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181 results on '"Kumasaka, Natsuhiko"'

2. Human skeletal muscle aging atlas

Author

Kedlian, Veronika R., Wang, Yaning, Liu, Tianliang, Chen, Xiaoping, Bolt, Liam, Tudor, Catherine, Shen, Zhuojian, Fasouli, Eirini S., Prigmore, Elena, Kleshchevnikov, Vitalii, Pett, Jan Patrick, Li, Tong, Lawrence, John E. G., Perera, Shani, Prete, Martin, Huang, Ni, Guo, Qin, Zeng, Xinrui, Yang, Lu, Polański, Krzysztof, Chipampe, Nana-Jane, Dabrowska, Monika, Li, Xiaobo, Bayraktar, Omer Ali, Patel, Minal, Kumasaka, Natsuhiko, Mahbubani, Krishnaa T., Xiang, Andy Peng, Meyer, Kerstin B., Saeb-Parsy, Kourosh, Teichmann, Sarah A., and Zhang, Hongbo

Published
2024
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3. Teenage and young adult pregnancy and depression: findings from the Japan environment and children’s study

Author

Ishitsuka, Kazue, Yamamoto-Hanada, Kiwako, Mezawa, Hidetoshi, Yang, Limin, Saito-Abe, Mayako, Nishizato, Minaho, Sato, Miori, Miyaji, Yumiko, Kumasaka, Natsuhiko, Ohya, Yukihiro, Kamijima, Michihiro, Yamazaki, Shin, Kishi, Reiko, Yaegashi, Nobuo, Hashimoto, Koichi, Mori, Chisato, Ito, Shuichi, Yamagata, Zentaro, Inadera, Hidekuni, Nakayama, Takeo, Iso, Hiroyasu, Shima, Masayuki, Nakamura, Hiroshige, Suganuma, Narufumi, Kusuhara, Koichi, and Katoh, Takahiko

Published
2024
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4. Modelling Technical and Biological Effects in scRNA-seq data with Scalable GPLVMs

Author

Lalchand, Vidhi, Ravuri, Aditya, Dann, Emma, Kumasaka, Natsuhiko, Sumanaweera, Dinithi, Lindeboom, Rik G. H., Madad, Shaista, Teichmann, Sarah A., and Lawrence, Neil D.

Subjects
Computer Science - Machine Learning, Quantitative Biology - Genomics, Statistics - Applications, Statistics - Machine Learning, 92D99, 92C99, J.3, I.5
Abstract

Single-cell RNA-seq datasets are growing in size and complexity, enabling the study of cellular composition changes in various biological/clinical contexts. Scalable dimensionality reduction techniques are in need to disentangle biological variation in them, while accounting for technical and biological confounders. In this work, we extend a popular approach for probabilistic non-linear dimensionality reduction, the Gaussian process latent variable model, to scale to massive single-cell datasets while explicitly accounting for technical and biological confounders. The key idea is to use an augmented kernel which preserves the factorisability of the lower bound allowing for fast stochastic variational inference. We demonstrate its ability to reconstruct latent signatures of innate immunity recovered in Kumasaka et al. (2021) with 9x lower training time. We further analyze a COVID dataset and demonstrate across a cohort of 130 individuals, that this framework enables data integration while capturing interpretable signatures of infection. Specifically, we explore COVID severity as a latent dimension to refine patient stratification and capture disease-specific gene expression., Comment: Machine Learning and Computational Biology Symposium (Oral), 2022

Published
2022

5. 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

7. 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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8. Mapping interindividual dynamics of innate immune response at single-cell resolution

Author

Kumasaka, Natsuhiko, Rostom, Raghd, Huang, Ni, Polanski, Krzysztof, Meyer, Kerstin B., Patel, Sharad, Boyd, Rachel, Gomez, Celine, Barnett, Sam N., Panousis, Nikolaos I., Schwartzentruber, Jeremy, Ghoussaini, Maya, Lyons, Paul A., Calero-Nieto, Fernando J., Göttgens, Berthold, Barnes, Josephine L., Worlock, Kaylee B., Yoshida, Masahiro, Nikolić, Marko Z., Stephenson, Emily, Reynolds, Gary, Haniffa, Muzlifah, Marioni, John C., Stegle, Oliver, Hagai, Tzachi, and Teichmann, Sarah A.

