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216 results on '"Mamanova, Lira"'

1. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, He, Peng, Lawrence, John E. G., Wang, Shuaiyu, Tuck, Elizabeth, Williams, Brian A., Roberts, Kenny, Kleshchevnikov, Vitalii, Mamanova, Lira, Bolt, Liam, Polanski, Krzysztof, Li, Tong, Elmentaite, Rasa, Fasouli, Eirini S., Prete, Martin, He, Xiaoling, Yayon, Nadav, Fu, Yixi, Yang, Hao, Liang, Chen, Zhang, Hui, Blain, Raphael, Chedotal, Alain, FitzPatrick, David R., Firth, Helen, Dean, Andrew, Bayraktar, Omer Ali, Marioni, John C., Barker, Roger A., Storer, Mekayla A., Wold, Barbara J., Zhang, Hongbo, and Teichmann, Sarah A.

Published
2024
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2. Systematic benchmarking of single-cell ATAC-sequencing protocols.

Author

De Rop, Florian, Hulselmans, Gert, Flerin, Chris, Soler-Vila, Paula, Rafels, Albert, Christiaens, Valerie, González-Blas, Carmen, Marchese, Domenica, Caratù, Ginevra, Poovathingal, Suresh, Rozenblatt-Rosen, Orit, Slyper, Michael, Luo, Wendy, Muus, Christoph, Duarte, Fabiana, Shrestha, Rojesh, Bagdatli, S, Corces, M, Mamanova, Lira, Knights, Andrew, Meyer, Kerstin, Mulqueen, Ryan, Taherinasab, Akram, Maschmeyer, Patrick, Pezoldt, Jörn, Lambert, Camille, Iglesias, Marta, Najle, Sebastián, Dossani, Zain, Martelotto, Luciano, Burkett, Zach, Lebofsky, Ronald, Martin-Subero, José, Pillai, Satish, Sebé-Pedrós, Arnau, Deplancke, Bart, Teichmann, Sarah, Ludwig, Leif, Braun, Theodore, Adey, Andrew, Greenleaf, William, Buenrostro, Jason, Regev, Aviv, Aerts, Stein, and Heyn, Holger

Subjects
Humans, Single-Cell Analysis, Benchmarking, Leukocytes, Mononuclear, Chromatin Immunoprecipitation Sequencing, Chromatin, Transposases, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing
Abstract

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.

Published
2024

3. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics

Author

Lindeboom, Rik G. H., Worlock, Kaylee B., Dratva, Lisa M., Yoshida, Masahiro, Scobie, David, Wagstaffe, Helen R., Richardson, Laura, Wilbrey-Clark, Anna, Barnes, Josephine L., Kretschmer, Lorenz, Polanski, Krzysztof, Allen-Hyttinen, Jessica, Mehta, Puja, Sumanaweera, Dinithi, Boccacino, Jacqueline M., Sungnak, Waradon, Elmentaite, Rasa, Huang, Ni, Mamanova, Lira, Kapuge, Rakesh, Bolt, Liam, Prigmore, Elena, Killingley, Ben, Kalinova, Mariya, Mayer, Maria, Boyers, Alison, Mann, Alex, Swadling, Leo, Woodall, Maximillian N. J., Ellis, Samuel, Smith, Claire M., Teixeira, Vitor H., Janes, Sam M., Chambers, Rachel C., Haniffa, Muzlifah, Catchpole, Andrew, Heyderman, Robert, Noursadeghi, Mahdad, Chain, Benny, Mayer, Andreas, Meyer, Kerstin B., Chiu, Christopher, Nikolić, Marko Z., and Teichmann, Sarah A.

Published
2024
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4. HOX gene expression in the developing human spine

Author

Lawrence, John E. G., Roberts, Kenny, Tuck, Elizabeth, Li, Tong, Mamanova, Lira, Balogh, Petra, Usher, Inga, Piapi, Alice, Mazin, Pavel, Anderson, Nathaniel D., Bolt, Liam, Richardson, Laura, Prigmore, Elena, He, Xiaoling, Barker, Roger A., Flanagan, Adrienne, Young, Matthew D., Teichmann, Sarah A., Bayraktar, Omer, and Behjati, Sam

Published
2024
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5. Early human lung immune cell development and its role in epithelial cell fate.

Author

Barnes, Josephine, Yoshida, Masahiro, He, Peng, Worlock, Kaylee, Lindeboom, Rik, Suo, Chenqu, Pett, J, Wilbrey-Clark, Anna, Dann, Emma, Mamanova, Lira, Richardson, Laura, Polanski, Krzysztof, Pennycuick, Adam, Allen-Hyttinen, Jessica, Herczeg, Iván, Arzili, Romina, Hynds, Robert, Teixeira, Vitor, Haniffa, Muzlifah, Lim, Kyungtae, Sun, Dawei, Rawlins, Emma, Oliver, Amanda, Lyons, Paul, Marioni, John, Ruhrberg, Christiana, Tuong, Zewen, Clatworthy, Menna, Reading, James, Janes, Sam, Teichmann, Sarah, Meyer, Kerstin, and Nikolić, Marko

Subjects
Humans, Immunity, Innate, Cell Differentiation, Lung, Killer Cells, Natural, Epithelial Cells
Abstract

Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.

Published
2023

6. A human embryonic limb cell atlas resolved in space and time.

Author

Zhang, Bao, He, Peng, Lawrence, John, Wang, Shuaiyu, Tuck, Elizabeth, Williams, Brian, Roberts, Kenny, Kleshchevnikov, Vitalii, Mamanova, Lira, Bolt, Liam, Polanski, Krzysztof, Li, Tong, Elmentaite, Rasa, Fasouli, Eirini, Prete, Martin, He, Xiaoling, Yayon, Nadav, Fu, Yixi, Yang, Hao, Liang, Chen, Zhang, Hui, Blain, Raphael, Chedotal, Alain, FitzPatrick, David, Firth, Helen, Dean, Andrew, Bayraktar, Omer, Marioni, John, Barker, Roger, Storer, Mekayla, Wold, Barbara, Zhang, Hongbo, and Teichmann, Sarah

Abstract

Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months1. This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common2. Decades of work with model organisms have defined the fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization of this process in humans has yet to be performed. Here we detail human embryonic limb development across space and time using single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells from a few multipotent progenitors to myriad differentiated cell states, including several novel cell populations. We uncover two waves of human muscle development, each characterized by different cell states regulated by separate gene expression programmes, and identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity. Through assembly of multiple anatomically continuous spatial transcriptomic samples using VisiumStitcher, we map cells across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of the mesenchyme in the autopod. Finally, we perform single-cell RNA sequencing on mouse embryonic limbs to facilitate cross-species developmental comparison, finding substantial homology between the two species.

