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1. Proteome Analysis for Inflammation Related to Acute and Convalescent Infection.

Author

Boada, Patrick, McDermott, Suzanne, Arlehamn, Cecilia, Murray, Kristy, Bockenstedt, Linda, Kerwin, Maggie, Harris, Eva, Stuart, Ken, Peters, Bjoern, Sesma, Ana, Montgomery, Ruth, Sigdel, Tara, Reed, Elaine, Sarwal, Minnie, and Sur, Swastika

Subjects
BK virus, CMV, Dengue, Lyme disease, Malaria, Pathogens, Proteomics, Tuberculosis, West Nile virus, Humans, Proteome, West Nile virus, Inflammation, Cytokines, Signal Transduction
Abstract

Infectious diseases are a significant burden in global healthcare. Pathogens engage with different host defense mechanisms. However, it is currently unknown if there are disease-specific immune signatures and/or if different pathogens elicit common immune-associated molecular entities to common therapeutic interventions. We studied patients enrolled through the Human Immunology Project Consortium (HIPC), which focuses on immune responses to various infections. Blood samples were collected and analyzed from patients during infection and follow-up time points at the convalescent stage. The study included samples from patients with Lyme disease (LD), tuberculosis (TB), malaria (MLA), dengue virus (DENV), and West Nile virus (WNV), as well as kidney transplant patients with cytomegalovirus (CMV) and polyomavirus (BKV) infections. Using an antibody-based assay, we quantified ~ 350 cell surface markers, cytokines, and chemokines involved in inflammation and immunity. Unique protein signatures were identified specific to the acute phase of infection irrespective of the pathogen type, with significant changes during convalescence. In addition, tumor necrosis factor receptor superfamily member 6 (TNR6), C-C Motif Chemokine Receptor 7 (CCR7), and C-C motif chemokine ligand-1 (CCL1) were increased in the acute and convalescent phases across all viral, bacterial, and protozoan compared to blood from healthy donors. Furthermore, despite the differences between pathogens, proteins were enriched in common biological pathways such as cell surface receptor signaling pathway and response to external stimulus. In conclusion, we demonstrated that irrespective of the pathogen type, there are common immunoregulatory and proinflammatory signals.

Published
2024

3. Plasma proteome perturbation for CMV DNAemia in kidney transplantation.

Author

Sigdel, Tara K, Boada, Patrick, Kerwin, Maggie, Rashmi, Priyanka, Gjertson, David, Rossetti, Maura, Sur, Swastika, Munar, Dane, Cimino, James, Ahn, Richard, Pickering, Harry, Sen, Subha, Parmar, Rajesh, Fatou, Benoit, Steen, Hanno, Schaenman, Joanna, Bunnapradist, Suphamai, Reed, Elaine F, Sarwal, Minnie M, and CMV Systems Immunobiology Group

Subjects
CMV Systems Immunobiology Group, Humans, Cytomegalovirus, Cytomegalovirus Infections, Proteome, Serpins, DNA, Viral, Kidney Transplantation, Proteomics, Infectious Diseases, Organ Transplantation, Biotechnology, Transplantation, Kidney Disease, Aetiology, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, 2.1 Biological and endogenous factors, Infection, Inflammatory and immune system, General Science & Technology
Abstract