Published
2023
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9. 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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11. 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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12. Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease

Author

Ji, Sun-Gou, Juran, Brian D, Mucha, Sören, Folseraas, Trine, Jostins, Luke, Melum, Espen, Kumasaka, Natsuhiko, Atkinson, Elizabeth J, Schlicht, Erik M, Liu, Jimmy Z, Shah, Tejas, Gutierrez-Achury, Javier, Boberg, Kirsten M, Bergquist, Annika, Vermeire, Severine, Eksteen, Bertus, Durie, Peter R, Farkkila, Martti, Müller, Tobias, Schramm, Christoph, Sterneck, Martina, Weismüller, Tobias J, Gotthardt, Daniel N, Ellinghaus, David, Braun, Felix, Teufel, Andreas, Laudes, Mattias, Lieb, Wolfgang, Jacobs, Gunnar, Beuers, Ulrich, Weersma, Rinse K, Wijmenga, Cisca, Marschall, Hanns-Ulrich, Milkiewicz, Piotr, Pares, Albert, Kontula, Kimmo, Chazouillères, Olivier, Invernizzi, Pietro, Goode, Elizabeth, Spiess, Kelly, Moore, Carmel, Sambrook, Jennifer, Ouwehand, Willem H, Roberts, David J, Danesh, John, Floreani, Annarosa, Gulamhusein, Aliya F, Eaton, John E, Schreiber, Stefan, Coltescu, Catalina, Bowlus, Christopher L, Luketic, Velimir A, Odin, Joseph A, Chopra, Kapil B, Kowdley, Kris V, Chalasani, Naga, Manns, Michael P, Srivastava, Brijesh, Mells, George, Sandford, Richard N, Alexander, Graeme, Gaffney, Daniel J, Chapman, Roger W, Hirschfield, Gideon M, de Andrade, Mariza, Rushbrook, Simon M, Franke, Andre, Karlsen, Tom H, Lazaridis, Konstantinos N, and Anderson, Carl A

Subjects
Human Genome, Digestive Diseases, Autoimmune Disease, Digestive Diseases - (Gallbladder), Genetics, Rare Diseases, Inflammatory Bowel Disease, 2.1 Biological and endogenous factors, Aetiology, Oral and gastrointestinal, Adaptor Proteins, Signal Transducing, Alleles, Cholangitis, Sclerosing, Colitis, Ulcerative, Genome-Wide Association Study, Humans, Inflammatory Bowel Diseases, Polymorphism, Single Nucleotide, RNA, Messenger, Risk Factors, UK-PSC Consortium, International IBD Genetics Consortium, International PSC Study Group, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; ∼75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified four new genome-wide significant loci. The most associated SNP at one locus affects splicing and expression of UBASH3A, with the protective allele (C) predicted to cause nonstop-mediated mRNA decay and lower expression of UBASH3A. Further analyses based on common variants suggested that the genome-wide genetic correlation (rG) between PSC and ulcerative colitis (UC) (rG = 0.29) was significantly greater than that between PSC and Crohn's disease (CD) (rG = 0.04) (P = 2.55 × 10-15). UC and CD were genetically more similar to each other (rG = 0.56) than either was to PSC (P < 1.0 × 10-15). Our study represents a substantial advance in understanding of the genetics of PSC.

Published
2017

13. A map of transcriptional heterogeneity and regulatory variation in human microglia

Author

Young, Adam M. H., Kumasaka, Natsuhiko, Calvert, Fiona, Hammond, Timothy R., Knights, Andrew, Panousis, Nikolaos, Park, Jun Sung, Schwartzentruber, Jeremy, Liu, Jimmy, Kundu, Kousik, Segel, Michael, Murphy, Natalia A., McMurran, Christopher E., Bulstrode, Harry, Correia, Jason, Budohoski, Karol P., Joannides, Alexis, Guilfoyle, Mathew R., Trivedi, Rikin, Kirollos, Ramez, Morris, Robert, Garnett, Matthew R., Timofeev, Ivan, Jalloh, Ibrahim, Holland, Katherine, Mannion, Richard, Mair, Richard, Watts, Colin, Price, Stephen J., Kirkpatrick, Peter J., Santarius, Thomas, Mountjoy, Edward, Ghoussaini, Maya, Soranzo, Nicole, Bayraktar, Omer A., Stevens, Beth, Hutchinson, Peter J., Franklin, Robin J. M., and Gaffney, Daniel J.

Published
2021
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16. Parental stress and food allergy phenotypes in young children: A National Birth Cohort (JECS).