Published
2023

7. Age-specific nasal epithelial responses to SARS-CoV-2 infection

Author

Woodall, Maximillian N. J., Cujba, Ana-Maria, Worlock, Kaylee B., Case, Katie-Marie, Masonou, Tereza, Yoshida, Masahiro, Polanski, Krzysztof, Huang, Ni, Lindeboom, Rik G. H., Mamanova, Lira, Bolt, Liam, Richardson, Laura, Cakir, Batuhan, Ellis, Samuel, Palor, Machaela, Burgoyne, Thomas, Pinto, Andreia, Moulding, Dale, McHugh, Timothy D., Saleh, Aarash, Kilich, Eliz, Mehta, Puja, O’Callaghan, Chris, Zhou, Jie, Barclay, Wendy, De Coppi, Paolo, Butler, Colin R., Cortina-Borja, Mario, Vinette, Heloise, Roy, Sunando, Breuer, Judith, Chambers, Rachel C., Heywood, Wendy E., Mills, Kevin, Hynds, Robert E., Teichmann, Sarah A., Meyer, Kerstin B., Nikolić, Marko Z., and Smith, Claire M.

Published
2024
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8. Author Correction: Age-specific nasal epithelial responses to SARS-CoV-2 infection

Author

Woodall, Maximillian N. J., Cujba, Ana-Maria, Worlock, Kaylee B., Case, Katie-Marie, Masonou, Tereza, Yoshida, Masahiro, Polanski, Krzysztof, Huang, Ni, Lindeboom, Rik G. H., Mamanova, Lira, Bolt, Liam, Richardson, Laura, Cakir, Batuhan, Ellis, Samuel, Palor, Machaela, Burgoyne, Thomas, Pinto, Andreia, Moulding, Dale, McHugh, Timothy D., Saleh, Aarash, Kilich, Eliz, Mehta, Puja, O’Callaghan, Chris, Zhou, Jie, Barclay, Wendy, De Coppi, Paolo, Butler, Colin R., Cortina-Borja, Mario, Vinette, Heloise, Roy, Sunando, Breuer, Judith, Chambers, Rachel C., Heywood, Wendy E., Mills, Kevin, Hynds, Robert E., Teichmann, Sarah A., Meyer, Kerstin B., Nikolić, Marko Z., and Smith, Claire M.

Published
2024
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9. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.

Author

Madissoon, Elo, Oliver, Amanda, Kleshchevnikov, Vitalii, Wilbrey-Clark, Anna, Polanski, Krzysztof, Richoz, Nathan, Ribeiro Orsi, Ana, Mamanova, Lira, Bolt, Liam, Elmentaite, Rasa, Pett, J, Huang, Ni, Xu, Chuan, He, Peng, Dabrowska, Monika, Pritchard, Sophie, Tuck, Liz, Prigmore, Elena, Perera, Shani, Knights, Andrew, Oszlanczi, Agnes, Hunter, Adam, Vieira, Sara, Patel, Minal, Lindeboom, Rik, Campos, Lia, Matsuo, Kazuhiko, Nakayama, Takashi, Yoshida, Masahiro, Worlock, Kaylee, Nikolić, Marko, Georgakopoulos, Nikitas, Mahbubani, Krishnaa, Saeb-Parsy, Kourosh, Bayraktar, Omer, Clatworthy, Menna, Stegle, Oliver, Kumasaka, Natsuhiko, Teichmann, Sarah, and Meyer, Kerstin

Subjects
Humans, Respiratory Mucosa, Lung, Epithelial Cells, B-Lymphocytes, Immunoglobulin A
Abstract

Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new gland-associated immune niche has implications for respiratory health.

Published
2023

10. Author Correction: Human SARS-CoV-2 challenge uncovers local and systemic response dynamics

Author

Lindeboom, Rik G. H., Worlock, Kaylee B., Dratva, Lisa M., Yoshida, Masahiro, Scobie, David, Wagstaffe, Helen R., Richardson, Laura, Wilbrey-Clark, Anna, Barnes, Josephine L., Kretschmer, Lorenz, Polanski, Krzysztof, Allen-Hyttinen, Jessica, Mehta, Puja, Sumanaweera, Dinithi, Boccacino, Jacqueline M., Sungnak, Waradon, Elmentaite, Rasa, Huang, Ni, Mamanova, Lira, Kapuge, Rakesh, Bolt, Liam, Prigmore, Elena, Killingley, Ben, Kalinova, Mariya, Mayer, Maria, Boyers, Alison, Mann, Alex, Swadling, Leo, Woodall, Maximillian N. J., Ellis, Samuel, Smith, Claire M., Teixeira, Vitor H., Janes, Sam M., Chambers, Rachel C., Haniffa, Muzlifah, Catchpole, Andrew, Heyderman, Robert, Noursadeghi, Mahdad, Chain, Benny, Mayer, Andreas, Meyer, Kerstin B., Chiu, Christopher, Nikolić, Marko Z., and Teichmann, Sarah A.

Published
2024
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11. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, Cranley, James, Muraro, Daniele, Miranda, Antonio M. A., Ho, Siew Yen, Wilbrey-Clark, Anna, Patrick Pett, Jan, Polanski, Krzysztof, Richardson, Laura, Litvinukova, Monika, Kumasaka, Natsuhiko, Qin, Yue, Jablonska, Zuzanna, Semprich, Claudia I., Mach, Lukas, Dabrowska, Monika, Richoz, Nathan, Bolt, Liam, Mamanova, Lira, Kapuge, Rakeshlal, Barnett, Sam N., Perera, Shani, Talavera-López, Carlos, Mulas, Ilaria, Mahbubani, Krishnaa T., Tuck, Liz, Wang, Lu, Huang, Margaret M., Prete, Martin, Pritchard, Sophie, Dark, John, Saeb-Parsy, Kourosh, Patel, Minal, Clatworthy, Menna R., Hübner, Norbert, Chowdhury, Rasheda A., Noseda, Michela, and Teichmann, Sarah A.

Published
2023
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12. 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

13. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer

Author

Li, Ruoyan, Ferdinand, John R., Loudon, Kevin W., Bowyer, Georgina S., Laidlaw, Sean, Muyas, Francesc, Mamanova, Lira, Neves, Joana B., Bolt, Liam, Fasouli, Eirini S., Lawson, Andrew R.J., Young, Matthew D., Hooks, Yvette, Oliver, Thomas R.W., Butler, Timothy M., Armitage, James N., Aho, Tev, Riddick, Antony C.P., Gnanapragasam, Vincent, Welsh, Sarah J., Meyer, Kerstin B., Warren, Anne Y., Tran, Maxine G.B., Stewart, Grant D., Cortés-Ciriano, Isidro, Behjati, Sam, Clatworthy, Menna R., Campbell, Peter J., Teichmann, Sarah A., and Mitchell, Thomas J.