BackgroundCytomegalovirus (CMV) infection, either de novo or as reactivation after allotransplantation and chronic immunosuppression, is recognized to cause detrimental alloimmune effects, inclusive of higher susceptibility to graft rejection and substantive impact on chronic graft injury and reduced transplant survival. To obtain further insights into the evolution and pathogenesis of CMV infection in an immunocompromised host we evaluated changes in the circulating host proteome serially, before and after transplantation, and during and after CMV DNA replication (DNAemia), as measured by quantitative polymerase chain reaction (QPCR).MethodsLC-MS-based proteomics was conducted on 168 serially banked plasma samples, from 62 propensity score-matched kidney transplant recipients. Patients were stratified by CMV replication status into 31 with CMV DNAemia and 31 without CMV DNAemia. Patients had blood samples drawn at protocol times of 3- and 12-months post-transplant. Additionally, blood samples were also drawn before and 1 week and 1 month after detection of CMV DNAemia. Plasma proteins were analyzed using an LCMS 8060 triple quadrupole mass spectrometer. Further, public transcriptomic data on time matched PBMCs samples from the same patients was utilized to evaluate integrative pathways. Data analysis was conducted using R and Limma.ResultsSamples were segregated based on their proteomic profiles with respect to their CMV Dnaemia status. A subset of 17 plasma proteins was observed to predict the onset of CMV at 3 months post-transplant enriching platelet degranulation (FDR, 4.83E-06), acute inflammatory response (FDR, 0.0018), blood coagulation (FDR, 0.0018) pathways. An increase in many immune complex proteins were observed at CMV infection. Prior to DNAemia the plasma proteome showed changes in the anti-inflammatory adipokine vaspin (SERPINA12), copper binding protein ceruloplasmin (CP), complement activation (FDR = 0.03), and proteins enriched in the humoral (FDR = 0.01) and innate immune responses (FDR = 0.01).ConclusionPlasma proteomic and transcriptional perturbations impacting humoral and innate immune pathways are observed during CMV infection and provide biomarkers for CMV disease prediction and resolution. Further studies to understand the clinical impact of these pathways can help in the formulation of different types and duration of anti-viral therapies for the management of CMV infection in the immunocompromised host.

Published
2023

4. Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection

Author

Lamarthée, Baptiste, Callemeyn, Jasper, Van Herck, Yannick, Antoranz, Asier, Anglicheau, Dany, Boada, Patrick, Becker, Jan Ulrich, Debyser, Tim, De Smet, Frederik, De Vusser, Katrien, Eloudzeri, Maëva, Franken, Amelie, Gwinner, Wilfried, Koshy, Priyanka, Kuypers, Dirk, Lambrechts, Diether, Marquet, Pierre, Mathias, Virginie, Rabant, Marion, Sarwal, Minnie M., Senev, Aleksandar, Sigdel, Tara K., Sprangers, Ben, Thaunat, Olivier, Tinel, Claire, Van Brussel, Thomas, Van Craenenbroeck, Amaryllis, Van Loon, Elisabet, Vaulet, Thibaut, Bosisio, Francesca, and Naesens, Maarten

Published
2023
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5. Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney

Author

Rashmi, Priyanka, Sur, Swastika, Sigdel, Tara K, Boada, Patrick, Schroeder, Andrew W, Damm, Izabella, Kretzler, Matthias, Hodgin, Jeff, Hartoularos, George, Ye, Chun Jimmie, Sarwal, Minnie M, and Project, For The Kidney Precision Medicine

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Immunology, Kidney Disease, Transplantation, Biotechnology, Organ Transplantation, Underpinning research, 1.1 Normal biological development and functioning, Renal and urogenital, Allografts, Endothelial Cells, Graft Rejection, Humans, Kidney, Kidney Transplantation, basic (laboratory) research, science, kidney (allograft) function, dysfunction, kidney biology, kidney transplantation, nephrology, rejection, translational research, Kidney Precision Medicine Project, basic (laboratory) research/science, kidney (allograft) function/dysfunction, kidney transplantation/nephrology, translational research/science, Medical and Health Sciences, Surgery, Clinical sciences
Abstract

Maintenance of systemic homeostasis by kidney requires the coordinated response of diverse cell types. The use of single-cell RNA sequencing (scRNAseq) for patient tissue samples remains fraught with difficulties with cell isolation, purity, and experimental bias. The ability to characterize immune and parenchymal cells during transplant rejection will be invaluable in defining transplant pathology where tissue availability is restricted to needle biopsy fragments. Herein, we present feasibility data for multiplexing approach for droplet scRNAseq (Mux-Seq). Mux-Seq has the potential to minimize experimental batch bias and variation even with very small sample input. In this first proof-of-concept study for this approach, explant tissues from six normal and two transplant recipients after multiple early post-transplant rejection episodes leading to nephrectomy due to aggressive antibody mediated rejection, were pooled for Mux-Seq. A computational tool, Demuxlet was applied for demultiplexing the individual cells from the pooled experiment. Each sample was also applied individually in a single microfluidic run (singleplex) to correlate results with the pooled data from the same sample. Our applied protocol demonstrated that data from Mux-Seq correlated highly with singleplex (Pearson coefficient 0.982) sequencing results, with the ability to identify many known and novel kidney cell types including different infiltrating immune cells. Trajectory analysis of proximal tubule and endothelial cells demonstrated separation between healthy and injured kidney from transplant explant suggesting evolving stages of cell- specific differentiation in alloimmune injury. This study provides the technical groundwork for understanding the pathogenesis of alloimmune injury and host tissue response in transplant rejection and normal human kidney and provides a protocol for optimized processing precious and low input human kidney biopsy tissue for larger scale studies.

