, Grewenow, Stephanie M., Himmelfarb, Jonathan, Hoofnagle, Andrew, Jefferson, Nichole, Larson, Brandon, Limonte, Christine, McClelland, Robyn, Mooney, Sean, Nam, Yunbi, Park, Christopher, Phuong, Jimmy, Rezaei, Kasra, Roberts, Glenda, Sarkisova, Natalya, Shankland, Stuart, Snyder, Jaime, Stutzke, Christy, Tuttle, Katherine, Wangperawong, Artit, Wilcox, Adam, Williams, Kayleen, Young, Bessie, Allen, Jamie, Caprioli, Richard M., de Caestecker, Mark, Djambazova, Katerina, Dufresne, Martin, Farrow, Melissa, Fogo, Agnes, Sharman, Kavya, Spraggins, Jeffrey, Basta, Jeannine, Conlon, Kristine, Diettman, Sabine M., Gaut, Joseph, Kaushal, Madhurima, Jain, Sanjay, Knoten, Amanda, Minor, Brittany, Nwanne, Gerald, Vijayan, Anitha, Zhang, Bo, Arora, Tanima, Cantley, Lloyd, Victoria Castro, Angela M., Kakade, Vijayakumar, Moeckel, Gilbert, Moledina, Dennis, Shaw, Melissa, Wilson, Francis P., El-Achkar, Tarek M., and Eadon, Michael T.

Published
2024
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11. An integrated organoid omics map extends modeling potential of kidney disease

Author

Lassé, Moritz, El Saghir, Jamal, Berthier, Celine C., Eddy, Sean, Fischer, Matthew, Laufer, Sandra D., Kylies, Dominik, Hutzfeldt, Arvid, Bonin, Léna Lydie, Dumoulin, Bernhard, Menon, Rajasree, Vega-Warner, Virginia, Eichinger, Felix, Alakwaa, Fadhl, Fermin, Damian, Billing, Anja M., Minakawa, Akihiro, McCown, Phillip J., Rose, Michael P., Godfrey, Bradley, Meister, Elisabeth, Wiech, Thorsten, Noriega, Mercedes, Chrysopoulou, Maria, Brandts, Paul, Ju, Wenjun, Reinhard, Linda, Hoxha, Elion, Grahammer, Florian, Lindenmeyer, Maja T., Huber, Tobias B., Schlüter, Hartmut, Thiel, Steffen, Mariani, Laura H., Puelles, Victor G., Braun, Fabian, Kretzler, Matthias, Demir, Fatih, Harder, Jennifer L., and Rinschen, Markus M.

Published
2023
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12. Molecular Signatures of Glomerular Neovascularization in a Patient with Diabetic Kidney Disease

Author

Ferkowicz, Michael J., Verma, Ashish, Barwinska, Daria, Melo Ferreira, Ricardo, Henderson, Joel M., Kirkpatrick, Mary, Silva, Paolo S., Steenkamp, Devin W., Phillips, Carrie L., Waikar, Sushrut S., Sutton, Timothy A., Lake, Blue, Zhang, Kun, Lecker, Stewart, Morales, Alexander, Stillman, Isaac, Bogen, Steve, Amodu, Afolarin A., Beck, Laurence, Henderson, Joel, Ilori, Titlayo, Maikhor, Shana, Onul, Ingrid, Schmidt, Insa, Verma, Ashish, Waikar, Sushrut, Yadati, Pranav, Yu, Guanghao, Colona, Mia R., McMahon, Gearoid, Weins, Astrid, Hacohen, Nir, Greka, Anna, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Bush, William, Chen, Yijiang, Crawford, Dana, Madabhushi, Anant, Viswanathan, Vidya S., Bush, Lakeshia, Cooperman, Leslie, Gadegbeku, Crystal, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’Malley, Charles, O’Toole, John, Palmer, Ellen, Poggio, Emilio, Spates-Harden, Kassandra, Sedor, John, Sendrey, Dianna, Taliercio, Jonathan, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan, Berroue, Cecilia, Bomback, Andrew, Canetta, Pietro A., D’Agati, Vivette, Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Sabatello, Maya, Shang, Ning, Varela, German, de Pinho Gonçalves, Joana, Lardenoije, Roy, Migas, Lukasz, Van de Plas, Raf, Barisoni, Laura, Rennke, Helmut, Azeloglu, Evren, Campbell, Kirk, Coca, Steven, He, Cijang, He, John, Iyengar, Srinivas Ravi, Lefferts, Seanee, Nadkarni, Girish, Patel, Marissa, Tokita, Joji, Ward, Stephen, Xiong, Yuguang, Verdoes, Abraham, Sabo, Angela, Barwinska, Daria, Gisch, Debora Lidia, Williams, James, Kelly, Katherine, Dunn, Kenneth, Asghari, Mahla, Eadon, Michael, Ferkowicz, Michael, Dagher, Pierre, Ferreira, Ricardo Melo, Winfree, Seth, Bledsoe, Sharon, Wofford, Stephanie, El-Achkar, Tarek, Sutton, Timothy, Bowen, William, Cheng, Ying-Hua, Slade, Austen, Record, Elizabeth, Cheng, Yinghua, Borner, Katy, Herr, Bruce, Jain, Yashvardhan, Quardokus, Ellen, Atta, Mohamed, Bernard, Lauren, Menez, Steven, Parikh, Chirag, Corona Villalobos, Celia Pamela, Wang, Ashley, Wen, Yumeng, Xu, Alan, Chen, Sarah, Donohoe, Isabel, Johansen, Camille, Rosas, Sylvia, Sun, Jennifer, Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Fox, Monica, Hayashi, Lynda, Jefferson, Nichole, Richard Knight, Jennifer Jones, Koewler, Robert, Pinkeney, Roy, Saul, John, Shpigel, Anna, Stutzke, Christy, Prasad, Pottumarthi, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher, Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George, Mao, Weiguang, Sealfon, Rachel, Troyanskaya, Olga, Wong, Aaron, Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Lutnick, Brendon, Anjani, Kavya, Laszik, Zoltan G., Mukatash, Tariq, Nolan, Garry, Beyda, David, Bracamonte, Erika, Brosius, Frank, Campos, Baltazar, Marquez, Nicole, Mendoza, Katherine, Scott, Raymond, Thajudeen, Bijin, Tsosie, Rebecca, Woodhead, Gregory, Saunders, Milda, Alloway, Rita R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Bjornstad, Petter, Hsieh, Elena, Kendrick, Jessica, Pyle, Laura, Thurman, Joshua, Vinovskis, Carissa, Wrobel, Julia, Lucarelli, Nicholas, Sarder, Pinaki, Bui, James, Carmona-Powell, Eunice, Gaba, Ron, Kelly, Tanika, Lash, James, Meza, Natalie, Redmond, Devona, Renteria, Amada, Ricardo, Ana, Setty, Suman, Srivastava, Anand, Alakwaa, Fadhl, Ascani, Heather, Balis, Ul, Bitzer, Markus, Blanc, Victoria, Bonevich, Nikki, Conser, Ninive, Demeke, Dawit, Dull, Rachel, Eddy, Sean, Frey, Renee, Hartman, John, He, Yongqun Oliver, Hodgin, Jeffrey, Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura, McCown, Phillip, Menon, Rajasree, Nair, Viji, Otto, Edgar, Reamy, Rebecca, Rose, Michael, Schaub, Jennifer, Steck, Becky, Wright, Zachary, Coleman, Alyson, Henderson-Brown, Dorisann, Berge, Jerica, Caramori, Maria Luiza, Adeyi, Oyedele, Nachman, Patrick, Safadi, Sami, Flanagan, Siobhan, Ma, Sisi, Klett, Susan, Wolf, Susan, Harindhanavudhi, Tasma, Rao, Via, Bream, Peter, Froment, Anne, Kelley, Sara, Mottl, Amy, Roy-Chaudhury, Prabir, Zeitler, Evan, Bender, Filitsa, Elder, Michele, Gilliam, Matthew, Hall, Daniel E., Kellum, John A., Murugan, Raghavan, Palevsky, Paul, Rosengart, Matthew, Tan, Roderick, Tublin, Mitchell, Winters, James, Bansal, Shweta, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Cai, Qi, Hendricks, Allen, Hedayati, Susan, and Asra

Published
2024
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13. Participant Experience with Protocol Research Kidney Biopsies in the Kidney Precision Medicine Project