Published
2022
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14. A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

Author

He, Peng, Lim, Kyungtae, Sun, Dawei, Pett, Jan Patrick, Jeng, Quitz, Polanski, Krzysztof, Dong, Ziqi, Bolt, Liam, Richardson, Laura, Mamanova, Lira, Dabrowska, Monika, Wilbrey-Clark, Anna, Madissoon, Elo, Tuong, Zewen Kelvin, Dann, Emma, Suo, Chenqu, Goh, Isaac, Yoshida, Masahiro, Nikolić, Marko Z., Janes, Sam M., He, Xiaoling, Barker, Roger A., Teichmann, Sarah A., Marioni, John C., Meyer, Kerstin B., and Rawlins, Emma L.

Published
2022
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15. Local and systemic responses to SARS-CoV-2 infection in children and adults

Author

Yoshida, Masahiro, Worlock, Kaylee B., Huang, Ni, Lindeboom, Rik G. H., Butler, Colin R., Kumasaka, Natsuhiko, Dominguez Conde, Cecilia, Mamanova, Lira, Bolt, Liam, Richardson, Laura, Polanski, Krzysztof, Madissoon, Elo, Barnes, Josephine L., Allen-Hyttinen, Jessica, Kilich, Eliz, Jones, Brendan C., de Wilton, Angus, Wilbrey-Clark, Anna, Sungnak, Waradon, Pett, J. Patrick, Weller, Juliane, Prigmore, Elena, Yung, Henry, Mehta, Puja, Saleh, Aarash, Saigal, Anita, Chu, Vivian, Cohen, Jonathan M., Cane, Clare, Iordanidou, Aikaterini, Shibuya, Soichi, Reuschl, Ann-Kathrin, Herczeg, Iván T., Argento, A. Christine, Wunderink, Richard G., Smith, Sean B., Poor, Taylor A., Gao, Catherine A., Dematte, Jane E., Reynolds, Gary, Haniffa, Muzlifah, Bowyer, Georgina S., Coates, Matthew, Clatworthy, Menna R., Calero-Nieto, Fernando J., Göttgens, Berthold, O’Callaghan, Christopher, Sebire, Neil J., Jolly, Clare, De Coppi, Paolo, Smith, Claire M., Misharin, Alexander V., Janes, Sam M., Teichmann, Sarah A., Nikolić, Marko Z., and Meyer, Kerstin B.

Published
2022
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16. Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses

Author

Rodríguez-Ubreva, Javier, Arutyunyan, Anna, Bonder, Marc Jan, Del Pino-Molina, Lucía, Clark, Stephen J., de la Calle-Fabregat, Carlos, Garcia-Alonso, Luz, Handfield, Louis-François, Ciudad, Laura, Andrés-León, Eduardo, Krueger, Felix, Català-Moll, Francesc, Rodríguez-Cortez, Virginia C., Polanski, Krzysztof, Mamanova, Lira, van Dongen, Stijn, Kiselev, Vladimir Yu., Martínez-Saavedra, María T., Heyn, Holger, Martín, Javier, Warnatz, Klaus, López-Granados, Eduardo, Rodríguez-Gallego, Carlos, Stegle, Oliver, Kelsey, Gavin, Vento-Tormo, Roser, and Ballestar, Esteban

Published
2022
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17. Cells of the human intestinal tract mapped across space and time

Author

Elmentaite, Rasa, Kumasaka, Natsuhiko, Roberts, Kenny, Fleming, Aaron, Dann, Emma, King, Hamish W., Kleshchevnikov, Vitalii, Dabrowska, Monika, Pritchard, Sophie, Bolt, Liam, Vieira, Sara F., Mamanova, Lira, Huang, Ni, Perrone, Francesca, Goh Kai’En, Issac, Lisgo, Steven N., Katan, Matilda, Leonard, Steven, Oliver, Thomas R. W., Hook, C. Elizabeth, Nayak, Komal, Campos, Lia S., Domínguez Conde, Cecilia, Stephenson, Emily, Engelbert, Justin, Botting, Rachel A., Polanski, Krzysztof, van Dongen, Stijn, Patel, Minal, Morgan, Michael D., Marioni, John C., Bayraktar, Omer Ali, Meyer, Kerstin B., He, Xiaoling, Barker, Roger A., Uhlig, Holm H., Mahbubani, Krishnaa T., Saeb-Parsy, Kourosh, Zilbauer, Matthias, Clatworthy, Menna R., Haniffa, Muzlifah, James, Kylie R., and Teichmann, Sarah A.

Published
2021
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19. Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

Author

Wells, Steven B., primary, Rainbow, Daniel B., additional, Mark, Michal, additional, Szabo, Peter A., additional, Ergen, Can, additional, Maceiras, Ana Raquel, additional, Caron, Daniel P., additional, Rahmani, Elior, additional, Benuck, Eli, additional, Amiri, Valeh Valiollah Pour, additional, Chen, David, additional, Wagner, Allon, additional, Howlett, Sarah K., additional, Jarvis, Lorna B., additional, Ellis, Karen L., additional, Kubota, Masaru, additional, Matsumoto, Rei, additional, Mahbubani, Krishnaa, additional, Saeb-Parsy, Kouresh, additional, Dominguez-Conde, Cecilia, additional, Richardson, Laura, additional, Xu, Chuan, additional, Li, Shuang, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Wilk, Alicja, additional, Teichmann, Sarah A., additional, Farber, Donna L., additional, Sims, Peter A., additional, Jones, Joanne L., additional, and Yosef, Nir, additional

Published
2024
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20. Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours

Author

Custers, Lars, Khabirova, Eleonora, Coorens, Tim H. H., Oliver, Thomas R. W., Calandrini, Camilla, Young, Matthew D., Vieira Braga, Felipe A., Ellis, Peter, Mamanova, Lira, Segers, Heidi, Maat, Arie, Kool, Marcel, Hoving, Eelco W., van den Heuvel-Eibrink, Marry M., Nicholson, James, Straathof, Karin, Hook, Liz, de Krijger, Ronald R., Trayers, Claire, Allinson, Kieren, Behjati, Sam, and Drost, Jarno

Published
2021
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21. Single cell derived mRNA signals across human kidney tumors

