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18 results on '"Tarashansky, Alexander J."'

4. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Author

Musser, Jacob M., primary, Schippers, Klaske J., additional, Nickel, Michael, additional, Mizzon, Giulia, additional, Kohn, Andrea B., additional, Pape, Constantin, additional, Ronchi, Paolo, additional, Papadopoulos, Nikolaos, additional, Tarashansky, Alexander J., additional, Hammel, Jörg U., additional, Wolf, Florian, additional, Liang, Cong, additional, Hernández-Plaza, Ana, additional, Cantalapiedra, Carlos P., additional, Achim, Kaia, additional, Schieber, Nicole L., additional, Pan, Leslie, additional, Ruperti, Fabian, additional, Francis, Warren R., additional, Vargas, Sergio, additional, Kling, Svenja, additional, Renkert, Maike, additional, Polikarpov, Maxim, additional, Bourenkov, Gleb, additional, Feuda, Roberto, additional, Gaspar, Imre, additional, Burkhardt, Pawel, additional, Wang, Bo, additional, Bork, Peer, additional, Beck, Martin, additional, Schneider, Thomas R., additional, Kreshuk, Anna, additional, Wörheide, Gert, additional, Huerta-Cepas, Jaime, additional, Schwab, Yannick, additional, Moroz, Leonid L., additional, and Arendt, Detlev, additional

Published
2021
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5. A cell atlas of the fly kidney

Author

Xu, Jun, primary, Liu, Yifang, additional, Li, Hongjie, additional, Tarashansky, Alexander J., additional, Kalicki, Colin H., additional, Hung, Ruei-Jiun, additional, Hu, Yanhui, additional, Comjean, Aram, additional, Kolluru, Sai Saroja, additional, Wang, Bo, additional, Quake, Stephen R, additional, Luo, Liqun, additional, McMahon, Andrew P., additional, Dow, Julian A.T., additional, and Perrimon, Norbert, additional

Published
2021
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7. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Author

Huerta-Cepas, Jaime [0000-0003-4195-5025], Hernández-Plaza, Ana, Musser, Jacob M., Schippers, Klaske J., Nickel, Michael, Mizzon, Giulia, Kohn, Andrea B., Pape, Constantin, Ronchi, Paolo, Papadopoulos, Nikolaos, Tarashansky, Alexander J., Hammel, Jörg U., Wolf, Florian, Liang, Cong, Cantalapiedra, Carlos P, Achim, Kaia, Schieber, Nicole L., Pan, Leslie, Ruperti, Fabian, Francis, Warren R., Vargas, Sergio, Kling, Svenja, Renkert, Maike, Polikarpov, Maxim, Bourenkov, Gleb, Feuda, Roberto, Gaspar, Imre, Burkhardt, Pawel, Wang, Bo, Bork, Peer, Beck, Martin, Schneider, Thomas R., Kreshuk, Anna, Wörheide, Gert, Huerta-Cepas, Jaime, Moroz, Leonid L., Arendt, Detlev, Huerta-Cepas, Jaime [0000-0003-4195-5025], Hernández-Plaza, Ana, Musser, Jacob M., Schippers, Klaske J., Nickel, Michael, Mizzon, Giulia, Kohn, Andrea B., Pape, Constantin, Ronchi, Paolo, Papadopoulos, Nikolaos, Tarashansky, Alexander J., Hammel, Jörg U., Wolf, Florian, Liang, Cong, Cantalapiedra, Carlos P, Achim, Kaia, Schieber, Nicole L., Pan, Leslie, Ruperti, Fabian, Francis, Warren R., Vargas, Sergio, Kling, Svenja, Renkert, Maike, Polikarpov, Maxim, Bourenkov, Gleb, Feuda, Roberto, Gaspar, Imre, Burkhardt, Pawel, Wang, Bo, Bork, Peer, Beck, Martin, Schneider, Thomas R., Kreshuk, Anna, Wörheide, Gert, Huerta-Cepas, Jaime, Moroz, Leonid L., and Arendt, Detlev

Abstract

The evolutionary origin of metazoan cell types such as neurons and muscles is not known. Using whole-body single-cell RNA sequencing in a sponge, an animal without nervous system and musculature, we identified 18 distinct cell types. These include nitric oxide-sensitive contractile pinacocytes, amoeboid phagocytes, and secretory neuroid cells that reside in close contact with digestive choanocytes that express scaffolding and receptor proteins. Visualizing neuroid cells by correlative x-ray and electron microscopy revealed secretory vesicles and cellular projections enwrapping choanocyte microvilli and cilia. Our data show a communication system that is organized around sponge digestive chambers, using conserved modules that became incorporated into the pre- and postsynapse in the nervous systems of other animals.

Published
2021

9. Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing.