Author

Victoria-Castro, Angela M., Corona-Villalobos, Celia P., Xu, Alan Y., Onul, Ingrid, Huynh, Courtney, Chen, Sarah W., Ugwuowo, Ugochukwu, Sarkisova, Natalya, Dighe, Ashveena L., Blank, Kristina N., Blanc, Victoria M., Rose, Michael P., Himmelfarb, Jonathan, de Boer, Ian H., Tuttle, Katherine R., Roberts, Glenda V., Alexandrov, Theodore, Alloway, Rita R., Alpers, Charles E., Amodu, Afolarin A., Anderton, Christopher R., Anjani, Kavya, Appelbaum, Paul, Ardayfio, Joseph, Arora, Tanima, Ascani, Heather, El-Achkar, Tarek M., Aulisio, Mark, Azeloglu, Evren U., Balderes, Olivia, Balis, Ulysses G.J., Bansal, Shweta, Barasch, Jonathan M., Bansal, Shweta, Barkell, Alex, Barwinska, Daria, Basit, Mujeeb, Basta, Jeanine, Bebiak, Jack, Beck, Laurence H., Bender, Filitsa, Berglund, Ashley, Bernard, Lauren, Berrouet, Cecilia, Berry, Brooke, Bjornstad, Petter M., Blanc, Victoria M., Blank, Kristina N., Bledsoe, Sharon, Boada, Patrick, Bogen, Steve, Bomback, Andrew S., Bonevich, Nikole, Borner, Katy, Brown, Keith, Bueckle, Andreas, Burg, Ashley R., Burgess, Adam, Bush, Lakeshia, Bush, William S., Campbell, Catherine E., Campbell, Taneisha, Canetta, Pietro A., Cantley, Lloyd G., Caprioli, Richard M., Carson, Jonas, Chen, Sarah, Chen, Yijiang M., Cheng, Yinghua, Cimino, Jim, Colona, Mia R., Conser, Ninive C., Cooperman, Leslie, Crawford, Dana C., DʼAgati, Vivette D., Dagher, Pierre C., Daniel, Stephen, Daratha, Kenn, de Boer, Ian H., Diettman, Sabine M., Dighe, Ashveena L., Donohoe, Isabel, Dowd, Frederick, Dunn, Kenneth W., Eadon, Michael T., Eddy, Sean, Elder, Michele M., Ferkowicz, Michael J., Frey, Renee, Gadegbeku, Crystal A., Gaut, Joseph P., Gilliam, Matthew, Ginley, Brandon, Gisch, Debora, Goltsev, Yury, Gonzalez-Vicente, Agustin, Greka, Anna, Grewenow, Stephanie M., Hacohen, Nir, Hall, Daniel E., Hansen, Jens, Hayashi, Lynda, He, Cijang, He, Yougqun, Hedayati, S. Susan, Henderson, Joel M., Hendricks, Allen H., Herlitz, Leal, Herr, Bruce W., Himmelfarb, Jonathan, Hodgin, Jeffrey B., Hoofnagle, Andrew N., Hoover, Paul J., Ilori, Titlayo, Iyengar, Ravi, Jain, Sanjay, Jain, Yashvardhan, Janowczyk, Andrew, Jefferson, Nichole, Johansen, Camille, Jolly, Stacey, Kakade, Vijaykumar R., Kellum, John A., Kelly, Katherine J., Kermani, Asra, Kiryluk, Krzysztof, Knight, Richard, Koewler, Robert, Kretzler, Matthias, Kudose, Satoru, Lake, Blue B., Larson, Brandon, Laszik, Zoltan G., Lecker, Stewart H., Lee, Paul J., Lee, Simon C., Lienczewski, Chrysta, Limonte, Christine, Lu, Christopher Y., Lucarelli, Nicholas, Lukowski, Jessica, Luo, Jinghui, Lutnick, Brendon, Ma, Shihong, Madabhushi, Anant, Madhavan, Sethu M., Maikhor, Shana, Mariani, Laura H., Marshall, Jamie L., McClelland, Robyn L., McMahon, Gearoid M., Mehl, Karla, Ferreira, Ricardo Melo, Menez, Steven, Menon, Rajasree, Miller, R. Tyler, Moe, Orson W., Moledina, Dennis, Montellano, Richard, Mooney, Sean D., Morales, Martha Catalina, Mukatash, Tariq, Murugan, Raghavan, Nam, Yunbi, Nguyen, Jane, Nolan, Garry, Oʼtoole, John, Oliver, George (Holt), Onul, Ingrid, Otto, Edgar, Palevsky, Paul M., Palmer, Ellen, Pamreddy, Annapurna, Parikh, Chirag R., Parikh, Samir, Park, Christopher, Park, Harold, Pasa-Tolic, Ljiljana, Patel, Jiten, Patterson, Nathan, Phuong, Jim, Pillai, Anil, Pinkeney, Roy, Poggio, Emilio, Pollack, Ari, Prasad, Pottumarthi, Pyle, Laura, Quardokus, Ellen M., Randhawa, Parmjeet, Rauchman, Michael I., Record, Elizabeth, Rennke, Helmut, Rezaei, Kasra, Rike, Adele, Rivera, Marcelino, Roberts, Glenda V., Rosas, Sylvia E., Rosenberg, Avi, Rosengart, Matthew, Rovin, Brad, Roy, Neil, Sabatello, Maya, Sambandam, Kamalanathan, Sarder, Pinaki, Sarkisova, Natalya, Sarwal, Minnie, Saul, John, Schaub, Jennifer, Schmidt, Insa, Sealfon, Rachel, Sedor, John, Sendrey, Dianna, Shang, Ning, Shankland, Stuart, Shapiro, John P., Sharma, Kumar, Sharman, Kavya, Shaw, Melissa M., Shi, Tiffany, Shpigel, Anna, Sigdel, Tara, Slade, Austen, Snyder, Jamie, Spates-Harden, Kassandra, Spraggins, Jeffrey M., Srivastava, Anand, Steck, Becky, Stillman, Isaac, Stutzke, Christy, Su, Jing, Sun, Jennifer, Sutton, Timothy A., Taliercio, Jonathan, Tan, Roderick, Torrealba, Jose, Toto, Robert D., Troyanskaya, Olga, Tublin, Mitchell, Tuttle, Katherine R., Ugwuowo, Ugochukwu, Valerius, M. Todd, Van de Plas, Raf, Varela, German, Vazquez, Miguel, Velickovic, Dusan, Venkatachalam, Manjeri, Verma, Ashish, Victoria-Castro, Angela M., Vijayan, Anitha, Corona-Villalobos, Celia P., Vinovskis, Carissa, Viswanathan, Vidya S., Vita, Tina, Waikar, Sushrut, Wang, Ashley, Wang, Ruikang, Wang, Nancy, Weins, Astrid, Wen, Natasha, Wen, Yumeng, Wilcox, Adam, Williams, James C., Jr., Kayleen Williams, Williams, Mark, Wilson, Francis P., Winfree, Seth, Winters, James, Wofford, Stephanie, Wong, Aaron, Woodle, E. Steve, Xiong, Yuguang, Xu, Alan, Yadati, Pranav, Ye, Hongping, Yu, Guanghao, Zhang, Dianbo, Zhang, Guanshi, and Zhang, Kun

Published
2024
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14. Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis

Author

Mariani, Laura H., Eddy, Sean, AlAkwaa, Fadhl M., McCown, Phillip J., Harder, Jennifer L., Nair, Viji, Eichinger, Felix, Martini, Sebastian, Ademola, Adebowale D., Boima, Vincent, Reich, Heather N., El Saghir, Jamal, Godfrey, Bradley, Ju, Wenjun, Tanner, Emily C., Vega-Warner, Virginia, Wys, Noel L., Adler, Sharon G., Appel, Gerald B., Athavale, Ambarish, Atkinson, Meredith A., Bagnasco, Serena M., Barisoni, Laura, Brown, Elizabeth, Cattran, Daniel C., Coppock, Gaia M., Dell, Katherine M., Derebail, Vimal K., Fervenza, Fernando C., Fornoni, Alessia, Gadegbeku, Crystal A., Gibson, Keisha L., Greenbaum, Laurence A., Hingorani, Sangeeta R., Hladunewich, Michelle A., Hodgin, Jeffrey B., Hogan, Marie C., Holzman, Lawrence B., Jefferson, J. Ashley, Kaskel, Frederick J., Kopp, Jeffrey B., Lafayette, Richard A., Lemley, Kevin V., Lieske, John C., Lin, Jen-Jar, Menon, Rajarasee, Meyers, Kevin E., Nachman, Patrick H., Nast, Cynthia C., O’Shaughnessy, Michelle M., Otto, Edgar A., Reidy, Kimberly J., Sambandam, Kamalanathan K., Sedor, John R., Sethna, Christine B., Singer, Pamela, Srivastava, Tarak, Tran, Cheryl L., Tuttle, Katherine R., Vento, Suzanne M., Wang, Chia-shi, Ojo, Akinlolu O., Adu, Dwomoa, Gipson, Debbie S., Trachtman, Howard, and Kretzler, Matthias