Author

Young, Matthew D., Mitchell, Thomas J., Custers, Lars, Margaritis, Thanasis, Morales-Rodriguez, Francisco, Kwakwa, Kwasi, Khabirova, Eleonora, Kildisiute, Gerda, Oliver, Thomas R. W., de Krijger, Ronald R., van den Heuvel-Eibrink, Marry M., Comitani, Federico, Piapi, Alice, Bugallo-Blanco, Eva, Thevanesan, Christine, Burke, Christina, Prigmore, Elena, Ambridge, Kirsty, Roberts, Kenny, Braga, Felipe A. Vieira, Coorens, Tim H. H., Del Valle, Ignacio, Wilbrey-Clark, Anna, Mamanova, Lira, Stewart, Grant D., Gnanapragasam, Vincent J., Rampling, Dyanne, Sebire, Neil, Coleman, Nicholas, Hook, Liz, Warren, Anne, Haniffa, Muzlifah, Kool, Marcel, Pfister, Stefan M., Achermann, John C., He, Xiaoling, Barker, Roger A., Shlien, Adam, Bayraktar, Omer A., Teichmann, Sarah A., Holstege, Frank C., Meyer, Kerstin B., Drost, Jarno, Straathof, Karin, and Behjati, Sam

Published
2021
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23. Single cell transcriptomics reveals chondrocyte differentiation dynamics in vivo and in vitro

Author

Lawrence, John E G, primary, Woods, Steven, additional, Roberts, Kenny, additional, Sumanaweera, Dinithi N, additional, Balogh, Petra, additional, Predeus, Alexander V, additional, He, Peng, additional, Li, Tong, additional, Polanski, Krzysztof, additional, Prigmore, Elena, additional, Tuck, Elizabeth, additional, Mamanova, Lira, additional, Zhou, Di, additional, Webb, Simone, additional, Jardine, Laura, additional, He, Xiaoling, additional, Barker, Roger A, additional, Haniffa, Muzlifah, additional, Flanagan, Adrienne M, additional, Young, Matthew D, additional, Behjati, Sam, additional, Bayraktar, Omer, additional, Kimber, Susan J, additional, and Teichmann, Sarah, additional

Published
2023
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24. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, primary, He, Peng, additional, Lawrence, John E. G., additional, Wang, Shuaiyu, additional, Tuck, Elizabeth, additional, Williams, Brian A., additional, Roberts, Kenny, additional, Kleshchevnikov, Vitalii, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Polanski, Krzysztof, additional, Li, Tong, additional, Elmentaite, Rasa, additional, Fasouli, Eirini S., additional, Prete, Martin, additional, He, Xiaoling, additional, Yayon, Nadav, additional, Fu, Yixi, additional, Yang, Hao, additional, Liang, Chen, additional, Zhang, Hui, additional, Blain, Raphael, additional, Chedotal, Alain, additional, FitzPatrick, David R., additional, Firth, Helen, additional, Dean, Andrew, additional, Bayraktar, Omer Ali, additional, Marioni, John C., additional, Barker, Roger A., additional, Storer, Mekayla A., additional, Wold, Barbara J., additional, Zhang, Hongbo, additional, and Teichmann, Sarah A., additional

Published
2023
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25. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

Author

Young, Matthew D., Mitchell, Thomas J., Braga, Felipe A. Vieira, Tran, Maxine G. B., Stewart, Benjamin J., Ferdinand, John R., Collord, Grace, Botting, Rachel A., Popescu, Dorin-Mirel, Loudon, Kevin W., Vento-Tormo, Roser, Stephenson, Emily, Cagan, Alex, Farndon, Sarah J., Del Castillo Velasco-Herrera, Martin, Guzzo, Charlotte, Richoz, Nathan, Mamanova, Lira, Aho, Tevita, Armitage, James N., Riddick, Antony C. P., Mushtaq, Imran, Farrell, Stephen, Rampling, Dyanne, Nicholson, James, Filby, Andrew, Burge, Johanna, Lisgo, Steven, Maxwell, Patrick H., Lindsay, Susan, Warren, Anne Y., Stewart, Grant D., Sebire, Neil, Coleman, Nicholas, Haniffa, Muzlifah, Teichmann, Sarah A., Clatworthy, Menna, and Behjati, Sam

Published
2018

26. Decoding human fetal liver haematopoiesis

Author

Popescu, Dorin-Mirel, Botting, Rachel A., Stephenson, Emily, Green, Kile, Webb, Simone, Jardine, Laura, Calderbank, Emily F., Polanski, Krzysztof, Goh, Issac, Efremova, Mirjana, Acres, Meghan, Maunder, Daniel, Vegh, Peter, Gitton, Yorick, Park, Jong-Eun, Vento-Tormo, Roser, Miao, Zhichao, Dixon, David, Rowell, Rachel, McDonald, David, Fletcher, James, Poyner, Elizabeth, Reynolds, Gary, Mather, Michael, Moldovan, Corina, Mamanova, Lira, Greig, Frankie, Young, Matthew D., Meyer, Kerstin B., Lisgo, Steven, Bacardit, Jaume, Fuller, Andrew, Millar, Ben, Innes, Barbara, Lindsay, Susan, Stubbington, Michael J. T., Kowalczyk, Monika S., Li, Bo, Ashenberg, Orr, Tabaka, Marcin, Dionne, Danielle, Tickle, Timothy L., Slyper, Michal, Rozenblatt-Rosen, Orit, Filby, Andrew, Carey, Peter, Villani, Alexandra-Chloé, Roy, Anindita, Regev, Aviv, Chédotal, Alain, Roberts, Irene, Göttgens, Berthold, Behjati, Sam, Laurenti, Elisa, Teichmann, Sarah A., and Haniffa, Muzlifah

Published
2019
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27. Systematic benchmarking of single-cell ATAC-sequencing protocols

Author

De Rop, Florian V., primary, Hulselmans, Gert, additional, Flerin, Chris, additional, Soler-Vila, Paula, additional, Rafels, Albert, additional, Christiaens, Valerie, additional, González-Blas, Carmen Bravo, additional, Marchese, Domenica, additional, Caratù, Ginevra, additional, Poovathingal, Suresh, additional, Rozenblatt-Rosen, Orit, additional, Slyper, Michael, additional, Luo, Wendy, additional, Muus, Christoph, additional, Duarte, Fabiana, additional, Shrestha, Rojesh, additional, Bagdatli, S. Tansu, additional, Corces, M. Ryan, additional, Mamanova, Lira, additional, Knights, Andrew, additional, Meyer, Kerstin B., additional, Mulqueen, Ryan, additional, Taherinasab, Akram, additional, Maschmeyer, Patrick, additional, Pezoldt, Jörn, additional, Lambert, Camille Lucie Germaine, additional, Iglesias, Marta, additional, Najle, Sebastián R., additional, Dossani, Zain Y., additional, Martelotto, Luciano G., additional, Burkett, Zach, additional, Lebofsky, Ronald, additional, Martin-Subero, José Ignacio, additional, Pillai, Satish, additional, Sebé-Pedrós, Arnau, additional, Deplancke, Bart, additional, Teichmann, Sarah A., additional, Ludwig, Leif S., additional, Braun, Theodore P., additional, Adey, Andrew C., additional, Greenleaf, William J., additional, Buenrostro, Jason D., additional, Regev, Aviv, additional, Aerts, Stein, additional, and Heyn, Holger, additional

