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20 results on '"Fiskin, Evgenij"'

1. Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells

Author

Lareau, Caleb A., Dubois, Sonia M., Buquicchio, Frank A., Hsieh, Yu-Hsin, Garg, Kopal, Kautz, Pauline, Nitsch, Lena, Praktiknjo, Samantha D., Maschmeyer, Patrick, Verboon, Jeffrey M., Gutierrez, Jacob C., Yin, Yajie, Fiskin, Evgenij, Luo, Wendy, Mimitou, Eleni P., Muus, Christoph, Malhotra, Rhea, Parikh, Sumit, Fleming, Mark D., Oevermann, Lena, Schulte, Johannes, Eckert, Cornelia, Kundaje, Anshul, Smibert, Peter, Vardhana, Santosha A., Satpathy, Ansuman T., Regev, Aviv, Sankaran, Vijay G., Agarwal, Suneet, and Ludwig, Leif S.

Published
2023
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2. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.

Author

Muus, Christoph, Luecken, Malte, Eraslan, Gökcen, Sikkema, Lisa, Waghray, Avinash, Heimberg, Graham, Kobayashi, Yoshihiko, Vaishnav, Eeshit, Subramanian, Ayshwarya, Smillie, Christopher, Jagadeesh, Karthik, Duong, Elizabeth, Fiskin, Evgenij, Torlai Triglia, Elena, Ansari, Meshal, Cai, Peiwen, Lin, Brian, Buchanan, Justin, Chen, Sijia, Shu, Jian, Haber, Adam, Chung, Hattie, Montoro, Daniel, Adams, Taylor, Aliee, Hananeh, Allon, Samuel, Andrusivova, Zaneta, Angelidis, Ilias, Ashenberg, Orr, Bassler, Kevin, Bécavin, Christophe, Benhar, Inbal, Bergenstråhle, Joseph, Bergenstråhle, Ludvig, Bolt, Liam, Braun, Emelie, Bui, Linh, Callori, Steven, Chaffin, Mark, Chichelnitskiy, Evgeny, Chiou, Joshua, Conlon, Thomas, Cuoco, Michael, Cuomo, Anna, Deprez, Marie, Duclos, Grant, Fine, Denise, Fischer, David, Ghazanfar, Shila, Gillich, Astrid, Giotti, Bruno, Gould, Joshua, Guo, Minzhe, Gutierrez, Austin, Habermann, Arun, Harvey, Tyler, He, Peng, Hou, Xiaomeng, Hu, Lijuan, Hu, Yan, Jaiswal, Alok, Ji, Lu, Jiang, Peiyong, Kapellos, Theodoros, Kuo, Christin, Larsson, Ludvig, Leney-Greene, Michael, Lim, Kyungtae, Litviňuková, Monika, Ludwig, Leif, Lukassen, Soeren, Luo, Wendy, Maatz, Henrike, Madissoon, Elo, Mamanova, Lira, Manakongtreecheep, Kasidet, Leroy, Sylvie, Mayr, Christoph, Mbano, Ian, McAdams, Alexi, Nabhan, Ahmad, Nyquist, Sarah, Penland, Lolita, Poirion, Olivier, Poli, Sergio, Qi, CanCan, Queen, Rachel, Reichart, Daniel, Rosas, Ivan, Schupp, Jonas, Shea, Conor, Shi, Xingyi, Sinha, Rahul, Sit, Rene, Slowikowski, Kamil, Slyper, Michal, Smith, Neal, Sountoulidis, Alex, Strunz, Maximilian, and Sullivan, Travis

Subjects
Adult, Aged, Aged, 80 and over, Alveolar Epithelial Cells, Angiotensin-Converting Enzyme 2, COVID-19, Cathepsin L, Datasets as Topic, Demography, Female, Gene Expression Profiling, Host-Pathogen Interactions, Humans, Lung, Male, Middle Aged, Organ Specificity, Respiratory System, SARS-CoV-2, Sequence Analysis, RNA, Serine Endopeptidases, Single-Cell Analysis, Virus Internalization
Abstract

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.