Author

Yamamoto‐Hanada, Kiwako, Pak, Kyongsun, Iwamoto, Shintaro, Konishi, Mizuho, Saito‐Abe, Mayako, Sato, Miori, Miyaji, Yumiko, Mezawa, Hidetoshi, Nishizato, Minaho, Yang, Limin, Kumasaka, Natsuhiko, Ohya, Yukihiro, Kamijima, Michihiro, Yamazaki, Shin, Kishi, Reiko, Yaegashi, Nobuo, Hashimoto, Koichi, Mori, Chisato, Ito, Shuichi, and Yamagata, Zentaro

Subjects
FOOD allergy, CHILDBIRTH, COHORT analysis, EGGS, PHENOTYPES, JUNK food, PSYCHOLOGICAL stress, CONDUCT disorders in children
Abstract

Background: Food allergy children and their families tend to have emotional distress and anxiety. There have been few reports of differences in parenting stress and a child's food allergy phenotypes. Methods: We examined the associations between food allergy phenotypes in children and parenting stress assessed by the Parenting Stress Index‐Short Form (PSI‐SF) from a national birth cohort (Japan Environment and Children's Study). Results: We included 65,805 children for statistical analysis. Of them, 7.2% of children had a food allergy diagnosis at 2 years old. The means of the total PSI‐SF (39.9 ± 10.3, 39.1 ± 9.9), CD‐SF (19.5 ± 5.4, 19.1 ± 5.2), and PD‐SF (20.5 ± 6.3, 20.0 ± 6.1) scores are similar for caregivers in the with and without food allergy groups. Food allergy diagnosis resulted in significantly higher total PSI scores (coefficient.47, 95% CI 0.19–0.75, p =.001), CD‐SF (coefficient.22, 95% CI 0.07–0.38, p =.004), and PD‐SF (coefficient.24, 95% CI 0.08–0.41, p =.004). A similar trend was observed for allergy reactions to hen's egg. However, there was no clear relationship between allergic reactions to milk, wheat, nuts, and PSI‐SF. Conclusions: Parental stress was significantly related to a child's food allergy. Furthermore, hen's egg allergy increased parental stress. Multiple food avoidance might also increase parental stress. Healthcare providers need to be aware of parental stress in our daily clinic. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.

Author

Panousis, Nikolaos I, primary, Garwany, Omar El, additional, Knights, Andrew, additional, Rop, Jesse Cheruiyot, additional, Kumasaka, Natsuhiko, additional, Imaz, Maria, additional, Vilarino, Lorena Boquete, additional, Tsingene, Anthi, additional, Barnett, Alice, additional, Gomez, Celine, additional, Anderson, Carl, additional, and Gaffney, Daniel J, additional

Published
2023
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21. 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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22. 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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23. 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

24. Maternal Dietary Zinc Intake during Pregnancy and Childhood Allergic Diseases up to Four Years: The Japan Environment and Children's Study.

Author

Yang, Limin, Sato, Miori, Saito-Abe, Mayako, Miyaji, Yumiko, Shimada, Mami, Sato, Chikako, Nishizato, Minaho, Kumasaka, Natsuhiko, Mezawa, Hidetoshi, Yamamoto-Hanada, Kiwako, and Ohya, Yukihiro

Abstract

Maternal dietary zinc intake and childhood allergy have inconsistent relationships. Thus, this study aimed to evaluate the influence of low maternal dietary zinc intake during pregnancy on developing pediatric allergic diseases. This study was designed using the Japan Environment and Children's Study dataset. The model building used data from 74,948 mother–child pairs. Maternal dietary zinc intake was estimated based on the food frequency questionnaire, collecting the intake information of 171 food and beverage items. Fitted logistic regression models and generalized estimating equation models (GEEs) estimated the association between energy-adjusted zinc intake and childhood allergic conditions. The energy-adjusted zinc intake did not affect the risk of developing allergic disorders (wheeze, asthma, atopic dermatitis, rhinitis, and food allergy) in offspring. The GEE model revealed similar insignificant odds ratios. No significant association was found between zinc intake during pregnancy and allergic diseases in offspring in early childhood. Further study remains necessary to examine the association between zinc and allergy with reliable zinc status biomarkers in the body. [ABSTRACT FROM AUTHOR]

Published
2023
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25. Endotoxin concentration and persistent eczema in early childhood.