Published
2023
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28. Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis

Author

Penkava, Frank, Velasco-Herrera, Martin Del Castillo, Young, Matthew D., Yager, Nicole, Nwosu, Lilian N., Pratt, Arthur G., Lara, Alicia Lledo, Guzzo, Charlotte, Maroof, Ash, Mamanova, Lira, Cole, Suzanne, Efremova, Mirjana, Simone, Davide, Filer, Andrew, Brown, Chrysothemis C., Croxford, Andrew L., Isaacs, John D., Teichmann, Sarah, Bowness, Paul, Behjati, Sam, and Hussein Al-Mossawi, M.

Published
2020
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30. Human SARS-CoV-2 challenge resolves local and systemic response dynamics

Author

Lindeboom, Rik G H, primary, Worlock, Kaylee B, additional, Dratva, Lisa M, additional, Yoshida, Masahiro, additional, Scobie, David, additional, Wagstaffe, Helen R, additional, Richardson, Laura, additional, Wilbrey-Clark, Anna L, additional, Barnes, Josephine L, additional, Polanski, Krzysztof, additional, Allen-Hyttinen, Jessica, additional, Mehta, Puja, additional, Sumanaweera, Dinithi, additional, Boccacino, Jacqueline M, additional, Sungnak, Waradon, additional, Huang, Ni, additional, Mamanova, Lira, additional, Kapuge, Rakeshlal, additional, Bolt, Liam, additional, Prigmore, Elena, additional, Killingley, Ben, additional, Kalinova, Mariya, additional, Mayer, Maria, additional, Boyers, Alison, additional, Mann, Alex, additional, Teixeira, Vitor H, additional, Janes, Sam M, additional, Chambers, Rachel C, additional, Haniffa, Muzlifah, additional, Catchpole, Andrew, additional, Heyderman, Robert S, additional, Noursadeghi, Mahdad, additional, Chain, Benny, additional, Mayer, Andreas, additional, Meyer, Kerstin B, additional, Chiu, Christopher, additional, Nikolić, Marko Z, additional, and Teichmann, Sarah A, additional

Published
2023
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31. Spatially resolved multiomics of human cardiac niches

Author

Kanemaru, Kazumasa, primary, Cranley, James, additional, Muraro, Daniele, additional, Miranda, Antonio M.A., additional, Pett, Jan Patrick, additional, Litvinukova, Monika, additional, Kumasaka, Natsuhiko, additional, Ho, Siew Yen, additional, Polanski, Krzysztof, additional, Richardson, Laura, additional, Mach, Lukas, additional, Dabrowska, Monika, additional, Richoz, Nathan, additional, Barnett, Sam N., additional, Perera, Shani, additional, Wilbrey-Clark, Anna L, additional, Talavera-López, Carlos, additional, Mulas, Ilaria, additional, Mahbubani, Krishnaa T., additional, Bolt, Liam, additional, Mamanova, Lira, additional, Tuck, Liz, additional, Wang, Lu, additional, Huang, Margaret M., additional, Prete, Martin, additional, Pritchard, Sophie, additional, Dark, John, additional, Saeb-Parsy, Kourosh, additional, Patel, Minal, additional, Clatworthy, Menna R., additional, Chowdhury, Rasheda A., additional, Noseda, Michela, additional, and Teichmann, Sarah A., additional

Published
2023
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32. The emergence of goblet inflammatory or ITGB6hinasal progenitor cells determines age-associated SARS-CoV-2 pathogenesis

Author

Woodall, Maximillian, primary, Cujba, Ana-Maria, additional, Worlock, Kaylee B., additional, Case, Katie-Marie, additional, Masonou, Tereza, additional, Yoshida, Masahiro, additional, Polanski, Krzysztof, additional, Huang, Ni, additional, Lindeboom, Rik G. H., additional, Mamanova, Lira, additional, Bolt, Liam, additional, Richardson, Laura, additional, Ellis, Samuel, additional, Palor, Machaela, additional, Burgoyne, Thomas, additional, Pinto, Andreia, additional, Moulding, Dale, additional, McHugh, Timothy D., additional, Saleh, Aarash, additional, Kilich, Eliz, additional, Mehta, Puja, additional, O’Callaghan, Chris, additional, Zhou, Jie, additional, Barclay, Wendy, additional, Coppi, Paolo De, additional, Butler, Colin R., additional, Vinette, Heloise, additional, Roy, Sunando, additional, Breuer, Judith, additional, Chambers, Rachel C., additional, Heywood, Wendy E., additional, Mills, Kevin, additional, Hynds, Robert E., additional, Teichmann, Sarah A., additional, Meyer, Kerstin B., additional, Nikolić, Marko Z., additional, and Smith, Claire M., additional

Published
2023
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34. Local and systemic responses to SARS-CoV-2 infection in children and adults

Author

Yoshida, Masahiro, Worlock, Kaylee B., Huang, Ni, Lindeboom, Rik G. H., Butler, Colin R., Kumasaka, Natsuhiko, Dominguez Conde, Cecilia, Mamanova, Lira, Bolt, Liam, Richardson, Laura, Polanski, Krzysztof, Madissoon, Elo, Barnes, Josephine L., Allen-Hyttinen, Jessica, Kilich, Eliz, Jones, Brendan C., de Wilton, Angus, Wilbrey-Clark, Anna, Sungnak, Waradon, Pett, J. Patrick, Weller, Juliane, Prigmore, Elena, Yung, Henry, Mehta, Puja, Saleh, Aarash, Saigal, Anita, Chu, Vivian, Cohen, Jonathan M., Cane, Clare, Iordanidou, Aikaterini, Shibuya, Soichi, Reuschl, Ann-Kathrin, Herczeg, Iván T., Argento, A. Christine, Wunderink, Richard G., Smith, Sean B., Poor, Taylor A., Gao, Catherine A., Dematte, Jane E., Budinger, G. R. Scott, Donnelly, Helen K., Markov, Nikolay S., Lu, Ziyan, Reynolds, Gary, Haniffa, Muzlifah, Bowyer, Georgina S., Coates, Matthew, Clatworthy, Menna R., Calero-Nieto, Fernando J., Göttgens, Berthold, O’Callaghan, Christopher, Sebire, Neil J., Jolly, Clare, De Coppi, Paolo, Smith, Claire M., Misharin, Alexander V., Janes, Sam M., Teichmann, Sarah A., Nikolić, Marko Z., and Meyer, Kerstin B.

