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Your search keyword '"Bull, Katherine"' showing total 15 results
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2. Multiscale topology classifies and quantifies cell types in subcellular spatial transcriptomics

Author

Benjamin, Katherine, Bhandari, Aneesha, Shang, Zhouchun, Xing, Yanan, An, Yanru, Zhang, Nannan, Hou, Yong, Tillmann, Ulrike, Bull, Katherine R., and Harrington, Heather A.

Subjects
Quantitative Biology - Quantitative Methods, Mathematics - Algebraic Topology, Quantitative Biology - Genomics, Statistics - Methodology, 92-08, 55N31, 62R40, 68T09
Abstract

Spatial transcriptomics has the potential to transform our understanding of RNA expression in tissues. Classical array-based technologies produce multiple-cell-scale measurements requiring deconvolution to recover single cell information. However, rapid advances in subcellular measurement of RNA expression at whole-transcriptome depth necessitate a fundamentally different approach. To integrate single-cell RNA-seq data with nanoscale spatial transcriptomics, we present a topological method for automatic cell type identification (TopACT). Unlike popular decomposition approaches to multicellular resolution data, TopACT is able to pinpoint the spatial locations of individual sparsely dispersed cells without prior knowledge of cell boundaries. Pairing TopACT with multiparameter persistent homology landscapes predicts immune cells forming a peripheral ring structure within kidney glomeruli in a murine model of lupus nephritis, which we experimentally validate with immunofluorescent imaging. The proposed topological data analysis unifies multiple biological scales, from subcellular gene expression to multicellular tissue organization., Comment: Main text: 8 pages, 4 figures. Supplement: 12 pages, 5 figures

Published
2022

3. In Their Own Words: Amplifying Critical Literacy and Social Justice Pedagogy through Spoken Word Poetry

Author

Curwood, Jen Scott and Bull, Katherine

Abstract

Drawn from an ethnographic study of spoken word poetry in Australia, this article offers case studies of two youth poets and follows their journeys with spoken word over three years as they performed in community-based slams, engaged with the New South Wales English Extension 2 curriculum, and served as mentor poets in culturally and linguistically diverse schools. Situated in western Sydney, this article considers how spoken word poetry can be integrated into the secondary English curriculum in order to enhance critical literacy and promote social justice pedagogy. As the first study that explores the intersection of spoken word poetry with high-stakes assessment, it offers insight into how social justice shapes young people's creative practices that interrogate and celebrate their intersectional identities.

Published
2023
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4. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Author

Pagnamenta, Alistair T., Camps, Carme, Giacopuzzi, Edoardo, Taylor, John M., Hashim, Mona, Calpena, Eduardo, Kaisaki, Pamela J., Hashimoto, Akiko, Yu, Jing, Sanders, Edward, Schwessinger, Ron, Hughes, Jim R., Lunter, Gerton, Dreau, Helene, Ferla, Matteo, Lange, Lukas, Kesim, Yesim, Ragoussis, Vassilis, Vavoulis, Dimitrios V., Allroggen, Holger, Ansorge, Olaf, Babbs, Christian, Banka, Siddharth, Baños-Piñero, Benito, Beeson, David, Ben-Ami, Tal, Bennett, David L., Bento, Celeste, Blair, Edward, Brasch-Andersen, Charlotte, Bull, Katherine R., Cario, Holger, Cilliers, Deirdre, Conti, Valerio, Davies, E. Graham, Dhalla, Fatima, Dacal, Beatriz Diez, Dong, Yin, Dunford, James E., Guerrini, Renzo, Harris, Adrian L., Hartley, Jane, Hollander, Georg, Javaid, Kassim, Kane, Maureen, Kelly, Deirdre, Kelly, Dominic, Knight, Samantha J. L., Kreins, Alexandra Y., Kvikstad, Erika M., Langman, Craig B., Lester, Tracy, Lines, Kate E., Lord, Simon R., Lu, Xin, Mansour, Sahar, Manzur, Adnan, Maroofian, Reza, Marsden, Brian, Mason, Joanne, McGowan, Simon J., Mei, Davide, Mlcochova, Hana, Murakami, Yoshiko, Németh, Andrea H., Okoli, Steven, Ormondroyd, Elizabeth, Ousager, Lilian Bomme, Palace, Jacqueline, Patel, Smita Y., Pentony, Melissa M., Pugh, Chris, Rad, Aboulfazl, Ramesh, Archana, Riva, Simone G., Roberts, Irene, Roy, Noémi, Salminen, Outi, Schilling, Kyleen D., Scott, Caroline, Sen, Arjune, Smith, Conrad, Stevenson, Mark, Thakker, Rajesh V., Twigg, Stephen R. F., Uhlig, Holm H., van Wijk, Richard, Vona, Barbara, Wall, Steven, Wang, Jing, Watkins, Hugh, Zak, Jaroslav, Schuh, Anna H., Kini, Usha, Wilkie, Andrew O. M., Popitsch, Niko, and Taylor, Jenny C.