Published
2021

4. Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis

Author

Fiskin, Evgenij, primary, Eraslan, Gökcen, additional, Alora-Palli, Maria B, additional, Leyva-Castillo, Juan Manuel, additional, Kim, Sean, additional, Choe, Heather, additional, Lareau, Caleb A, additional, Lau, Helena, additional, Finan, Emily P, additional, Teixeira-Soldano, Isabella, additional, LaBere, Brenna, additional, Chu, Anne, additional, Woods, Brian, additional, Chou, Janet, additional, Slyper, Michal, additional, Waldman, Julia, additional, Islam, Sabina, additional, Schneider, Lynda, additional, Phipatanakul, Wanda, additional, Platt, Craig, additional, Rozenblatt-Rosen, Orit, additional, Delorey, Toni M, additional, Deguine, Jacques, additional, Smith, Gideon P, additional, Geha, Raif, additional, Regev, Aviv, additional, and Xavier, Ramnik, additional

Published
2023
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6. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Author

Massachusetts Institute of Technology. Department of Biology, Eraslan, Gökcen, Drokhlyansky, Eugene, Anand, Shankara, Fiskin, Evgenij, Subramanian, Ayshwarya, Slyper, Michal, Wang, Jiali, Van Wittenberghe, Nicholas, Rouhana, John M, Waldman, Julia, Ashenberg, Orr, Lek, Monkol, Dionne, Danielle, Win, Thet Su, Cuoco, Michael S, Kuksenko, Olena, Tsankov, Alexander M, Branton, Philip A, Marshall, Jamie L, Greka, Anna, Getz, Gad, Segrè, Ayellet V, Aguet, François, Rozenblatt-Rosen, Orit, Ardlie, Kristin G, Regev, Aviv, Massachusetts Institute of Technology. Department of Biology, Eraslan, Gökcen, Drokhlyansky, Eugene, Anand, Shankara, Fiskin, Evgenij, Subramanian, Ayshwarya, Slyper, Michal, Wang, Jiali, Van Wittenberghe, Nicholas, Rouhana, John M, Waldman, Julia, Ashenberg, Orr, Lek, Monkol, Dionne, Danielle, Win, Thet Su, Cuoco, Michael S, Kuksenko, Olena, Tsankov, Alexander M, Branton, Philip A, Marshall, Jamie L, Greka, Anna, Getz, Gad, Segrè, Ayellet V, Aguet, François, Rozenblatt-Rosen, Orit, Ardlie, Kristin G, and Regev, Aviv

Abstract

Understanding gene function and regulation in homeostasis and disease requires knowledge of the cellular and tissue contexts in which genes are expressed. Here, we applied four single-nucleus RNA sequencing methods to eight diverse, archived, frozen tissue types from 16 donors and 25 samples, generating a cross-tissue atlas of 209,126 nuclei profiles, which we integrated across tissues, donors, and laboratory methods with a conditional variational autoencoder. Using the resulting cross-tissue atlas, we highlight shared and tissue-specific features of tissue-resident cell populations; identify cell types that might contribute to neuromuscular, metabolic, and immune components of monogenic diseases and the biological processes involved in their pathology; and determine cell types and gene modules that might underlie disease mechanisms for complex traits analyzed by genome-wide association studies.

Published
2023

7. Single-cell multi-omics reveals dynamics of purifying selection of pathogenic mitochondrial DNA across human immune cells

Author

Lareau, Caleb A., primary, Dubois, Sonia M., additional, Buquicchio, Frank A., additional, Hsieh, Yu-Hsin, additional, Garg, Kopal, additional, Kautz, Pauline, additional, Nitsch, Lena, additional, Praktiknjo, Samantha D., additional, Maschmeyer, Patrick, additional, Verboon, Jeffrey M., additional, Gutierrez, Jacob C., additional, Yin, Yajie, additional, Fiskin, Evgenij, additional, Luo, Wendy, additional, Mimitou, Eleni, additional, Muus, Christoph, additional, Malhotra, Rhea, additional, Parikh, Sumit, additional, Fleming, Mark D., additional, Oevermann, Lena, additional, Schulte, Johannes, additional, Eckert, Cornelia, additional, Kundaje, Anshul, additional, Smibert, Peter, additional, Satpathy, Ansuman T., additional, Regev, Aviv, additional, Sankaran, Vijay G., additional, Agarwal, Suneet, additional, and Ludwig, Leif S., additional

Published
2022
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9. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Author