Published
2023
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15. A Participant-Centered Approach to Understanding Risks and Benefits of Participation in Research Informed by the Kidney Precision Medicine Project

Author

Alexandrov, Theodore, Alpers, Charles E., Anderton, Christopher R., Ardayfio, Joseph, Arora, Tanima, El-Achkar, Tarek M., Azeloglu, Evren U., Balderes, Olivia, Balis, Ulysses G.J., Bansal, Shweta, Barasch, Jonathan M., Barwinska, Daria, Bebiak, Jack, Blanc, Victoria M., Blank, Kristina N., Bomback, Andrew S., Brown, Keith D., Bush, William S., Campbell, Taneisha, Canetta, Pietro A., Carson, Jonas, Cooperman, Leslie, Crawford, Dana C., D’Agati, Vivette D., Dagher, Pierre C., Daniel, Stephen, Dowd, Frederick, Dunn, Kenneth W., Eadon, Michael T., Eddy, Sean, Elder, Michele M., Ferkowicz, Michael J., Gaut, Joe P., Goltsev, Yury, Gonzalez-Vicente, Agustin, Hacohen, Nir, Hansen, Jens, Hayashi, Lynda, He, Oliver, He, Cijang, Hedayati, S. Susan, Herlitz, Leal, Hodgin, Jeffrey B., Hoofnagle, Andrew N., Hoover, Paul J., Iyengar, Ravi, Jain, Sanjay, Jefferson, Nichole, Jolly, Stacey, Kellum, John A., Kelly, Katherine J., Kermani, Asra, Kiryluk, Krzysztof, Koewler, Robert, Kretzler, Matthias, Lake, Blue B., Laszik, Zoltan G., Lecker, Stewart H., Lee, Simon C., Lienczewski, Chrysta, Lu, Christopher Y., Mariani, Laura H., McClelland, Robyn L., McMahon, Gearoid M., Menez, Steven, Menon, Rajasree, Miller, Tyler, Moe, Orson W., Moledina, Dennis, Mooney, Sean D., Nguyen, Jane, Nolan, Garry, Oliver, George, Otto, Edgar, Palevsky, Paul M., Palmer, Ellen, Pamreddy, Annapurna, Parikh, Chirag R., Parikh, Samir, Park, Christopher, Park, Harold, Pasa-Tolic, Ljiljana, Pinkeney, Roy, Poggio, Emilio, Randhawa, Parmjeet, Rennke, Helmut, Roberts, Glenda V., Rosenberg, Avi, Rosengart, Matthew, Rovin, Brad, Roy, Neil, Sambandam, Kamalanathan, Sarwal, Minnie, Saul, John, Schaub, Jennifer, Sealfon, Rachel, Shang, Ning, Shankland, Stuart, Sharma, Kumar, Shpigel, Anna, Sigdel, Tara, Steck, Becky, Stillman, Isaac, Stutzke, Edith Christine, Sutton, Timothy A., Torrealba, Jose, Toto, Robert D., Troyanskaya, Olga, Tublin, Mitchell, Ugwuowo, Ugochukwu, Vazquez, Miguel, Velickovic, Dusan, Venkatachalam, Manjeri, Vijayan, Anitha, Corona-Villalobos, Celia P., Wang, Nancy, Weins, Astrid, Wilcox, Adam, Williams, Kayleen, Williams, Mark, Wilson, Francis P., Winfree, Seth, Xiong, Yuguang, Zhang, Kun, Zhang, Guanshi, Butler, Catherine R., Appelbaum, Paul S., Ascani, Heather, Aulisio, Mark, Campbell, Catherine E., de Boer, Ian H., Dighe, Ashveena L., Hall, Daniel E., Himmelfarb, Jonathan, Knight, Richard, Mehl, Karla, Murugan, Raghavan, Rosas, Sylvia E., Sedor, John R., O’Toole, John F., Tuttle, Katherine R., Waikar, Sushrut S., and Freeman, Michael

Published
2022
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17. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome

Author

Dell, K., Sedor, J., Schachere, M., Negrey, J., Lemley, K., Lim, E., Srivastava, T., Garrett, A., Sethna, C., Laurent, K., Canetta, P., Pradhan, A., Greenbaum, L., Wang, C., Kang, C., Adler, S., LaPage, J., Athavale, A., Itteera, M., Atkinson, M., Boynton, S., Fervenza, F., Hogan, M., Lieske, J., Chernitskiy, V., Kaskel, F., Ross, M., Flynn, P., Kopp, J., Blake, J., Trachtman, H., Zhdanova, O., Modersitzki, F., Vento, S., Bray, M., Kelton, M., Cooper, A., Lafayette, R., Mehta, K., Gadegbeku, C., Quinn-Boyle, S., Hladunewich, M., Reich, H., Ling, P., Romano, M., Fornoni, A., Bidot, C., Kretzler, M., Gipson, D., Williams, A., LaVigne, J., Derebail, V., Gibson, K., Cole, E., Ormond-Foster, J., Holzman, L., Meyers, K., Kallem, K., Swenson, A., Sambandam, K., Wang, Z., Rogers, M., Jefferson, A., Hingorani, S., Tuttle, K., Lin, J.J., Barisoni, L., Bixler, J., Desmond, H., Eddy, S., Fermin, D., Gillespie, B., Kurtz, V., Larkina, M., Lavigne, J., Li, S., Lienczewski, C.C., Liu, J., Mainieri, T., Mariani, L., Sampson, M., Smith, A., Zee, J., Avila-Casado, Carmen, Bagnasco, Serena, Gaut, Joseph, Hewitt, Stephen, Hodgin, Jeff, Lemley, Kevin, Mariani, Laura, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Thomas, David, Zee, Jarcy, Barisoni, Laura, Nast, Cynthia, Hodgin, Jeffrey B., Mariani, Laura H., Liu, Qian, Smith, Abigail R., Eddy, Sean, Hartman, John, Hamidi, Habib, Gaut, Joseph P., Palmer, Matthew B., Nast, Cynthia C., Chang, Anthony, Gillespie, Brenda W., Kretzler, Matthias, and Holzman, Lawrence B.

Published
2022
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18. Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures

Author

Latt, Khun Zaw, Heymann, Jurgen, Jessee, Joseph H., Rosenberg, Avi Z., Berthier, Celine C., Arazi, Arnon, Eddy, Sean, Yoshida, Teruhiko, Zhao, Yongmei, Chen, Vicky, Nelson, George W., Cam, Margaret, Kumar, Parimal, Mehta, Monika, Kelly, Michael C., Kretzler, Matthias, Ray, Patricio E., Moxey-Mims, Marva, Gorman, Gregory H., Lechner, Brent L., Regunathan-Shenk, Renu, Raj, Dominic S., Susztak, Katalin, Winkler, Cheryl A., and Kopp, Jeffrey B.

Published
2022
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20. Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis

Author

Knight, Richard, Lecker, Stewart H., Stillman, Isaac, Bogen, Steve, Amodu, Afolarin A., Ilori, Titlayo, Maikhor, Shana, Schmidt, Insa M., Beck, Laurence H., Henderson, Joel M., Onul, Ingrid, Verma, Ashish, McMahon, Gearoid M., Valerius, M. Todd, Waikar, Sushrut, Weins, Astrid, Colona, Mia R., Greka, Anna, Hacohen, Nir, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Chen, Yijiang M., Janowczyk, Andrew, Jayapandian, Catherine, Viswanathan, Vidya S., Bush, William S., Crawford, Dana C., Madabhushi, Anant, Bush, Lakeshia, Cooperman, Leslie, Gonzalez-Vicente, Agustin, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’toole, John, Palmer, Ellen, Poggio, Emilio, Sedor, John, Sendrey, Dianna, Spates-Harden, Kassandra, Taliercio, Jonathan, Bjornstad, Petter M., Pyle, Laura, Vinovskis, Carissa, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan M., Bomback, Andrew S., Canetta, Pietro A., D’Agati, Vivette D., Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Shang, Ning, Bansal, Shweta, Alexandrov, Theodore, Rennke, Helmut, El-Achkar, Tarek M., Barwinska, Daria, Bledso, Sharon, Borner, Katy, Bueckle, Andreas, Cheng, Yinghua, Dagher, Pierre C., Dunn, Kenneth W., Eadon, Michael T., Ferkowicz, Michael J., Herr, Bruce W., Kelly, Katherine J., Ferreira, Ricardo Melo, Quardokus, Ellen M., Record, Elizabeth, Rivera, Marcelino, Su, Jing, Sutton, Timothy A., Williams, James C., Jr., Winfree, Seth, Jain, Yashvardhan, Menez, Steven, Parikh, Chirag R., Rosenberg, Avi, Corona-Villalobos, Celia P., Wen, Yumeng, Johansen, Camille, Rosas, Sylvia E., Roy, Neil, Sun, Jennifer, Williams, Mark, Azeloglu, Evren U., Hansen, Jens, He, Cijang, Iyengar, Ravi, Xiong, Yuguang, Prasad, Pottumarthi, Srivastava, Anand, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher R., Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George (Holt), Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Campbell, Catherine E., Hayashi, Lynda, Jefferson, Nichole, Roberts, Glenda V., Saul, John, Shpigel, Anna, Stutzke, Christy, Koewler, Robert, Pinkeney, Roy, Sealfon, Rachel, Troyanskaya, Olga, Wong, Aaron, Tuttle, Katherine R., Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Lucarelli, Nicholas, Lutnick, Brendon, Sarder, Pinaki, Lake, Blue B., Zhang, Kun, Boada, Patrick, Laszik, Zoltan G., Nolan, Garry, Anjani, Kavya, Sarwal, Minnie, Mukatash, Tariq, Sigdel, Tara, Alloway, Rita R., Burg, Ashley R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Ascani, Heather, Balis, Ulysses G.J., Blanc, Victoria M., Conser, Ninive C., Eddy, Sean, Frey, Renee, He, Yougqun, Hodgin, Jeffrey B., Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura H., Menon, Rajasree, Otto, Edgar, Schaub, Jennifer, Steck, Becky, Elder, Michele M., Gilliam, Matthew, Hall, Daniel E., Murugan, Raghavan, Palevsky, Paul M., Randhawa, Parmjeet, Rosengart, Matthew, Tublin, Mitchell, Vita, Tina, Winters, James, Kellum, John A., Alpers, Charles E., Berglund, Ashley, Berry, Brooke, Blank, Kristina N., Carson, Jonas, Daniel, Stephen, De Boer, Ian H., Dighe, Ashveena L., Dowd, Frederick, Grewenow, Stephanie M., Himmelfarb, Jonathan, Hoofnagle, Andrew N., Limonte, Christine, McClelland, Robyn L., Mooney, Sean D., Rezaei, Kasra, Shankland, Stuart, Snyder, Jamie, Wang, Ruikang, Wilcox, Adam, Williams, Kayleen, Park, Christopher, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Hedayati, S. Susan, Kermani, Asra, Lee, Simon C., Lu, Christopher Y., Miller, R. Tyler, Moe, Orson W., Patel, Jiten, Pillai, Anil, Sambandam, Kamalanathan, Torrealba, Jose, Toto, Robert D., Vazquez, Miguel, Wang, Nancy, Wen, Natasha, Zhang, Dianbo, Park, Harold, Caprioli, Richard M., Patterson, Nathan, Sharman, Kavya, Spraggins, Jeffrey M., Van de Plas, Raf, Basta, Jeanine, Diettman, Sabine M., Gaut, Joseph P., Jain, Sanjay, Rauchman, Michael I., Vijayan, Anitha, Cantley, Lloyd G., Kakade, Vijaykumar R., Moledina, Dennis, Shaw, Melissa M., Ugwuowo, Ugochukwu, Wilson, Francis P., Arora, Tanima, Kestenbaum, Bryan R., Alexopoulos, Leonidas G., Palsson, Ragnar, Liu, Jing, Stillman, Isaac E., Rennke, Helmut G., Vaidya, Vishal S., Wu, Haojia, Humphreys, Benjamin D., and Waikar, Sushrut S.

Published
2021
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22. SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth-onset type 2 diabetes

Author

Schaub, Jennifer A., AlAkwaa, Fadhl M., McCown, Phillip J., Naik, Abhijit S., Nair, Viji, Eddy, Sean, Menon, Rajasree, Otto, Edgar A., Demeke, Dawit, Hartman, John, Fermin, Damian, O'Connor, Christopher L., Subramanian, Lalita, Bitzer, Markus, Harned, Roger, Ladd, Patricia, Pyle, Laura, Pennathur, Subramaniam, Inoki, Ken, Hodgin, Jeffrey B., Brosius, Frank C., III, Nelson, Robert G., Kretzler, Matthias, and Bjornstad, Petter

Subjects
Hypoglycemic agents -- Usage -- Physiological aspects, Type 2 diabetes -- Drug therapy -- Complications and side effects, Pediatric research, Diabetic nephropathies -- Risk factors -- Development and progression -- Prevention, Health care industry
Abstract

The molecular mechanisms of sodium-glucose cotransporter-2 (SGLT2) inhibitors (SGLT2i) remain incompletely understood. Single-cell RNA sequencing and morphometric data were collected from research kidney biopsies donated by young persons with type 2 diabetes (T2D), aged 12 to 21 years, and healthy controls (HCs). Participants with T2D were obese and had higher estimated glomerular filtration rates and mesangial and glomerular volumes than HCs. Ten T2D participants had been prescribed SGLT2i (T2Di[+]) and 6 not (T2Di[-]). Transcriptional profiles showed SGLT2 expression exclusively in the proximal tubular (PT) cluster with highest expression in T2Di(-) patients. However, transcriptional alterations with SGLT2i treatment were seen across nephron segments, particularly in the distal nephron. SGLT2i treatment was associated with suppression of transcripts in the glycolysis, gluconeogenesis, and tricarboxylic acid cycle pathways in PT, but had the opposite effect in thick ascending limb. Transcripts in the energy-sensitive mTORC1-signaling pathway returned toward HC levels in all tubular segments in T2Di(+), consistent with a diabetes mouse model treated with SGLT2i. Decreased levels of phosphorylated S6 protein in proximal and distal tubules in T2Di(+) patients confirmed changes in mTORC1 pathway activity. We propose that SGLT2i treatment benefits the kidneys by mitigating diabetes-induced metabolic perturbations via suppression of mTORC1 signaling in kidney tubules., Introduction The incedence of youth-onset type 2 diabetes (T2D) is rapidly rising among children and adolescents globally (1). It is associated with a more severe clinical course than youth-onset type [...]

Published
2023
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23. SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease

Author

Menon, Rajasree, Otto, Edgar A., Sealfon, Rachel, Nair, Viji, Wong, Aaron K., Theesfeld, Chandra L., Chen, Xi, Wang, Yuan, Boppana, Avinash S., Luo, Jinghui, Yang, Yingbao, Kasson, Peter M., Schaub, Jennifer A., Berthier, Celine C., Eddy, Sean, Lienczewski, Chrysta C., Godfrey, Bradley, Dagenais, Susan L., Sohaney, Ryann, Hartman, John, Fermin, Damian, Subramanian, Lalita, Looker, Helen C., Harder, Jennifer L., Mariani, Laura H., Hodgin, Jeffrey B., Sexton, Jonathan Z., Wobus, Christiane E., Naik, Abhijit S., Nelson, Robert G., Troyanskaya, Olga G., and Kretzler, Matthias

Published
2020
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24. Urinary Epidermal Growth Factor as a Marker of Disease Progression in Children With Nephrotic Syndrome

Author

Gipson, Debbie S., Trachtman, Howard, Waldo, Anne, Gibson, Keisha L., Eddy, Sean, Dell, Katherine M., Srivastava, Tarak, Lemley, Kevin V., Greenbaum, Larry A., Hingorani, Sangeeta, Meyers, Kevin E., Kaskel, Frederick J., Reidy, Kimberly J., Sethna, Christine B., Tran, Cheryl L., Wang, Chia-shi, Tuttle, Katherine R., Oh, Gia, Neu, Alicia M., Brown, Elizabeth, Lin, Jen-Jar, Yee, Jennifer Lai, Roth, Therese M., Troost, Jonathan P., Gillespie, Brenda W., Sampson, Matthew G., Kretzler, Matthias, and Ju, Wenjun

Published
2020
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26. Glomerular Elasticity and Gene Expression Patterns Define Two Phases of Alport Nephropathy

Author

Yoon, Joonho, primary, Liu, Zhenan, additional, Alaba, Matthew, additional, Bruggeman, Leslie A., additional, Janmey, Paul A., additional, Arana, Carlos A., additional, Ayenuyo, Oluwatoyosi, additional, Medeiros, Isabela, additional, Eddy, Sean, additional, Kretzler, Matthias, additional, Henderson, Joel M., additional, Naik, Abhijit, additional, Chang, Audrey N., additional, and Miller, R. Tyler, additional

Published
2024
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27. Rationale and design of the Nephrotic Syndrome Study Network (NEPTUNE) Match in glomerular diseases: designing the right trial for the right patient, today