Published
2022

6. 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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7. FcER1: A Novel Molecule Implicated in the Progression of Human Diabetic Kidney Disease

Author

Sur, Swastika, Nguyen, Mark, Boada, Patrick, Sigdel, Tara K, Sollinger, Hans, and Sarwal, Minnie M

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Kidney Disease, Biotechnology, Diabetes, Genetics, Aetiology, 2.1 Biological and endogenous factors, Metabolic and endocrine, Renal and urogenital, Adult, Aged, Cohort Studies, Diabetic Nephropathies, Disease Progression, Female, Gene Expression Profiling, Gene Regulatory Networks, Humans, Immunohistochemistry, Kidney, Leukocytes, Mononuclear, Male, Middle Aged, Oligonucleotide Array Sequence Analysis, Receptors, IgE, Signal Transduction, diabetes, DKD, FcER1, chronic kidney disease, mast cells, Immunology, Medical Microbiology, Biochemistry and cell biology
Abstract

Diabetic kidney disease (DKD) is a key microvascular complication of diabetes, with few therapies for targeting renal disease pathogenesis and progression. We performed transcriptional and protein studies on 103 unique blood and kidney tissue samples from patients with and without diabetes to understand the pathophysiology of DKD injury and its progression. The study was based on the use of 3 unique patient cohorts: peripheral blood mononuclear cell (PBMC) transcriptional studies were conducted on 30 patients with DKD with advancing kidney injury; Gene Expression Omnibus (GEO) data was downloaded, containing transcriptional measures from 51 microdissected glomerulous from patients with DKD. Additionally, 12 independent kidney tissue sections from patients with or without DKD were used for validation of target genes in diabetic kidney injury by kidney tissue immunohistochemistry and immunofluorescence. PBMC DKD transcriptional analysis, identified 853 genes (p < 0.05) with increasing expression with progression of albuminuria and kidney injury in patients with diabetes. GEO data was downloaded, normalized, and analyzed for significantly changed genes. Of the 325 significantly up regulated genes in DKD glomerulous (p < 0.05), 28 overlapped in PBMC and diabetic kidney, with perturbed FcER1 signaling as a significantly enriched canonical pathway. FcER1 was validated to be significantly increased in advanced DKD, where it was also seen to be specifically co-expressed in the kidney biopsy with tissue mast cells. In conclusion, we demonstrate how leveraging public and private human transcriptional datasets can discover and validate innate immunity and inflammation as key mechanistic pathways in DKD progression, and uncover FcER1 as a putative new DKD target for rational drug design.

Published
2021

8. 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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12. Proteome Analysis for Inflammation Related to Acute and Convalescent Infection

Author

Sigdel, Tara K., primary, Sur, Swastika, additional, Boada, Patrick, additional, McDermott, Suzanne M., additional, Arlehamn, Cecilia S. Lindestam, additional, Murray, Kristy O., additional, Bockenstedt, Linda K., additional, Kerwin, Maggie, additional, Reed, Elaine F., additional, Harris, Eva, additional, Stuart, Ken, additional, Peters, Bjoern, additional, Sesma, Ana, additional, Montgomery, Ruth R., additional, and Sarwal, Minnie M., additional

Published
2023
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13. Bone marrow from focal segmental glomerulosclerosis displays activation of inflammatory pathway