Subjects
Multidisciplinary Sciences, Science & Technology, Multidisciplinary, Science & Technology - Other Topics, COVID-19, CELL
Abstract

It is not fully understood why COVID-19 is typically milder in children1–3. Here, to examine the differences between children and adults in their response to SARS-CoV-2 infection, we analysed paediatric and adult patients with COVID-19 as well as healthy control individuals (total n = 93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In the airways of healthy paediatric individuals, we observed cells that were already in an interferon-activated state, which after SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon responses restrict viral replication and disease progression. The systemic response in children was characterized by increases in naive lymphocytes and a depletion of natural killer cells, whereas, in adults, cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signalling in early infection, and identify epithelial cell states associated with COVID-19 and age. Our matching nasal and blood data show a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were substantially reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children.

Published
2021
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35. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Richoz, Nathan, additional, Ribeiro Orsi, Ana, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, Xu, Chuan, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Perera, Shani, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Lindeboom, Rik G. H., additional, Campos, Lia S., additional, Matsuo, Kazuhiko, additional, Nakayama, Takashi, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Nikolić, Marko Z., additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa T., additional, Saeb-Parsy, Kourosh, additional, Bayraktar, Omer Ali, additional, Clatworthy, Menna R., additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2022
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36. Early human lung immune cell development and its role in epithelial cell fate

Author

Barnes, Josephine L., primary, He, Peng, additional, Yoshida, Masahiro, additional, Worlock, Kaylee B., additional, Lindeboom, Rik G.H., additional, Suo, Chenqu, additional, Pett, J. Patrick, additional, Wilbrey-Clark, Anna, additional, Dann, Emma, additional, Mamanova, Lira, additional, Richardson, Laura, additional, Oliver, Amanda J., additional, Pennycuick, Adam, additional, Allen-Hyttinen, Jessica, additional, Herczeg, Iván T., additional, Hynds, Robert E., additional, Teixeira, Vitor H., additional, Haniffa, Muzlifah, additional, Lim, Kyungtae, additional, Sun, Dawei, additional, Rawlins, Emma L., additional, Polanski, Krzysztof, additional, Lyons, Paul A., additional, Marioni, John C., additional, Tuong, Zewen Kelvin, additional, Clatworthy, Menna R., additional, Reading, James L., additional, Janes, Sam M., additional, Teichmann, Sarah A., additional, Meyer, Kerstin B., additional, and Nikolić, Marko Z., additional

Published
2022
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37. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, He, Peng, Lawrence, John E., Wang, Shuaiyu, Tuck, Elizabeth, Williams, Brian, Roberts, Kenny, Kleshchevnikov, Vitalii, Mamanova, Lira, Bolt, Liam, Polanski, Krzysztof, Elmentaite, Rasa, Fasouli, Eirini S., Prete, Martin, He, Xiaoling, Yayon, Nadav, Fu, Yixi, Yang, Hao, Liang, Chen, Zhang, Hui, FitzPatrick, David R., Firth, Helen, Dean, Andrew, Barker, Roger A., Storer, Mekayla A., Wold, Barbara J., Zhang, Hongbo, Teichmann, Sarah A., Zhang, Bao, He, Peng, Lawrence, John E., Wang, Shuaiyu, Tuck, Elizabeth, Williams, Brian, Roberts, Kenny, Kleshchevnikov, Vitalii, Mamanova, Lira, Bolt, Liam, Polanski, Krzysztof, Elmentaite, Rasa, Fasouli, Eirini S., Prete, Martin, He, Xiaoling, Yayon, Nadav, Fu, Yixi, Yang, Hao, Liang, Chen, Zhang, Hui, FitzPatrick, David R., Firth, Helen, Dean, Andrew, Barker, Roger A., Storer, Mekayla A., Wold, Barbara J., Zhang, Hongbo, and Teichmann, Sarah A.

Abstract

Human limbs emerge during the fourth post-conception week as mesenchymal buds which develop into fully-formed limbs over the subsequent months. Limb development is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common. Decades of work with model organisms has outlined the fundamental processes underlying vertebrate limb development, but an in-depth characterisation of this process in humans has yet to be performed. Here we detail the development of the human embryonic limb across space and time, using both single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells, progressing from a restricted number of multipotent progenitors to myriad mature cell states, and identify several novel cell populations, including perineural fibroblasts and multiple distinct mesenchymal states. We uncover two waves of human muscle development, each characterised by different cell states regulated by separate gene expression programmes. We identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity and validate this by performing MSC knock down in human embryonic myoblasts, which results in significant upregulation of late myogenic genes. Spatially mapping the cell types of the limb across a range of gestational ages demonstrates a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncovers two transcriptionally and spatially distinct populations of the progress zone, which we term “outer” and “transitional” layers. The latter exhibits a transcriptomic profile similar to that of the chondrocyte lineage, but lacking the key chondrogenic transcription factors SOX5,6 & 9. Finally, we perform scRNA-seq on murine embryonic limbs to facilitate cross-species developmental comparison at single-cell resolution, finding substantial homology between the two species.

Published
2022

38. Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses.

Author

Generalitat de Catalunya, Fundación Josep Carreras, Ministerio de Ciencia e Innovación (España), Instituto de Salud Carlos III, Jeffrey Modell Foundation, Chan Zuckerberg Initiative, Wellcome Sanger Institute, European Commission, Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), Rodríguez-Ubreva, Javier, Arutyunyan, Anna, Bonder, Marc J., Pino-Molina, Lucía del, Clark, Stephen J., Calle-Fabregat, Carlos de la, García-Alonso, Luz, Handfield, Louis-François, Ciudad, Laura, Andrés-León, Eduardo, Krueger, Felix, Català-Moll, Francesc, Rodríguez-Cortez, Virginia C., Polanski, Krzysztof, Mamanova, Lira, Dongen, Stijn van, Kiselev, Vladimir Yu, Martínez-Saavedra, María T., Heyn, Holger, Martin, Javier, Warnatz, Klaus, López-Granados, Eduardo, Rodriguez-Gallego, Carlos, Stegle, Oliver, Kelsey, Gavin, Vento-Tormo, Roser, Ballestar, Esteban, Generalitat de Catalunya, Fundación Josep Carreras, Ministerio de Ciencia e Innovación (España), Instituto de Salud Carlos III, Jeffrey Modell Foundation, Chan Zuckerberg Initiative, Wellcome Sanger Institute, European Commission, Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), Rodríguez-Ubreva, Javier, Arutyunyan, Anna, Bonder, Marc J., Pino-Molina, Lucía del, Clark, Stephen J., Calle-Fabregat, Carlos de la, García-Alonso, Luz, Handfield, Louis-François, Ciudad, Laura, Andrés-León, Eduardo, Krueger, Felix, Català-Moll, Francesc, Rodríguez-Cortez, Virginia C., Polanski, Krzysztof, Mamanova, Lira, Dongen, Stijn van, Kiselev, Vladimir Yu, Martínez-Saavedra, María T., Heyn, Holger, Martin, Javier, Warnatz, Klaus, López-Granados, Eduardo, Rodriguez-Gallego, Carlos, Stegle, Oliver, Kelsey, Gavin, Vento-Tormo, Roser, and Ballestar, Esteban