Author

Trachtman, Howard, primary, Desmond, Hailey, additional, Williams, Amanda L., additional, Mariani, Laura H., additional, Eddy, Sean, additional, Ju, Wenjun, additional, Barisoni, Laura, additional, Ascani, Heather K., additional, Uhlmann, Wendy R., additional, Spino, Cathie, additional, Holzman, Lawrence B., additional, Sedor, John R., additional, Gadegbeku, Crystal, additional, Subramanian, Lalita, additional, Lienczewski, Chrysta C., additional, Manieri, Tina, additional, Roberts, Scott J., additional, Gipson, Debbie S., additional, Kretzler, Matthias, additional, Massengill, Susan, additional, Lo, Layla, additional, Dell, Katherine, additional, O’Toole, John, additional, Sedor, John, additional, Martin, Blair, additional, Macumber, Ian, additional, Sharma, Silpa, additional, Srivastava, Tarak, additional, Markus, Kelsey, additional, Sethna, Christine, additional, Vento, Suzanne, additional, Canetta, Pietro, additional, Olabisi, Opeyemi, additional, Gbadegesin, Rasheed, additional, Smith, Maurice, additional, Greenbaum, Laurence, additional, Wang, Chia-shi, additional, Yun, Emily, additional, Adler, Sharon, additional, LaPage, Janine, additional, Amarah, Amatur, additional, Itteera, Mathew, additional, Atkinson, Meredith, additional, Williams, Miahje, additional, Lieske, John, additional, Hogan, Marie, additional, Fervenza, Fernando, additional, Selewski, David, additional, Alston, Cheryl, additional, Reidy, Kim, additional, Ross, Michael, additional, Kaskel, Frederick, additional, Flynn, Patricia, additional, Malaga-Dieguez, Laura, additional, Zhdanova, Olga, additional, Pehrson, Laura Jane, additional, Miranda, Melanie, additional, Almaani, Salem, additional, Roberts, Laci, additional, Lafayette, Richard, additional, Dave, Shiktij, additional, Lee, Iris, additional, Shah, Shweta, additional, Batla, Sadaf, additional, Reich, Heather, additional, Hladunewich, Michelle, additional, Ling, Paul, additional, Romano, Martin, additional, Brakeman, Paul, additional, Dylewski, James, additional, Rogers, Nathan, additional, McCarthy, Ellen, additional, Creed, Catherine, additional, Fornoni, Alessia, additional, Bandes, Miguel, additional, Mariani, Laura, additional, Modi, Zubin, additional, Williams, A., additional, Ni, Roxy, additional, Nachman, Patrick, additional, Rheault, Michelle, additional, Kowalski, Amy, additional, Rauwolf, Nicolas, additional, Derebail, Vimal, additional, Gibson, Keisha, additional, Froment, Anne, additional, Kelley, Sara, additional, Holzman, Lawrence, additional, Meyers, Kevin, additional, Kallem, Krishna, additional, Edwards, Aliya, additional, Sharma, Samin, additional, Roehm, Elizabeth, additional, Sambandam, Kamalanathan, additional, Brown, Elizabeth, additional, Hellewege, Jamie, additional, Jefferson, Ashley, additional, Hingorani, Sangeeta, additional, Tuttle, Katherine, additional, Manahan, Linda, additional, Pao, Emily, additional, Kuykendall, Kelli, additional, Lin, Jen Jar, additional, Dharnidharka, Vikas, additional, Gillespie, Brenda, additional, Salmon, Eloise, additional, Trachtman, Howard, additional, Mainieri, Tina, additional, Alter, Gabrielle, additional, Arbit, Michael, additional, Fermin, Damian, additional, Larkina, Maria, additional, Lienczewski, Chrysta, additional, Scherr, Rebecca, additional, Troost, Jonathan, additional, Williams, Amanda, additional, Zhai, Yan, additional, Kincaid, Colleen, additional, Li, Shengqian, additional, Li, Shannon, additional, Sampson, Matthew G., additional, Smith, Abigail, additional, Zee, Jarcy, additional, Avila-Casado, Carmen, additional, Bagnasco, Serena, additional, Bu, Lihong, additional, Caltharp, Shelley, additional, Cassol, Clarissa, additional, Demeke, Dawit, additional, Hassler, Jared, additional, Herlitz, Leal, additional, Hewitt, Stephen, additional, Hodgin, Jeff, additional, Holanda, Danni, additional, Kambham, Neeraja, additional, Lemley, Kevin, additional, Messias, Nidia, additional, Mikhailov, Alexei, additional, Moreno, Vanessa, additional, Najafian, Behzad, additional, Palmer, Matthew, additional, Rosenberg, Avi, additional, Royal, Virginie, additional, Sekulik, Miroslav, additional, Stokes, Barry, additional, Thomas, David, additional, Wu, Ming, additional, Yamashita, Michifumi, additional, Yin, Hong, additional, Zuo . Cochairs, Yiqin, additional, and Nast, Cynthia, additional

Published
2024
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28. Epigenomic landscapes of retinal rods and cones.

Author

Mo, Alisa, Luo, Chongyuan, Davis, Fred P, Mukamel, Eran A, Henry, Gilbert L, Nery, Joseph R, Urich, Mark A, Picard, Serge, Lister, Ryan, Eddy, Sean R, Beer, Michael A, Ecker, Joseph R, and Nathans, Jeremy

Subjects
Animals, Mice, Histones, Transcription Factors, DNA, Gene Expression Profiling, Epigenesis, Genetic, Methylation, Retinal Rod Photoreceptor Cells, Retinal Cone Photoreceptor Cells, DNA methylation, chromatin, evolutionary biology, genomics, mouse, neuroscience, retinal development, retinal photoreceptors, transcription factors, Epigenesis, Genetic, Biochemistry and Cell Biology
Abstract

Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.

Published
2016

29. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Author

Mo, Alisa, Mukamel, Eran A, Davis, Fred P, Luo, Chongyuan, Henry, Gilbert L, Picard, Serge, Urich, Mark A, Nery, Joseph R, Sejnowski, Terrence J, Lister, Ryan, Eddy, Sean R, Ecker, Joseph R, and Nathans, Jeremy

Subjects
Genetics, Biotechnology, Human Genome, Neurosciences, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Cell Nucleolus, Chromatin Immunoprecipitation, DNA Methylation, Epigenomics, Gene Expression Profiling, Gene Expression Regulation, Developmental, Green Fluorescent Proteins, Mice, Mice, Transgenic, Microtubule-Associated Proteins, Neocortex, Nerve Tissue Proteins, Neurons, Proto-Oncogene Proteins c-myc, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.