Author

Irahara, Makoto, Yamamoto‐Hanada, Kiwako, Sato, Miori, Saito‐Abe, Mayako, Miyaji, Yumiko, Yang, Limin, Nishizato, Minaho, Kumasaka, Natsuhiko, Mezawa, Hidetohi, Ohya, Yukihiro, Kamijima, Michihiro, Yamazaki, Shin, Kishi, Reiko, Yaegashi, Nobuo, Hashimoto, Koichi, Mori, Chisato, Ito, Shuichi, Yamagata, Zentaro, Inadera, Hidekuni, and Nakayama, Takeo

Abstract

Although endotoxin concentration in the environment is negatively associated with atopic dermatitis (AD) onset in early childhood, the association between endotoxin concentration in the environment and eczema resolution in children with preexisting eczema is unclear. The aim of this study was to evaluate the association between endotoxin concentration in house dust and eczema persistence in young children. The authors used data from children participating in JECS (Japan Environment and Children's Study). In children who had AD or AD‐like lesions at the age of 1 year, the authors investigated the association between the prevalence of eczema at the age of 3 years and endotoxin concentration (categorized by quartiles) in the dust on children's mattresses at the ages of 1.5 and 3 years. This study included 605 children. Eczema was significantly less prevalent among children whose mattresses were in the second and third quartiles of endotoxin concentration when they were 18 months old than among children whose mattresses were in the first quartile (adjusted odds ratio, 0.57 [95% confidence interval, 0.35‐0.93] and adjusted odds ratio, 0.49 [95% confidence interval, 0.29–0.83], respectively). Moreover, of the children with eczema at age 3 years, those whose mattresses had endotoxin concentrations in the first quartile had significantly worse sleep disturbance caused by itchy rash (>1 time per week) than did those whose mattresses were in the third and fourth quartiles (20.0% vs 3.3% and 3.7%, both p values < 0.01). The findings indicate that low endotoxin exposure is associated with a higher prevalence of persistent eczema during early childhood. [ABSTRACT FROM AUTHOR]

Published
2023
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26. Single-cell multi-omics analysis of the immune response in COVID-19

Author

Stephenson, Emily, Reynolds, Gary, Botting, Rachel A., Calero-Nieto, Fernando J., Morgan, Michael D., Tuong, Zewen Kelvin, Bach, Karsten, Sungnak, Waradon, Worlock, Kaylee B., Yoshida, Masahiro, Kumasaka, Natsuhiko, Kania, Katarzyna, Engelbert, Justin, Olabi, Bayanne, Spegarova, Jarmila Stremenova, Wilson, Nicola K., Mende, Nicole, Jardine, Laura, Gardner, Louis C. S., Goh, Issac, Horsfall, Dave, McGrath, Jim, Webb, Simone, Mather, Michael W., Lindeboom, Rik G. H., Dann, Emma, Huang, Ni, Polanski, Krzysztof, Prigmore, Elena, Gothe, Florian, Scott, Jonathan, Payne, Rebecca P., Baker, Kenneth F., Hanrath, Aidan T., Schim van der Loeff, Ina C. D., Barr, Andrew S., Sanchez-Gonzalez, Amada, Bergamaschi, Laura, Mescia, Federica, Barnes, Josephine L., Kilich, Eliz, de Wilton, Angus, Saigal, Anita, Saleh, Aarash, Janes, Sam M., Smith, Claire M., Gopee, Nusayhah, Wilson, Caroline, Coupland, Paul, Coxhead, Jonathan M., Kiselev, Vladimir Yu, van Dongen, Stijn, Bacardit, Jaume, King, Hamish W., Rostron, Anthony J., Simpson, A. John, Hambleton, Sophie, Laurenti, Elisa, Lyons, Paul A., Meyer, Kerstin B., Nikolić, Marko Z., Duncan, Christopher J. A., Smith, Kenneth G. C., Teichmann, Sarah A., Clatworthy, Menna R., Marioni, John C., Göttgens, Berthold, and Haniffa, Muzlifah

Subjects
Proteome, COVID-19, Cross-Sectional Studies, Humans, Monocytes, Receptors, Antigen, B-Cell, Receptors, Antigen, T-Cell, SARS-CoV-2, Single-Cell Analysis, T-Lymphocytes, Transcriptome, CD34, Biology, Peripheral blood mononuclear cell, Article, General Biochemistry, Genetics and Molecular Biology, Immune system, Antigen, Receptors, Platelet activation, Progenitor cell, B-Cell, RNA sequencing, General Medicine, T-Cell, Haematopoiesis, Viral infection, Immunology, Infection, CD8
Abstract

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy., Transcriptomic and proteomic profiling of blood samples from individuals with COVID-19 reveals immune cell and hematopoietic progenitor cell alterations that are differentially associated with disease severity.