Eraslan, Gökcen, primary, Drokhlyansky, Eugene, additional, Anand, Shankara, additional, Fiskin, Evgenij, additional, Subramanian, Ayshwarya, additional, Slyper, Michal, additional, Wang, Jiali, additional, Van Wittenberghe, Nicholas, additional, Rouhana, John M., additional, Waldman, Julia, additional, Ashenberg, Orr, additional, Lek, Monkol, additional, Dionne, Danielle, additional, Win, Thet Su, additional, Cuoco, Michael S., additional, Kuksenko, Olena, additional, Tsankov, Alexander M., additional, Branton, Philip A., additional, Marshall, Jamie L., additional, Greka, Anna, additional, Getz, Gad, additional, Segrè, Ayellet V., additional, Aguet, François, additional, Rozenblatt-Rosen, Orit, additional, Ardlie, Kristin G., additional, and Regev, Aviv, additional

Published
2022
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11. Single-nucleus cross-tissue molecular reference maps to decipher disease gene function

Author

Eraslan, Gokcen, primary, Drokhlyansky, Eugene, additional, Anand, Shankara, additional, Subramanian, Ayshwarya, additional, Fiskin, Evgenij, additional, Slyper, Michal, additional, Wang, Jiali, additional, Wittenberghe, Nicholas Van, additional, Rouhana, John M., additional, Waldman, Julia, additional, Ashenberg, Orr, additional, Dionne, Danielle, additional, Win, Thet Su, additional, Cuoco, Michael S., additional, Kuksenko, Olena, additional, Branton, Philip A., additional, Marshall, Jamie L., additional, Greka, Anna, additional, Getz, Gad, additional, Segrè, Ayellet V., additional, Aguet, François, additional, Rozenblatt-Rosen, Orit, additional, Ardlie, Kristin G., additional, and Regev, Aviv, additional

Published
2021
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18. Structural basis for phosphorylation-triggered autophagic clearance of Salmonella

Author

Rogov, Vladimir V., primary, Suzuki, Hironori, additional, Fiskin, Evgenij, additional, Wild, Philipp, additional, Kniss, Andreas, additional, Rozenknop, Alexis, additional, Kato, Ryuichi, additional, Kawasaki, Masato, additional, McEwan, David G., additional, Löhr, Frank, additional, Güntert, Peter, additional, Dikic, Ivan, additional, Wakatsuki, Soichi, additional, and Dötsch, Volker, additional

Published
2013
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20. Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis.

Author

Fiskin E, Eraslan G, Alora-Palli MB, Leyva-Castillo JM, Kim S, Choe H, Lareau CA, Lau H, Finan EP, Teixeira-Soldano I, LaBere B, Chu A, Woods B, Chou J, Slyper M, Waldman J, Islam S, Schneider L, Phipatanakul W, Platt C, Rozenblatt-Rosen O, Delorey TM, Deguine J, Smith GP, Geha R, Regev A, and Xavier R

Abstract

In healthy skin, a cutaneous immune system maintains the balance between tolerance towards innocuous environmental antigens and immune responses against pathological agents. In atopic dermatitis (AD), barrier and immune dysfunction result in chronic tissue inflammation. Our understanding of the skin tissue ecosystem in AD remains incomplete with regard to the hallmarks of pathological barrier formation, and cellular state and clonal composition of disease-promoting cells. Here, we generated a multi-modal cell census of 310,691 cells spanning 86 cell subsets from whole skin tissue of 19 adult individuals, including non-lesional and lesional skin from 11 AD patients, and integrated it with 396,321 cells from four studies into a comprehensive human skin cell atlas in health and disease. Reconstruction of human keratinocyte differentiation from basal to cornified layers revealed a disrupted cornification trajectory in AD. This disrupted epithelial differentiation was associated with signals from a unique immune and stromal multicellular community comprised of MMP12 + dendritic cells (DCs), mature migratory DCs, cycling ILCs, NK cells, inflammatory CCL19 + IL4I1 + fibroblasts, and clonally expanded IL13 + IL22 + IL26 + T cells with overlapping type 2 and type 17 characteristics. Cell subsets within this immune and stromal multicellular community were connected by multiple inter-cellular positive feedback loops predicted to impact community assembly and maintenance. AD GWAS gene expression was enriched both in disrupted cornified keratinocytes and in cell subsets from the lesional immune and stromal multicellular community including IL13 + IL22 + IL26 + T cells and ILCs, suggesting that epithelial or immune dysfunction in the context of the observed cellular communication network can initiate and then converge towards AD. Our work highlights specific, disease-associated cell subsets and interactions as potential targets in progression and resolution of chronic inflammation.

Published
2023
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