Abstract

Common variable immunodeficiency (CVID), the most prevalent symptomatic primary immunodeficiency, displays impaired terminal B-cell differentiation and defective antibody responses. Incomplete genetic penetrance and ample phenotypic expressivity in CVID suggest the participation of additional pathogenic mechanisms. Monozygotic (MZ) twins discordant for CVID are uniquely valuable for studying the contribution of epigenetics to the disease. Here, we generate a single-cell epigenomics and transcriptomics census of naïve-to-memory B cell differentiation in a CVID-discordant MZ twin pair. Our analysis identifies DNA methylation, chromatin accessibility and transcriptional defects in memory B-cells mirroring defective cell-cell communication upon activation. These findings are validated in a cohort of CVID patients and healthy donors. Our findings provide a comprehensive multi-omics map of alterations in naïve-to-memory B-cell transition in CVID and indicate links between the epigenome and immune cell cross-talk. Our resource, publicly available at the Human Cell Atlas, gives insight into future diagnosis and treatments of CVID patients.

Published
2022

39. A spatial multi-omics atlas of the human lung reveals a novel gland-associated immune niche

Author

Meyer, Kerstin, primary, Madissoon, Elo, additional, Oliver, Amanda, additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polański, Krzysztof, additional, Richoz, Nathan, additional, Orsi, Ana Elisa Ribeiro, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Elmentaite, Rasa, additional, Pett, Jan, additional, Huang, Ni, additional, Xu, Chuan, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Elizabeth, additional, Prigmore, Elena, additional, Perera, Shani, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara Filipa, additional, Patel, Minal, additional, Yoshida, Masahiro, additional, Worlock, Kaylee, additional, Lindeboom, Rik, additional, Nikolic, Marko, additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishna, additional, Saeb-Parsy, Kourosh, additional, Bayraktar, Omer Ali, additional, Clatworthy, Menna, additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, and Teichmann, Sarah, additional

Published
2022
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40. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, primary, He, Peng, additional, Lawrence, John E, additional, Wang, Shuaiyu, additional, Tuck, Elizabeth, additional, Williams, Brian A, additional, Roberts, Kenny, additional, Kleshchevnikov, Vitalii, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Polanski, Krzysztof, additional, Elmentaite, Rasa, additional, Fasouli, Eirini S, additional, Prete, Martin, additional, He, Xiaoling, additional, Yayon, Nadav, additional, Fu, Yixi, additional, Yang, Hao, additional, Liang, Chen, additional, Zhang, Hui, additional, Blain, Raphael, additional, Chedotal, Alain, additional, FitzPatrick, David R., additional, Firth, Helen, additional, Dean, Andrew, additional, Marioni, John C, additional, Barker, Roger A, additional, Storer, Mekayla A, additional, Wold, Barbara J, additional, Zhang, Hongbo, additional, and Teichmann, Sarah A, additional

Published
2022
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41. The multi-omics spatial lung atlas reveales new cell states and their functions in airway mesenchyme

Author

Madissoon, Elo, primary, Oliver, Amanda, additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polnski, Krzysztof, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Pett, Patrick, additional, Dabrowska, Monika, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Patel, Minal, additional, Mahbubani, Krishnaa, additional, Saeb-Parsy, Kourosh, additional, Ali Bayraktar, Omer, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah, additional, and Meyer, Kerstin, additional

Published
2022
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42. A novel IgA plasma cell niche in the human airways

Author

Oliver, Amanda, primary, Madissoon, Elo, additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Kryzysztof, additional, Ribeiro Orsi, Ana Elisa, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Pett, J. Patrick, additional, Huang, Ni, additional, Elmentaite, Rasa, additional, Richoz, Nathan, additional, He, Peng, additional, Dabrowska, Monika, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Pritchard, Sophie, additional, Vieira, Sara Filipa, additional, Patel, Minal, additional, Mahbubani, Krishnaa, additional, Georgakapopoulos, Nikitas, additional, Clatworthy, Menna, additional, Stegle, Oliver, additional, Saeb-Parsy, Kourosh, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah, additional, and Meyer, Kerstin, additional

Published
2022
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43. Local and systemic responses to SARS-CoV-2 infection in children and adults

Author

Yoshida, Masahiro, primary, Worlock, Kaylee, additional, Huang, Ni, additional, Lindeboom, Rik, additional, Butler, Colin, additional, Kumasaka, Natsuhiko, additional, Dominguez Conde, Cecilia, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Richardson, Laura, additional, Polanski, Krzysztof, additional, Madissoon, Elo, additional, Barnes, Josephine, additional, Allen-Hyttinen, Jessica, additional, Kilich, Eliz, additional, Jones, Brendan, additional, De Wilton, Angus, additional, Wilbrey-Clark, Anna, additional, Sungnak, Waradon, additional, Pett, Jan Patrick, additional, Weller, Juliane, additional, Prigmore, Elena, additional, Yung, Henry, additional, Mehta, Puja, additional, Saleh, Aarash, additional, Saigal, Anita, additional, Chu, Vivian, additional, Cohen, Jonathan, additional, Cane, Clare, additional, Iordanidou, Aikaterini, additional, Shibuya, Soichi, additional, Reuschl, Ann-Kathrin, additional, Herczeg, Iván, additional, Argento, Christine, additional, Wunderink, Richard, additional, Smith, Sean, additional, Poor, Taylor, additional, Gao, Catherine, additional, Dematte, Jane, additional, Reynolds, Gary, additional, Haniffa, Muzlifah, additional, Bowyer, Georgina, additional, Coates, Matthew, additional, Clatworthy, Menna, additional, Calero-Nieto, Fernando, additional, Göttgens, Berthold, additional, O'Callaghan, Christopher, additional, Sebire, Neil, additional, Jolly, Clare, additional, De Coppi, Paolo, additional, Smith, Claire, additional, Misharin, Alexander, additional, Janes, Sam, additional, Teichmann, Sarah, additional, Meyer, Kerstin, additional, and Nikolić, Marko, additional