Author

Rashmi, Priyanka, primary, Boada, Patrick, additional, Soni, Arvind, additional, Sigdel, Tara K, additional, Rychkov, Dmitry, additional, Hahm, Eunsil, additional, Da Silva, Andrea Alice, additional, Damm, Izabella, additional, Paul, Rohan, additional, Vincenti, Flavio, additional, Ye, Jimmie, additional, Reiser, Jochen, additional, wolf, Jeffrey, additional, and Sarwal, Minnie M., additional

Published
2023
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14. Longitudinal serum proteomics analyses identify unique and overlapping host response pathways in Lyme disease and West Nile virus infection

Author

Boada, Patrick, primary, Fatou, Benoit, additional, Belperron, Alexia A., additional, Sigdel, Tara K., additional, Smolen, Kinga K., additional, Wurie, Zainab, additional, Levy, Ofer, additional, Ronca, Shannon E., additional, Murray, Kristy O., additional, Liberto, Juliane M., additional, Rashmi, Priyanka, additional, Kerwin, Maggie, additional, Montgomery, Ruth R., additional, Bockenstedt, Linda K., additional, Steen, Hanno, additional, and Sarwal, Minnie M., additional

Published
2022
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15. 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

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

Published
2022
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16. 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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17. Cover, Volume 43, Issue 2

Author

Sarafrazi, Soodabeh, primary, Daugherty, Sean C., additional, Miller, Nicole, additional, Boada, Patrick, additional, Carpenter, Thomas O., additional, Chunn, Lauren, additional, Dill, Kariena, additional, Econs, Michael J., additional, Eisenbeis, Scott, additional, Imel, Erik A., additional, Johnson, Britt, additional, Kiel, Mark J., additional, Krolczyk, Stan, additional, Ramesan, Prameela, additional, Truty, Rebecca, additional, and Sabbagh, Yves, additional

Published
2022
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18. Novel PHEX gene locus‐specific database: Comprehensive characterization of vast number of variants associated with X‐linked hypophosphatemia (XLH)

Author

Sarafrazi, Soodabeh, primary, Daugherty, Sean C., additional, Miller, Nicole, additional, Boada, Patrick, additional, Carpenter, Thomas O., additional, Chunn, Lauren, additional, Dill, Kariena, additional, Econs, Michael J., additional, Eisenbeis, Scott, additional, Imel, Erik A., additional, Johnson, Britt, additional, Kiel, Mark J., additional, Krolczyk, Stan, additional, Ramesan, Prameela, additional, Truty, Rebecca, additional, and Sabbagh, Yves, additional

Published
2021
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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

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

Published
2021
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21. A comprehensive locus specific database of PHEX gene variants associated with X-linked hypophosphatemia vastly increases the number of known variants

Author

Miller, Nicole, primary, Daugherty, Sean, additional, Sarafrazi, Soodabeh, additional, Boada, Patrick, additional, Carpenter, Thomas, additional, Chunn, Lauren, additional, Econs, Michael, additional, Eisenbeis, Scott, additional, Imel, Erik, additional, Johnson, Britt, additional, Kiel, Mark, additional, Krolczyk, Stan, additional, Ramesan, Prameela, additional, Truty, Rebecca, additional, and Sabbagh, Yves, additional

Published
2021
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22. Novel PHEX gene locus‐specific database: Comprehensive characterization of vast number of variants associated with X‐linked hypophosphatemia (XLH).

Author

Sarafrazi, Soodabeh, Daugherty, Sean C., Miller, Nicole, Boada, Patrick, Carpenter, Thomas O., Chunn, Lauren, Dill, Kariena, Econs, Michael J., Eisenbeis, Scott, Imel, Erik A., Johnson, Britt, Kiel, Mark J., Krolczyk, Stan, Ramesan, Prameela, Truty, Rebecca, and Sabbagh, Yves