Published
2015

31. Protein N-Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease

Author

Veličković, Dušan, Shapiro, John P., Parikh, Samir V., Rovin, Brad, Toto, Robert D., Vazquez, Miguel A., Poggio, Emilio D., O'Toole, John F., Sedor, John R., Alexandrov, Theodore, Jain, Sanjay, Bitzer, Markus, Hodgin, Jeffrey, Veličković, Marija, Sharma, Kumar, Anderton, Christopher R., Adeyi, Oyedele A., Alakwaa, Fadhl, Alexandrov, Theodore, Allen, Jamie L., Alpers, Charles E., Alvear, Alison Bunio, Ambekar, Akhil, Ancheta, Joed, Anderton, Christopher R., Angus, Sophia A., Anjani, Kavya, Appelbaum, Paul S., Ardayfio, Joseph, Arora, Tanima, Ascani, Heather K., Asghari, Mahla, El-Achkar, Tarek M., Athar, Humra, Atta, Mohamed G., Aulisio, Mark P., Aw, Stephanie J., Azeloglu, Evren U., Bagne, Cathy A., Balderes, Olivia, Balis, Ulysses G.J., Barasch, Jonathan, Barisoni, Laura, Barwinska, Daria, Basta, Jeannine, Bebiak, Jack, Beck, Laurence H., Berge, Jerica M., Berglund, Ashley C., Bernard, Lauren, Berry, Brooke, Beyda, David H., Bhanushali, Jini Ashok, Bitzer, Markus, Bjornstad, Petter, Blanc, Victoria M., Blank, Kristina N., Bledsoe, Sharon B., Bogen, Steve, Bomback, Andrew S., Bonevich, Nikole, Border, Samuel, Börner, Katy, Bowen, William S., Boys, Charlotte, Bracamonte, Erika R., Bream, Peter R., Brosius, Frank C., Brown, Keith D., Budiman, Tifanny, Bueckle, Andreas, Bui, J.T., James, T., Burg, Ashley R., Burgess, Adam, Bush, Lakeshia, Bush, William S., Cai, Qi, Calixte, Marie Florence, Cameron-Wheeler, Tashas, Campbell, Kirk N, Campbell, Taneisha, Campbell, Catherine, Campos, Baltazar, Canetta, Pietro A., Cantley, Lloyd G, Caramori, M. Luiza, Carmona-Powell, Eunice, Carson, Jonas M, Chan, Lili, Chen, Sarah W, Chen, Yijiang, Cheng, Ying-Hua, Bejarano, Maria Chilo, Choe, Kisurb, Cimino, James G., Coca, Steven G., Coleman, Alyson, Colley, Madeline E., Collie, Mary M., Colona, Mia R., Commander, Clayton W., Conlon, Kristine, Conser, Ninive, Cooperman, Leslie, Corona-Villalobos, Celia P., Crawford, Dana C., Creger, Nathan, Cuevas-Rios, Yarieli, D'Agati, Vivette ., Dagher, Pierre c., de Boer, Ian H., de Caestecker, M.P, de Cos, Marina, Gonçalves, Joana P., Dekker, Matthew, Demeke, Dawit, Dighe, Ashveena L, Ding, Yanli, Djambazova, Katerina V., Donohoe, Isabel, Dowd, Frederick, Drawz, P.E., Dufresne, Martin, Dull, Rachel, Dunn, Kenneth W., Duran, Daniel Damian, Eadon, Michael T, Eddy, Sean, Elder, Michele M, Fallegger, Robin, Farrow, Melissa A, Ferkowicz, Michael, Fine, Derek M., Flanagan, Siobhan M., Fogo, Agnes B., Fox, Monica L., Frey, Renee, Froment, Anne, Gaba, Ron C., Gadegbeku, Crystal A, Gaut, Joseph P., Gehlenborg, Nils, Geraghty, Molly C, Ghag, Reetika, Gilliam, Matthew, Ginley, Brandon, Gisch, Debora, Gordon, Ronald E., Gorman, Brittney L., Greka, Anna, Grewenow, Stephanie M., Gurung, Bhupendra Kumar, Guthrie, Leah, Hacohen, Nir, Haddad, Samuel, Hall, Daniel E., Hansen, Jens, Harindhanavudhi, Tasma, Hartman, John, Hayashi, Lynda, Haydak, Jonathan, He, John Cijiang, He, Yongqun, Hedayati, S. Susan, Henderson, Dori, Henderson, Joel M, Hendricks, Allen R, Henshaw, Asari, Herlitz, Leal, Hernandez, Jeanine, Herr, Bruce W., Himmelfarb, Jonathan, Hodgin, Jeffrey B., Hoofnagle, Andrew N, Horowitz, Carol R., Hsieh, E.W.Y., Huynh, Courtney, Iyengar, Ravi, Jain, Sanjay, Janowczyk, Andrew, Jeffers, Vivian, Jefferson, Nichole M., Jennette, J Charles, Johansen, Camille, Jolly, Stacey, Jones, Christopher J., Jones, Jennifer L., Jones, Kiasha, Joyeux, Cienn N., Ju, Wenjun, Judd, Audra M., Kakade, Vijayakumar R, Kakarla, Dhatri, Kaspari, Rachel R., Kaushal, Madhurima, Keefe, Nicole, Keller, Mark S., Kelley, Sara S., Kellum, John A., Kelly, K. J., Kelly, Tanika N., Kermani, Asra, Kiryluk, Krzysztof, Klett, Susan, Knight, Richard A., Knoten, Amanda, Koch, Gina, Koewler, Robert, Kretzler, Matthias, Kruse, Angela R.S., Küchenhoff, Leonie, Lake, Blue B., Lardenoije, Roy, Larson, Astrid, Larson, Brandon G, Lash, James P., Laszik, Zoltan G., Lecker, Stewart H., Lee, Simon C., Lee, Sora, Lefferts, Sean, Li, Xiang, Lienczewski, Chrysta C, Limonte, Christine P, Lucarelli, Nicholas, Lukowski, Jessica, Lutnick, Brendon, Ma, Shihong, Ma, Sisi, Madabhushi, Anant, Maikhor, Shana, Mao, Weiguang, Mariani, Laura H., Markovic, Marina, Marquez, Nicole, Marshall, Jamie L., McAdams, Meredith C, McClelland, Robyn L., McCown, Phillip J., McMahon, Gearoid Michael, McMurray, Amy, Mehl, Karla, Meliambro, Kristin, Ferreira, Ricardo Melo, Mendoza, Katherine, Menez, Steven, Menon, Rajasree, Meza, Natalie, Migas, Lukasz G., Miller, R. Tyler, Mimar, Sayat, Minor, Brittany C, Mody, Priya, Moeckel, Gilbert W., Moledina, D.G., Molina-Guzman, Jenny, Monroy-Trujillo, Jose M, Morales, Alexander, Moreno, Vanessa, Mottl, Amy K., Mukatash, Tariq, Munar, Dane, Murugan, Raghavan, Nachman, Patrick H., Nadkarni, Girish N, Naglah, Ahmed, Nair, Viji, Nam, Yunbi, Narasimhan, R., Nwanne, Gerald, O'Malley, Charles, O'Toole, John F., Toro, Fernanda Ochoa, Oliver, George (Holt), Onul, Ingrid F, Otto, Edgar A., Palevsky, Paul M., Palmer, Ellen, Pamreddy, Annapurna, Parikh, Chirag R., Parikh, Samir V, Park, Christopher, Park, Harold, Paša-Tolić, Ljiljana, Patel, Jiten, Patel, Marissa, Patlis, Boris S., Paul, Anindya S., Phuong, Jimmy, Pillai, Anil, Pinkeney, Roy, Plisiewicz, Alexa, Poggio, Emilio D, Pollack, Ari, Prasad, Pottumarthi V, Pyle, Laura, Quardokus, Ellen M., Quiroga, Arabela, Ragi, Nagarjunachary, Randhawa, Parmjeet, Randle, Teresa, Rao, Via, Rauchman, Michael, Rauwolf, Nicolas J, Reamy, Rebecca, Record, Elizabeth G., Redmond, Devona, Rennke, Helmut, Renteria, Amada, Rezaei, Kasra A, Rhodes, Rosamond, Ricardo, Ana C., Rice, Samuel, Rivera, Marcelino, Roberts, Glenda V., Rosas, R., Sylvia, E., Rose, Michael P., Rosen, Seymour, Rosenberg, Avi Z., Rosenberg, Michael S., Rosengart, Matthew R., Rovin, Brad H., Roy, Neil, Roy-Chaudhury, Prabir, Rubinsky, Melissa D., Sabo, Angela R., Saez-Rodriguez, Julio, Safadi, Sami, Samari, Imane H., Sanora, Ana Celina, Sarder, Pinaki, Sarkisova, Natalya, Sarwal, Minnie M, Saul, John, Saunders, Milda R., Schaub, Jennifer A., Schmidt, IM, Scott, Raymond, Scroggins, Aaron, Sealfon, Rachel S. G., Sedor, John R., Sendrey, Dianna, Setty, Suman, Shah, Sonya, Shariff, Saad Mohammed, Sharma, Kumar, Shaw, Melissa M., Sigdel, Tara K, Silva, Paolo S., Snyder, Jaime, Snyder, Michelle L., Spates-Harden, Kassandra, Sperati, C. John, Spraggins, Jeffrey M., Srivastava, Anand, Stashevsky, Jennifer, Steck, Becky, Stillman, Isaac E, Stutzke, Christy, Subramanian, Lalita, Sun, Jennifer K., Rajan, Sandhya Sundar, Sutton, Timothy A., Taliercio, Jonathan J, Tan, Roderick, Tanevski, Jovan, Thajudeen, Bijin, Thurman, Joshua M., Tokita, Joji, Torrealba, Jose R., Toto, Robert D, Tout, Haneen, Troyanskaya, Olga G, Tsosie, Rebecca, Turner, Jeffrey M, Tuttle, Katherine R., Ugwuowo, Ugochukwu, Upadhyay, Ashish, Valerius, M. Todd, Van de Plas, Raf, Varela, German, Vazquez, Miguel A., Velickovic, Dusan, Venkatachalam, Manjeri, Verdoes, Abraham, Verma, Ashish, Victoria-Castro, Angela M., Vijayan, Anitha, Villalobos, Alexander, Viloria, Noralinda B., Vinovskis, Carissa, Vita, Tina, Waikar, Sushrut S., Wang, Ashley R., Wang, Bangchen, Wang, Nancy, Wang, Ruikang, Wangperawong, Artit, Ward, Stephen C, Warfield, Curtis, Weins, Astrid, Wen, Natasha, Wen, Yumeng, Wilcox, Adam, Williams, James C., Williams, Kayleen, Williams, Mark E., Wilson, F. Perry, Winfree, Seth, Winters, James, Wofford, Stephanie, Wolf, Susan M., Wong, Aaron, Woodhead, Gregory, Wright, Devin M., Wright, Zach, Wright, Zoe, Wrobel, Julia, Xing, Fuyong, Xu, Alan, Yadati, Pranav, Ye, Hongping, Young, Bessie A., Yu, Guanghao, Mon-Wei Yu, Samuel, Zeinoun, Gabriel, Zeitler, Evan M., Zhang, Bo, Zhang, Guanshi, and Zhang, Yi