Published
2022
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44. A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates

Author

He, Peng, primary, Lim, Kyungtae, additional, Sun, Dawei, additional, Pett, Jan Patrick, additional, Jeng, Quitz, additional, Polanski, Krzysztof, additional, Dong, Ziqi, additional, Bolt, Liam, additional, Richardson, Laura, additional, Mamanova, Lira, additional, Dabrowska, Monika, additional, Wilbrey-Clark, Anna, additional, Madissoon, Elo, additional, Tuong, Zewen Kelvin, additional, Dann, Emma, additional, Suo, Chenqu, additional, Goh, Isaac, additional, Yoshida, Masahiro, additional, Nikolić, Marko Z, additional, Janes, Sam M, additional, He, Xiaoling, additional, Barker, Roger A, additional, Teichmann, Sarah A, additional, Marioni, John C., additional, Meyer, Kerstin B, additional, and Rawlins, Emma L, additional

Published
2022
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45. Mapping Single Cell Transcriptomes in the Intra-Tumoural and Associated Territories of Kidney Cancer

Author

Li, Ruoyan, primary, Ferdinand, John R., additional, Loudon, Kevin, additional, Bowyer, Georgina S., additional, Laidlaw, Sean, additional, Mamanova, Lira, additional, Neves, Joana B., additional, Bolt, Liam, additional, Fasouli, Eirini, additional, Lawson, Andrew, additional, Young, Matthew, additional, Hooks, Yvette, additional, Oliver, Thomas, additional, Butler, Timothy M., additional, Armitage, James, additional, Aho, Tev, additional, Riddick, Anthony C. P., additional, Gnanapragasam, Vincent, additional, Welsh, Sarah, additional, Meyer, Kerstin, additional, Warren, Anne, additional, Tran, Maxine G. B., additional, Stewart, Grant, additional, Behjati, Sam, additional, Clatworthy, Menna R., additional, Campbell, Peter J., additional, Teichmann, Sarah, additional, and Mitchell, Thomas, additional

Published
2022
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46. Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses

Author

Rodriguez-Ubreva, Javier, primary, Arutyunyan, Anna, additional, Bonder, Marc Jan, additional, Del Pino-Molina, Lucia, additional, Clark, Stephen, additional, de la Calle-Fabregat, Carlos, additional, Garcia-Alonso, Luz, additional, Handfield, Louis-Francois, additional, Ciudad, Laura, additional, Andres-Leon, Eduardo, additional, Krueger, Felix, additional, Catala-Moll, Francesc, additional, Rodriguez-Cortez, Virginia C, additional, Polanski, Krzysztof, additional, Mamanova, Lira, additional, van Dongen, Stijn, additional, Kiselev, Vladimir Yu, additional, Martinez-Saavedra, Maria T, additional, Heyn, Holger, additional, Martin, Javier, additional, Warnatz, Klaus, additional, Lopez-Granados, Eduardo, additional, Rodriguez-Gallego, Carlos, additional, Stegle, Oliver, additional, Kelsey, Gavin D, additional, Vento-Tormo, Roser, additional, and Ballestar, Esteban, additional

Published
2021
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47. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche

Author

Madissoon, Elo, primary, Oliver, Amanda J., additional, Kleshchevnikov, Vitalii, additional, Wilbrey-Clark, Anna, additional, Polanski, Krzysztof, additional, Orsi, Ana Ribeiro, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Richoz, Nathan, additional, Elmentaite, Rasa, additional, Pett, J. Patrick, additional, Huang, Ni, additional, He, Peng, additional, Dabrowska, Monika, additional, Pritchard, Sophie, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Knights, Andrew, additional, Oszlanczi, Agnes, additional, Hunter, Adam, additional, Vieira, Sara F., additional, Patel, Minal, additional, Georgakopoulos, Nikitas, additional, Mahbubani, Krishnaa, additional, Saeb-Parsy, Kourosh, additional, Clatworthy, Menna, additional, Bayraktar, Omer Ali, additional, Stegle, Oliver, additional, Kumasaka, Natsuhiko, additional, Teichmann, Sarah A., additional, and Meyer, Kerstin B., additional

Published
2021
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48. Multi-regional characterisation of renal cell carcinoma and microenvironment at single cell resolution

Author

Li, Ruoyan, primary, Ferdinand, John R., additional, Loudon, Kevin W., additional, Bowyer, Georgina S., additional, Mamanova, Lira, additional, Neves, Joana B., additional, Bolt, Liam, additional, Fasouli, Eirini S., additional, Lawson, Andrew R. J., additional, Young, Matthew D., additional, Hooks, Yvette, additional, Oliver, Thomas R. W., additional, Butler, Timothy M., additional, Armitage, James N., additional, Aho, Tev, additional, Riddick, Antony C. P., additional, Gnanapragasam, Vincent, additional, Welsh, Sarah J., additional, Meyer, Kerstin B., additional, Warren, Anne Y., additional, Tran, Maxine G. B., additional, Stewart, Grant D., additional, Behjati, Sam, additional, Clatworthy, Menna R., additional, Campbell, Peter J., additional, Teichmann, Sarah A., additional, and Mitchell, Thomas J., additional

Published
2021
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49. Late Breaking Abstract - A multiomic micro- and macro-anatomical cell atlas of the human lungs and airways

Author

Meyer, Kerstin, primary, Madisoon, Elo, additional, Wilbrey-Clark, Anna, additional, Kleshchevnikov, Vitalii, additional, Ribeiro Orsi, Ana, additional, Polanski, Krzysztof, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Oliver, Amanda, additional, Kumasaka, Natsuhiko, additional, Huang, Ni, additional, Elmentaite, Rasa, additional, Weller, Juliana, additional, Pett, Jan Patrick, additional, He, Peng, additional, Dabrowska, Monika, additional, Tuck, Liz, additional, Prigmore, Elena, additional, Knights, Andrew, additional, Pritchard, Sophie, additional, Hunter, Adam, additional, Vieira, Sarah, additional, Patel, Minal, additional, Georgakopoulos, Nikitas, additional, Muhbubani, Krishnaa, additional, Saeb-Parsy, Kourosh, additional, Stegle, Oliver, additional, and Teichmann, Sarah, additional

Published
2021
Full Text
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