Published
2021

28. Human skeletal muscle ageing atlas

Author

Kedlian, Veronika R., primary, Wang, Yaning, additional, Liu, Tianliang, additional, Chen, Xiaoping, additional, Bolt, Liam, additional, Shen, Zhuojian, additional, Fasouli, Eirini S., additional, Prigmore, Elena, additional, Kleshchevnikov, Vitalii, additional, Li, Tong, additional, Lawrence, John E, additional, Huang, Ni, additional, Guo, Qin, additional, Yang, Lu, additional, Polański, Krzysztof, additional, Dabrowska, Monika, additional, Tudor, Catherine, additional, Li, Xiaobo, additional, Bayraktar, Omer, additional, Patel, Minal, additional, Meyer, Kerstin B., additional, Kumasaka, Natsuhiko, additional, Mahbubani, Krishnaa T., additional, Xiang, Andy Peng, additional, Saeb-Parsy, Kourosh, additional, Teichmann, Sarah A, additional, and Zhang, Hongbo, additional

Published
2022
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29. 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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30. Relationship between Food Allergy and Endotoxin Concentration and the Toleration Status at 2 Years: The Japan Environment and Children’s Study

Author

Irahara, Makoto, Yamamoto-Hanada, Kiwako, Sato, Miori, Saito-Abe, Mayako, Miyaji, Yumiko, Yang, Limin, Nishizato, Minaho, Kumasaka, Natsuhiko, Mezawa, Hidetoshi, Ohya, Yukihiro, and Group, on behalf of the Japan Environment and Children’s Study (JECS) Group on behalf of the Japan Environment and Children’s Study (JECS)

Subjects
IgG4, endotoxin, food allergy, hen’s egg, egg white, Nutrition and Dietetics, IgE, cow’s milk, Food Science
Abstract

Changes in household endotoxin concentration may affect the prognosis of food allergy (FA), but data on the association between household endotoxin concentration and an already-developed FA are scarce. Thus, we investigated the association between environmental endotoxin exposure and tolerance to hen’s egg (HE) and cow’s milk (CM) using data from children participating in the Japan Environment and Children’s Study who had HE allergies (n = 204) and CM allergy (n = 72) in their first year of life. We grouped the endotoxin results into quartiles 1–4 (Q1–Q4). In children with HE allergy and with CM allergy, there was no significant difference in the prevalence of tolerance to HE and CM at 2 years old when comparing endotoxin levels of the children in Q1 with those in Q2, Q3, and Q4, respectively. However, subgroup analyses by the presence of eczema and causal foods revealed that children in Q1 had a lower prevalence of tolerance to foods in some subgroup analyses and lower causal allergen-specific immunoglobulin G4 levels. Although an individually based approach against endotoxin according to background characteristics, such as eczema and causal foods, is necessary, preventing excessive endotoxin removal might contribute to FA resolution in some children.

Published
2023

31. 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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32. 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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33. 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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34. 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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35. 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
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36. Mapping interindividual dynamics of innate immune response at single-cell resolution

Author

Kumasaka, Natsuhiko, primary, Rostom, Raghd, additional, Huang, Ni, additional, Polanski, Krzysztof, additional, Meyer, Kerstin B., additional, Patel, Sharad, additional, Boyd, Rachel, additional, Gomez, Celine, additional, Barnett, Sam N., additional, Panousis, Nikolaos I, additional, Schwartzentruber, Jeremy, additional, Ghoussaini, Maya, additional, Lyons, Paul A., additional, Calero-Nieto, Fernando J., additional, Göttgens, Berthold, additional, Barnes, Josephine L., additional, Worlock, Kaylee B., additional, Yoshida, Masahiro, additional, Nikolic, Marko Z., additional, Stephenson, Emily, additional, Reynolds, Gary, additional, Haniffa, Muzlifah, additional, Marioni, John, additional, Stegle, Oliver, additional, Hagai, Tzachi, additional, and Teichmann, Sarah A., additional

Published
2021
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38. Allergic Disorders and Risk of Anemia in Japanese Children: Findings from the Japan Environment and Children's Study.