Published
2024
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32. Identification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms

Author

Tisch, Adam, primary, Madapoosi, Siddharth, additional, Blough, Stephen, additional, Rosa, Jan, additional, Eddy, Sean, additional, Mariani, Laura, additional, Naik, Abhijit, additional, Limonte, Christine, additional, Mccown, Philip, additional, Menon, Rajasree, additional, Rosas, Sylvia, additional, Parikh, Chirag, additional, Kretzler, Matthias, additional, Mahfouz, Ahmed, additional, and Alakwaa, Fadhl, additional

Published
2024
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33. Hydroxypropyl-β-cyclodextrin protects from kidney disease in experimental Alport syndrome and focal segmental glomerulosclerosis

Author

Mitrofanova, Alla, Molina, Judith, Varona Santos, Javier, Guzman, Johanna, Morales, Ximena A., Ducasa, G. Michelle, Bryn, Jonathan, Sloan, Alexis, Volosenco, Ion, Kim, Jin-Ju, Ge, Mengyuan, Mallela, Shamroop K., Kretzler, Matthias, Eddy, Sean, Martini, Sebastian, Wahl, Patricia, Pastori, Santiago, Mendez, Armando J., Burke, George W., Merscher, Sandra, and Fornoni, Alessia

Published
2018
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35. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome

Author

Sedor, John, Dell, Katherine, Schachere, Marleen, Lemley, Kevin, Whitted, Lauren, Srivastava, Tarak, Haney, Connie, Sethna, Christine, Grammatikopoulos, Kalliopi, Appel, Gerald, Toledo, Michael, Greenbaum, Laurence, Wang, Chia-shi, Lee, Brian, Adler, Sharon, Nast, Cynthia, LaPage, Janine, Athavale, Ambarish, Neu, Alicia, Boynton, Sara, Fervenza, Fernando, Hogan, Marie, Lieske, John C., Chernitskiy, Vladimir, Kaskel, Frederick, Kumar, Neelja, Flynn, Patricia, Kopp, Jeffrey, Castro-Rubio, Eveleyn, Blake, Jodi, Trachtman, Howard, Zhdanova, Olga, Modersitzki, Frank, Vento, Suzanne, Lafayette, Richard, Mehta, Kshama, Gadegbeku, Crystal, Johnstone, Duncan, Cattran, Daniel, Hladunewich, Michelle, Reich, Heather, Ling, Paul, Romano, Martin, Fornoni, Alessia, Barisoni, Laura, Bidot, Carlos, Kretzler, Matthias, Gipson, Debbie, Williams, Amanda, Pitter, Renee, Nachman, Patrick, Gibson, Keisha, Grubbs, Sandra, Froment, Anne, Holzman, Lawrence, Meyers, Kevin, Kallem, Krishna, Cerecino, Fumei, Sambandam, Kamal, Brown, Elizabeth, Johnson, Natalie, Jefferson, Ashley, Hingorani, Sangeeta, Tuttle, Kathleen, Curtin, Laura, Dismuke, S., Cooper, Ann, Freedman, Barry, Lin, Jen Jar, Gray, Stefanie, Barisoni, Larua, Gillespie, Brenda, Mariani, Laura, Sampson, Matthew G., Song, Peter, Troost, Johnathan, Zee, Jarcy, Herreshoff, Emily, Kincaid, Colleen, Lienczewski, Chrysta, Mainieri, Tina, Abbott, Kevin, Roy, Cindy, Urv, Tiina, Brooks, John, Gillies, Christopher E., Putler, Rosemary, Menon, Rajasree, Otto, Edgar, Yasutake, Kalyn, Nair, Viji, Hoover, Paul, Lieb, David, Li, Shuqiang, Eddy, Sean, Fermin, Damian, McNulty, Michelle T., Hacohen, Nir, Kiryluk, Krzysztof, and Wen, Xiaoquan

Published
2018
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37. A dynamic programming algorithm for RNA structure prediction including pseudoknots

Author

Rivas, Elena and Eddy, Sean R.

Subjects
Physics - Biological Physics, Quantitative Biology
Abstract

We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the algorithm is complex, which led us to adopt a useful graphical representation (Feynman diagrams) borrowed from quantum field theory. We present an implementation of the algorithm that generates the optimal minimum energy structure for a single RNA sequence, using standard RNA folding thermodynamic parameters augmented by a few parameters describing the thermodynamic stability of pseudoknots. We demonstrate the properties of the algorithm by using it to predict structures for several small pseudoknotted and non-pseudoknotted RNAs. Although the time and memory demands of the algorithm are steep, we believe this is the first algorithm to be able to fold optimal (minimum energy) pseudoknotted RNAs with the accepted RNA thermodynamic model., Comment: 34 pages, 18 figures. Uses LaTex and metapost

Published
1998

41. Rationale and design of the Nephrotic Syndrome Study Network (NEPTUNE) Match in glomerular diseases: designing the right trial for the right patient, today

Author

Massengill, Susan, Lo, Layla, Dell, Katherine, O’Toole, John, Sedor, John, Martin, Blair, Macumber, Ian, Sharma, Silpa, Srivastava, Tarak, Markus, Kelsey, Sethna, Christine, Vento, Suzanne, Canetta, Pietro, Olabisi, Opeyemi, Gbadegesin, Rasheed, Smith, Maurice, Greenbaum, Laurence, Wang, Chia-shi, Yun, Emily, Adler, Sharon, LaPage, Janine, Amarah, Amatur, Itteera, Mathew, Atkinson, Meredith, Williams, Miahje, Lieske, John, Hogan, Marie, Fervenza, Fernando, Selewski, David, Alston, Cheryl, Reidy, Kim, Ross, Michael, Kaskel, Frederick, Flynn, Patricia, Malaga-Dieguez, Laura, Zhdanova, Olga, Pehrson, Laura Jane, Miranda, Melanie, Almaani, Salem, Roberts, Laci, Lafayette, Richard, Dave, Shiktij, Lee, Iris, Shah, Shweta, Batla, Sadaf, Reich, Heather, Hladunewich, Michelle, Ling, Paul, Romano, Martin, Brakeman, Paul, Dylewski, James, Rogers, Nathan, McCarthy, Ellen, Creed, Catherine, Fornoni, Alessia, Bandes, Miguel, Kretzler, Matthias, Mariani, Laura, Modi, Zubin, Williams, A., Ni, Roxy, Nachman, Patrick, Rheault, Michelle, Kowalski, Amy, Rauwolf, Nicolas, Derebail, Vimal, Gibson, Keisha, Froment, Anne, Kelley, Sara, Holzman, Lawrence, Meyers, Kevin, Kallem, Krishna, Edwards, Aliya, Sharma, Samin, Roehm, Elizabeth, Sambandam, Kamalanathan, Brown, Elizabeth, Hellewege, Jamie, Jefferson, Ashley, Hingorani, Sangeeta, Tuttle, Katherine, Manahan, Linda, Pao, Emily, Kuykendall, Kelli, Lin, Jen Jar, Dharnidharka, Vikas, Gillespie, Brenda, Salmon, Eloise, Trachtman, Howard, Mainieri, Tina, Alter, Gabrielle, Arbit, Michael, Desmond, Hailey, Eddy, Sean, Fermin, Damian, Ju, Wenjun, Larkina, Maria, Lienczewski, Chrysta, Scherr, Rebecca, Troost, Jonathan, Williams, Amanda, Zhai, Yan, Kincaid, Colleen, Li, Shengqian, Li, Shannon, Gadegbeku, Crystal, Barisoni, Laura, Sampson, Matthew G., Smith, Abigail, Zee, Jarcy, Avila-Casado, Carmen, Bagnasco, Serena, Bu, Lihong, Caltharp, Shelley, Cassol, Clarissa, Demeke, Dawit, Hassler, Jared, Herlitz, Leal, Hewitt, Stephen, Hodgin, Jeff, Holanda, Danni, Kambham, Neeraja, Lemley, Kevin, Messias, Nidia, Mikhailov, Alexei, Moreno, Vanessa, Najafian, Behzad, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Sekulik, Miroslav, Stokes, Barry, Thomas, David, Wu, Ming, Yamashita, Michifumi, Yin, Hong, Zuo . Cochairs, Yiqin, Nast, Cynthia, Williams, Amanda L., Mariani, Laura H., Ascani, Heather K., Uhlmann, Wendy R., Spino, Cathie, Holzman, Lawrence B., Sedor, John R., Subramanian, Lalita, Lienczewski, Chrysta C., Manieri, Tina, Roberts, Scott J., and Gipson, Debbie S.