Author

Jun Xu, Yifang Liu, Hongjie Li, Tarashansky, Alexander J., Kalicki, Colin H., Ruei-Jiun Hung, Yanhui Hu, Comjean, Aram, Kolluru, Sai Saroja, Bo Wang, Quake, Stephen R., Liqun Luo, McMahon, Andrew P., Dow, Julian A. T., and Perrimon, Norbert

Subjects
GUANINE nucleotide exchange factors, HEPATOCYTE nuclear factors, RNA sequencing, KIDNEY physiology, EXCHANGE, CELL morphology
Abstract

Recent advances in single-cell sequencing provide a unique opportunity to gain novel insights into the diversity, lineage, and functions of cell types constituting a tissue/organ. Here, we performed a single-nucleus study of the adult Drosophila renal system, consisting of Malpighian tubules and nephrocytes, which shares similarities with the mammalian kidney. We identified 11 distinct clusters representing renal stem cells, stellate cells, regionally specific principal cells, garland nephrocyte cells, and pericardial nephrocytes. Characterization of the transcription factors specific to each cluster identified fruitless (fru) as playing a role in stem cell regeneration and Hepatocyte nuclear factor 4 (Hnf4) in regulating glycogen and triglyceride metabolism. In addition, we identified a number of genes, including Rho guanine nucleotide exchange factor at 64C (RhoGEF64c), Frequenin 2 (Frq2), Prip, and CG1093 that are involved in regulating the unusual star shape of stellate cells. Importantly, the single-nucleus dataset allows visualization of the expression at the organ level of genes involved in ion transport and junctional permeability, providing a systems-level view of the organization and physiological roles of the tubules. Finally, a cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia, knowledge that will help the generation of kidney disease models. Altogether, our study provides a comprehensive resource for studying the fly kidney. [ABSTRACT FROM AUTHOR]

Published
2022
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10. A Cell Atlas of the Fly Kidney

Author

Xi, Jun, primary, Liu, Yifang, additional, Li, Hongjie, additional, Tarashansky, Alexander J., additional, Kalicki, Colin H., additional, Hung, Ruei-Jiun, additional, Hu, Yanhui, additional, Comjean, Aram, additional, Kolluru, Sai Saroja, additional, Wang, Bo, additional, Quake, Stephen R., additional, Luo, Liqun, additional, McMahon, Andrew P., additional, Dow, Julian A.T., additional, and Perrimon, Norbert, additional

Published
2021
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17. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Author

Jones RC, Karkanias J, Krasnow MA, Pisco AO, Quake SR, Salzman J, Yosef N, Bulthaup B, Brown P, Harper W, Hemenez M, Ponnusamy R, Salehi A, Sanagavarapu BA, Spallino E, Aaron KA, Concepcion W, Gardner JM, Kelly B, Neidlinger N, Wang Z, Crasta S, Kolluru S, Morri M, Tan SY, Travaglini KJ, Xu C, Alcántara-Hernández M, Almanzar N, Antony J, Beyersdorf B, Burhan D, Calcuttawala K, Carter MM, Chan CKF, Chang CA, Chang S, Colville A, Culver RN, Cvijović I, D'Amato G, Ezran C, Galdos FX, Gillich A, Goodyer WR, Hang Y, Hayashi A, Houshdaran S, Huang X, Irwin JC, Jang S, Juanico JV, Kershner AM, Kim S, Kiss B, Kong W, Kumar ME, Kuo AH, Li B, Loeb GB, Lu WJ, Mantri S, Markovic M, McAlpine PL, de Morree A, Mrouj K, Mukherjee S, Muser T, Neuhöfer P, Nguyen TD, Perez K, Puluca N, Qi Z, Rao P, Raquer-McKay H, Schaum N, Scott B, Seddighzadeh B, Segal J, Sen S, Sikandar S, Spencer SP, Steffes LC, Subramaniam VR, Swarup A, Swift M, Van Treuren W, Trimm E, Veizades S, Vijayakumar S, Vo KC, Vorperian SK, Wang W, Weinstein HNW, Winkler J, Wu TTH, Xie J, Yung AR, Zhang Y, Detweiler AM, Mekonen H, Neff NF, Sit RV, Tan M, Yan J, Bean GR, Charu V, Forgó E, Martin BA, Ozawa MG, Silva O, Toland A, Vemuri VNP, Afik S, Awayan K, Botvinnik OB, Byrne A, Chen M, Dehghannasiri R, Gayoso A, Granados AA, Li Q, Mahmoudabadi G, McGeever A, Olivieri JE, Park M, Ravikumar N, Stanley G, Tan W, Tarashansky AJ, Vanheusden R, Wang P, Wang S, Xing G, Dethlefsen L, Ezran C, Gillich A, Hang Y, Ho PY, Irwin JC, Jang S, Leylek R, Liu S, Maltzman JS, Metzger RJ, Phansalkar R, Sasagawa K, Sinha R, Song H, Swarup A, Trimm E, Veizades S, Wang B, Beachy PA, Clarke MF, Giudice LC, Huang FW, Huang KC, Idoyaga J, Kim SK, Kuo CS, Nguyen P, Rando TA, Red-Horse K, Reiter J, Relman DA, Sonnenburg JL, Wu A, Wu SM, and Wyss-Coray T

Subjects
B-Lymphocytes metabolism, Humans, T-Lymphocytes metabolism, Atlases as Topic, Cells metabolism, Organ Specificity genetics, RNA Splicing, Single-Cell Analysis, Transcriptome
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022
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18. Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

Author

Tsitsiklis A, Zha BS, Byrne A, DeVoe C, Rackaityte E, Levan S, Sunshine S, Mick E, Ghale R, Love C, Tarashansky AJ, Pisco A, Albright J, Jauregui A, Sarma A, Neff N, Serpa PH, Deiss TJ, Kistler A, Carrillo S, Ansel KM, Leligdowicz A, Christenson S, Detweiler A, Jones NG, Wu B, Darmanis S, Lynch SV, DeRisi JL, Matthay MA, Hendrickson CM, Kangelaris KN, Krummel MF, Woodruff PG, Erle DJ, Rosenberg O, Calfee CS, and Langelier CR

Abstract

Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.

Published
2021
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