Published
2023
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5. Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model

Author

Bierzynska, Agnieszka, Bull, Katherine, Miellet, Sara, Dean, Philip, Neal, Chris, Colby, Elizabeth, McCarthy, Hugh J., Hegde, Shivaram, Sinha, Manish D., Bugarin Diz, Carmen, Stirrups, Kathleen, Megy, Karyn, Mapeta, Rutendo, Penkett, Chris, Marsh, Sarah, Forrester, Natalie, Afzal, Maryam, Stark, Hannah, BioResource, NIHR, Williams, Maggie, Welsh, Gavin I., Koziell, Ania B., Hartley, Paul S., and Saleem, Moin A.

Published
2022
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6. Demultiplexing of Single-Cell RNA sequencing data using interindividual variation in gene expression

Author

Nassiri, Isar, primary, Kwok, Andrew J, additional, Bhandari, Aneesha, additional, Bull, Katherine R, additional, Garner, Lucy C, additional, Klenerman, Paul, additional, Webber, Caleb, additional, Parkkinen, Laura, additional, Lee, Angela W, additional, Wu, Yanxia, additional, Fairfax, Benjamin, additional, Knight, Julian C, additional, Buck, David, additional, and Piazza, Paolo, additional

Published
2024
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8. B cells require DOCK8 to elicit and integrate T cell help when antigen is limiting.

Author

Deobagkar-Lele, Mukta, Crawford, Greg, Crockford, Tanya L., Back, Jennifer, Hodgson, Rose, Bhandari, Aneesha, Bull, Katherine R., and Cornall, Richard J.

Subjects
GUANINE nucleotide exchange factors, T helper cells, IMMUNOLOGIC memory, HUMORAL immunity, B cells, AGAMMAGLOBULINEMIA
Abstract

Dedicator of cytokinesis 8 (DOCK8) immunodeficiency syndrome is characterized by a failure of the germinal center response, a process involving the proliferation and positive selection of antigen-specific B cells. Here, we describe how DOCK8-deficient B cells are blocked at a light-zone checkpoint in the germinal centers of immunized mice, where they are unable to respond to T cell–dependent survival and selection signals and consequently differentiate into plasma cells or memory B cells. Although DOCK8-deficient B cells can acquire and present antigen to initiate activation of cognate T cells, integrin up-regulation, B cell–T cell conjugate formation, and costimulation are insufficient for sustained B cell and T cell activation when antigen availability is limited. Our findings provide an explanation for the failure of the humoral response in DOCK8 immunodeficiency syndrome and insight into how the level of available antigen modulates B cell–T cell cross-talk to fine-tune humoral immune responses and immunological memory. Editor's summary: In humans, loss-of-function mutations in dedicator of cytokinesis 8 (DOCK8) cause a rare, autosomal recessive primary immunodeficiency characterized, in part, by the failure of B cells to persist in germinal centers (GCs). Deobagkar-Lele et al. used Dock8-null mice to show that B cell–intrinsic DOCK8 bolsters the ability of antigen-specific B cells to receive and integrate survival signals from T follicular helper cells in the GC when the amount of antigen is limiting. This work provides insights into how the selection and affinity maturation of antigen-specific B cells can occur in the context of low antigen levels in the GC. —Seth Thomas Scanlon [ABSTRACT FROM AUTHOR]

Published
2024
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9. Prolidase Deficiency Causes Spontaneous T Cell Activation and Lupus-like Autoimmunity