Abstract

X‐linked hypophosphatemia (XLH), the most common form of hereditary hypophosphatemia, is caused by disrupting variants in the PHEX gene, located on the X chromosome. XLH is inherited in an X‐linked pattern with complete penetrance observed for both males and females. Patients experience lifelong symptoms resulting from chronic hypophosphatemia, including impaired bone mineralization, skeletal deformities, growth retardation, and diminished quality of life. This chronic condition requires life‐long management with disease‐specific therapies, which can improve patient outcomes especially when initiated early in life. To centralize and disseminate PHEX variant information, we have established a new PHEX gene locus‐specific database, PHEX LSDB. As of April 30, 2021, 870 unique PHEX variants, compiled from an older database of PHEX variants, a comprehensive literature search, a sponsored genetic testing program, and XLH clinical trials, are represented in the PHEX LSDB. This resource is publicly available on an interactive, searchable website (https://www.rarediseasegenes.com/), which includes a table of variants and associated data, graphical/tabular outputs of genotype‐phenotype analyses, and an online submission form for reporting new PHEX variants. The database will be updated regularly with new variants submitted on the website, identified in the published literature, or shared from genetic testing programs. [ABSTRACT FROM AUTHOR]

Published
2022
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23. Acute and Chronic Changes in Gene Expression After CMV DNAemia in Kidney Transplant Recipients.

Author

Ahn, Richard, Schaenman, Joanna, Qian, Zachary, Pickering, Harry, Groysberg, Victoria, Rossetti, Maura, Llamas, Megan, Hoffmann, Alexander, Gjertson, David, Deng, Mario, Bunnapradist, Suphamai, Reed, Elaine F., Arakawa-Hoyt, Janice, Boada, Patrick, Brook, Jenny, Cimino, Jim, Damm, Izabella, Datta, Nakul, Diamond, Don J., and Doung, Tin

Subjects
KIDNEY transplantation, GENE expression, BK virus, CYTOTOXIC T cells, CYTOMEGALOVIRUS diseases, CELLULAR signal transduction
Abstract

Cytomegalovirus (CMV) viremia continues to cause significant morbidity and mortality in kidney transplant patients with clinical complications including organ rejection and death. Whole blood gene expression dynamics in CMV viremic patients from onset of DNAemia through convalescence has not been well studied to date in humans. To evaluate how CMV infection impacts whole blood leukocyte gene expression over time, we evaluated a matched cohort of 62 kidney transplant recipients with and without CMV DNAemia using blood samples collected at multiple time points during the 12-month period after transplant. While transcriptomic differences were minimal at baseline between DNAemic and non-DNAemic patients, hundreds of genes were differentially expressed at the long-term timepoint, including genes enriching for pathways important for macrophages, interferon, and IL-8 signaling. Amongst patients with CMV DNAemia, the greatest amount of transcriptomic change occurred between baseline and 1-week post-DNAemia, with increase in pathways for interferon signaling and cytotoxic T cell function. Time-course gene set analysis of these differentially expressed genes revealed that most of the enriched pathways had a significant time-trend. While many pathways that were significantly down- or upregulated at 1 week returned to baseline-like levels, we noted that several pathways important in adaptive and innate cell function remained upregulated at the long-term timepoint after resolution of CMV DNAemia. Differential expression analysis and time-course gene set analysis revealed the dynamics of genes and pathways involved in the immune response to CMV DNAemia in kidney transplant patients. Understanding transcriptional changes caused by CMV DNAemia may identify the mechanism behind patient vulnerability to CMV reactivation and increased risk of rejection in transplant recipients and suggest protective strategies to counter the negative immunologic impact of CMV. These findings provide a framework to identify immune correlates for risk assessment and guiding need for extending antiviral prophylaxis. [ABSTRACT FROM AUTHOR]

Published
2021
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24. eP202 - A comprehensive locus specific database of PHEX gene variants associated with X-linked hypophosphatemia vastly increases the number of known variants.

Author

Miller, Nicole, Daugherty, Sean, Sarafrazi, Soodabeh, Boada, Patrick, Carpenter, Thomas, Chunn, Lauren, Econs, Michael, Eisenbeis, Scott, Imel, Erik, Johnson, Britt, Kiel, Mark, Krolczyk, Stan, Ramesan, Prameela, Truty, Rebecca, and Sabbagh, Yves

Subjects
*GENES, *HYPOPHOSPHATEMIA, *DATABASES, *LOCUS (Genetics)
Published
2021
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