Published
2024
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47. Activation of Stimulator of IFN Genes (STING) Causes Proteinuria and Contributes to Glomerular Diseases

Author

Mitrofanova, Alla, primary, Fontanella, Antonio, additional, Tolerico, Matthew, additional, Mallela, Shamroop, additional, Molina David, Judith, additional, Zuo, Yiqin, additional, Boulina, Marcia, additional, Kim, Jin-Ju, additional, Santos, Javier, additional, Ge, Mengyuan, additional, Sloan, Alexis, additional, Issa, Wadih, additional, Gurumani, Margaret, additional, Pressly, Jeffrey, additional, Ito, Marie, additional, Kretzler, Matthias, additional, Eddy, Sean, additional, Nelson, Robert, additional, Merscher, Sandra, additional, Burke, George, additional, and Fornoni, Alessia, additional

Published
2022
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48. Local TNF causes NFATc1-dependent cholesterol-mediated podocyte injury

Author

Pedigo, Christopher E., Ducasa, Gloria Michelle, Leclercq, Farah, Sloan, Alexis, Mitrofanova, Alla, Hashmi, Tahreem, Molina-David, Judith, Ge, Mengyuan, Lassenius, Mariann I., Forsblom, Carol, Lehto, Markku, Groop, Per- Henrik, Kretzler, Matthias, Eddy, Sean, Martini, Sebastian, Reich, Heather, Wahl, Patricia, Ghiggeri, GianMarco, Faul, Christian, Burke, III, George W., Kretz, Oliver, Huber, Tobias B., Mendez, Armando J., Merscher, Sandra, and Fornoni, Alessia

Subjects
Inflammation -- Research -- Risk factors, Chronic diseases -- Research -- Care and treatment -- Complications and side effects, Tumor necrosis factor -- Research -- Influence, Apoptosis -- Analysis, Health care industry
Abstract

High levels of circulating TNF and its receptors, TNFR1 and TNFR2, predict the progression of diabetic kidney disease (DKD), but their contribution to organ damage in DKD remains largely unknown. Here, we investigated the function of local and systemic TNF in podocyte injury. We cultured human podocytes with sera collected from DKD patients, who displayed elevated TNF levels, and focal segmental glomerulosclerosis (FSGS) patients, whose TNF levels resembled those of healthy patients. Exogenous TNF administration or local TNF expression was equally sufficient to cause free cholesteroldependent apoptosis in podocytes by acting through a dual mechanism that required a reduction in ATP-binding cassette transporter A1-mediated (ABCA1-mediated) cholesterol efflux and reduced cholesterol esterification by sterol- O-acyltransferase 1 (SOAT1). TNF-induced albuminuria was aggravated in mice with podocyte-specific ABCA1 deficiency and was partially prevented by cholesterol depletion with cyclodextrin. TNF-stimulated free cholesterol-dependent apoptosis in podocytes was mediated by nuclear factor of activated T cells 1 (NFATc1). ABCA1 overexpression or cholesterol depletion was sufficient to reduce albuminuria in mice with podocyte-specific NFATc1 activation. Our data implicate an NFATc1/ ABCA1-dependent mechanism in which local TNF is sufficient to cause free cholesterol-dependent podocyte injury irrespective of TNF, TNFR1, or TNFR2 serum levels., Introduction Chronic low-grade inflammation and elevated TNF levels have been associated with several diseases, such as rheumatoid arthritis (1), multiple sclerosis (2), and atherosclerosis (3). However, the complex nature of [...]

Published
2016
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49. An integrated organoid omics map extends modeling potential of kidney disease

Author

Lassé, Moritz, primary, Eddy, Sean, additional, Saghir, Jamal El, additional, Fischer, Matthew, additional, Hutzfeldt, Arvid, additional, Berthier, Celine, additional, Bonin, Léna, additional, Dumoulin, Bernhard, additional, Menon, Rajasree, additional, Vega-Warner, Virginia, additional, Eichinger, Felix, additional, Alakwaa, Fadhl, additional, Fermin, Damian, additional, McCown, Phillip, additional, Godfrey, Bradley, additional, Brandts, Paul, additional, Ju, Wenjen, additional, Reinhard, Linda, additional, Hoxha, Elion, additional, Grahammer, Florian, additional, Lindenmeyer, Maja, additional, Huber, Tobias, additional, Schlüter, Hartmut, additional, Thiel, Steffen, additional, Mariani, Laura, additional, Kretzler, Matthias, additional, Demir, Fatih, additional, Harder, Jennifer, additional, and Rinschen, Markus, additional

Published
2022
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50. Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation

Author

Knight, Richard, Lecker, Stewart H., Stillman, Isaac, Bogen, Steve, Beck, Laurence H., Waikar, Sushrut, McMahon, Gearoid M., Weins, Astrid, Colona, Mia R., Hacohen, Nir, Hoover, Paul J., Aulisio, Mark, Bush, William S., Crawford, Dana C., O'toole, John, Poggio, Emilio, Sedor, John, Cooperman, Leslie, Jolly, Stacey, Herlitz, Leal, Nguyen, Jane, Gonzalez-Vicente, Agustin, Palmer, Ellen, Sendrey, Dianna, Vinovskis, Carissa, Bjornstad, Petter M., Appelbaum, Paul, Barasch, Jonathan M., Bomback, Andrew S., D'Agati, Vivette D., Kiryluk, Krzysztof, Mehl, Karla, Canetta, Pietro A., Shang, Ning, Balderes, Olivia, Kudose, Satoru, Bansal, Shweta, Alexandrov, Theodore, Rennke, Helmut, El-Achkar, Tarek M., Cheng, Yinghua, Dagher, Pierre C., Eadon, Michael T., Dunn, Kenneth W., Kelly, Katherine J., Sutton, Timothy A., Barwinska, Daria, Ferkowicz, Michael J., Winfree, Seth, Bledsoe, Sharon, Rivera, Marcelino, Williams, James C., Jr., Ferreira, Ricardo Melo, Parikh, Chirag R., Corona-Villalobos, Celia P., Menez, Steven, Rosenberg, Avi, Rosas, Sylvia E., Roy, Neil, Williams, Mark, Azeloglu, Evren U., He, Cijang, Iyengar, Ravi, Hansen, Jens, Xiong, Yuguang, Rovin, Brad, Parikh, Samir, Shapiro, John P., Anderton, Christopher R., Pasa-Tolic, Ljiljana, Velickovic, Dusan, Lukowski, Jessica, Oliver, George, Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Catherine E., Saul, John, Shpigel, Anna, Stutzke, Christy, Koewler, Robert, Campbell, Taneisha, Hayashi, Lynda, Jefferson, Nichole, Roberts, Glenda V., Pinkeney, Roy, Troyanskaya, Olga, Sealfon, Rachel, Tuttle, Katherine R., Goltsev, Yury, Zhang, Kun, Lake, Blue B., Laszik, Zoltan G., Nolan, Garry, Boada, Patrick, Sarwal, Minnie, Sigdel, Tara, Lee, Paul J., Alloway, Rita R., Woodle, E. Steve, Ascani, Heather, Balis, Ulysses G.J., Hodgin, Jeffrey B., Kretzler, Matthias, Lienczewski, Chrysta, Mariani, Laura H., Menon, Rajasree, Steck, Becky, He, Yougqun, Otto, Edgar, Schaub, Jennifer, Blanc, Victoria M., Eddy, Sean, Conser, Ninive C., Luo, Jinghui, Palevsky, Paul M., Rosengart, Matthew, Kellum, John A., Hall, Daniel E., Randhawa, Parmjeet, Tublin, Mitchell, Murugan, Raghavan, Elder, Michele M., Winters, James, Alpers, Charles E., Blank, Kristina N., Carson, Jonas, De Boer, Ian H., Dighe, Ashveena L., Himmelfarb, Jonathan, Mooney, Sean D., Shankland, Stuart, Williams, Kayleen, Park, Christopher, Dowd, Frederick, McClelland, Robyn L., Daniel, Stephen, Hoofnagle, Andrew N., Wilcox, Adam, Grewenow, Stephanie M., Sharma, Kumar, Venkatachalam, Manjeri, Zhang, Guanshi, Pamreddy, Annapurna, Ye, Hongping, Montellano, Richard, Toto, Robert D., Vazquez, Miguel, Lee, Simon C., Miller, R. Tyler, Moe, Orson W., Torrealba, Jose, Wang, Nancy, Kermani, Asra, Sambandam, Kamalanathan, Park, Harold, Hedayati, S. Susan, Lu, Christopher Y., Jain, Sanjay, Vijayan, Anitha, Gaut, Joseph P., Moledina, Dennis, Wilson, Francis P., Ugwuowo, Ugochukwu, Arora, Tanima, and D’Agati, Vivette D.

Published
2022
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