Author

Hodgson, Rose, primary, Crockford, Tanya L., additional, Bhandari, Aneesha, additional, Kepple, Jessica D., additional, Back, Jennifer, additional, Cawthorne, Eleanor, additional, Abeler-Dörner, Lucie, additional, Laing, Adam G., additional, Clare, Simon, additional, Speak, Anneliese, additional, Adams, David J., additional, Dougan, Gordon, additional, Hayday, Adrian C., additional, Deobagkar-Lele, Mukta, additional, Cornall, Richard J., additional, and Bull, Katherine R., additional

Published
2023
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10. Determining the Relationship Between Blood Pressure, Kidney Function, and Chronic Kidney Disease: Insights From Genetic Epidemiology

Author

Staplin, Natalie, primary, Herrington, William G., additional, Murgia, Federico, additional, Ibrahim, Maysson, additional, Bull, Katherine R., additional, Judge, Parminder K., additional, Ng, Sarah Y.A., additional, Turner, Michael, additional, Zhu, Doreen, additional, Emberson, Jonathan, additional, Landray, Martin J., additional, Baigent, Colin, additional, Haynes, Richard, additional, and Hopewell, Jemma C., additional

Published
2022
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11. SARS-CoV-2-Specific T Cell Responses Are Not Associated with Protection against Reinfection in Hemodialysis Patients

Author

Shankar, Sushma, primary, Beckett, Joseph, additional, Tipton, Tom, additional, Ogbe, Ane, additional, Kasanyinga, Mwila, additional, Dold, Christina, additional, Lumley, Sheila, additional, Dengu, Fungai, additional, Rompianesi, Gianluca, additional, Elgilani, Faysal, additional, Longet, Stephanie, additional, Deeks, Alexandra, additional, Payne, Rebecca P., additional, Duncan, Christopher J.A., additional, Richter, Alex, additional, de Silva, Thushan I., additional, Turtle, Lance, additional, Bull, Katherine, additional, Barnardo, Martin, additional, Friend, Peter J., additional, Dunachie, Susanna J., additional, Hester, Joanna, additional, Issa, Fadi, additional, Barnes, Eleanor, additional, Carroll, Miles W., additional, and Klenerman, Paul, additional

Published
2022
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15. SARS-CoV-2-Specific T Cell Responses Are Not Associated with Protection against Reinfection in Hemodialysis Patients

Author

Shankar, S, Beckett, J, Tipton, T, Ogbe, A, Kasanyinga, M, Dold, C, Lumley, S, Dengu, F, Rompianesi, G, Elgilani, F, Longet, S, Deeks, A, Payne, RP, Duncan, CJA, Richter, A, de Silva, TI, Turtle, L, Bull, K, Barnardo, M, Friend, PJ, Dunachie, SJ, Hester, J, Issa, F, Barnes, E, Carroll, MW, Klenerman, P, Shankar, Sushma, Beckett, Joseph, Tipton, Tom, Ogbe, Ane, Kasanyinga, Mwila, Dold, Christina, Lumley, Sheila, Dengu, Fungai, Rompianesi, Gianluca, Elgilani, Faysal, Longet, Stephanie, Deeks, Alexandra, Payne, Rebecca P, Duncan, Christopher J A, Richter, Alex, de Silva, Thushan I, Turtle, Lance, Bull, Katherine, Barnardo, Martin, Friend, Peter J, Dunachie, Susanna J, Hester, Joanna, Issa, Fadi, Barnes, Eleanor, Carroll, Miles W, and Klenerman, Paul

Subjects
hemodialysi, Nephrology, Renal Dialysis, SARS-CoV-2, Reinfection, T-Lymphocytes, Research Letter, T cell, COVID-19, Humans, General Medicine, protection
Abstract

Patients on hemodialysis (HD) are vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mount poor neutralizing antibody responses after two-dose vaccination. Although serological responses have been associated with reduced rates of reinfection, the relationship between cellular immunogenicity and protection has not been established. We report, for the first time, high incidence of reinfection in patients on HD who are vaccine naive (25%), which identifies that T cell responses do not predict protection against reinfection. Instead, patients on HD who went on to become reinfected had mounted highly variable and sometimes robust proliferative T cell responses to a broad array of SARS-CoV-2 peptide pools during the primary infection. The understanding that SARS-CoV-2–specific T cell responses are not predictive of protection against future infection will be a critical issue when measuring clinical efficacy of vaccination in these vulnerable cohorts, particularly when facing rapidly emerging variants of concern.

Published
2023

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