Author

Yang, Limin, Sato, Miori, Saito-Abe, Mayako, Miyaji, Yumiko, Shimada, Mami, Sato, Chikako, Nishizato, Minaho, Kumasaka, Natsuhiko, Mezawa, Hidetoshi, Yamamoto-Hanada, Kiwako, and Ohya, Yukihiro

Abstract

Previous epidemiological studies have reported an increased risk of anemia in people with allergic disorders. However, previous studies have followed a cross-sectional design. The aim of this study was to investigate the association between the two conditions with a cohort dataset. We used data of 80,943 children in the Japan Environment and Children's Study, the largest birth cohort in Japan. The association between anemia and allergic disorders was evaluated with a logistic regression model and propensity score analysis. After adjusting for potential confounders, children with asthma (odds ratio [OR], 1.85; 95% confidence interval [CI], 1.32–2.60), atopic dermatitis (OR, 2.18; 95% CI, 1.66–2.85), allergic rhinitis (OR, 1.35; 95% CI, 1.05–1.74), allergic rhinoconjunctivitis (OR, 2.95; 95% CI, 1.91–4.54), and food allergies (OR, 1.92; 95% CI, 1.44–2.56) at 2 years of age predicted high odds of developing anemia in the next year. Any allergy at 2 years of age was associated with an increased risk of anemia at the age of 3 years (OR, 1.80; 95% CI, 1.41–2.29). The findings remained stable in the propensity score analysis. Results suggest that allergic diseases were related to caregiver-reported anemia in children. [ABSTRACT FROM AUTHOR]

Published
2022
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39. How a Family History of Allergic Diseases Influences Food Allergy in Children: The Japan Environment and Children's Study.

Author

Saito-Abe, Mayako, Yamamoto-Hanada, Kiwako, Pak, Kyongsun, Iwamoto, Shintaro, Sato, Miori, Miyaji, Yumiko, Mezawa, Hidetoshi, Nishizato, Minaho, Yang, Limin, Kumasaka, Natsuhiko, Kobayashi, Tohru, and Ohya, Yukihiro

Abstract

The influence of family allergic history on food allergy in offspring in Japan is unknown. We analyzed data from a nationwide birth cohort study using logistic regression models to examine the associations of maternal, paternal, and both parental histories of allergic diseases (food allergy, atopic dermatitis, asthma, and rhinitis) with their child's food allergy at 1.5 and 3 years of age. This analysis included 69,379 singleton full-term mothers and 37,179 fathers and their children. All parental histories of allergic diseases showed significant positive associations with their child's food allergy. When both parents had a history of allergic diseases, the adjusted odds ratio (aOR) tended to be higher than when either parent had allergic diseases (p for trend < 0.0001). The highest aOR was detected when both parents had food allergy (2.60; 95% confidential interval, 1.58–4.27), and the aOR was 1.71 when either parent had food allergy (95% confidential interval, 1.54–1.91). The aORs were attenuated but still had significant positive associations after adjusting for the child's atopic dermatitis, a risk factor for allergy development. In conclusion, all parental allergic diseases were significantly positively associated with their child's food allergy. The effect of family history showed a stepwise increase in risk from either parent to both parents, and the highest risk of allergic disease was a parental history of food allergy. [ABSTRACT FROM AUTHOR]

Published
2022
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41. A genome-wide association identified the common genetic variants influence disease severity in β0-thalassemia/hemoglobin E

Author

Nuinoon, Manit, Makarasara, Wattanan, Mushiroda, Taisei, Setianingsih, Iswari, Wahidiyat, Pustika Amalia, Sripichai, Orapan, Kumasaka, Natsuhiko, Takahashi, Atsushi, Svasti, Saovaros, Munkongdee, Thongperm, Mahasirimongkol, Surakameth, Peerapittayamongkol, Chayanon, Viprakasit, Vip, Kamatani, Naoyuki, Winichagoon, Pranee, Kubo, Michiaki, Nakamura, Yusuke, and Fucharoen, Suthat

Published
2010
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43. Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer’s disease risk genes

Author

Schwartzentruber, Jeremy, primary, Cooper, Sarah, additional, Liu, Jimmy Z, additional, Barrio-Hernandez, Inigo, additional, Bello, Erica, additional, Kumasaka, Natsuhiko, additional, Johnson, Toby, additional, Estrada, Karol, additional, Gaffney, Daniel J., additional, Beltrao, Pedro, additional, and Bassett, Andrew, additional

Published
2020
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44. A map of transcriptional heterogeneity and regulatory variation in human microglia

Author

Young, Adam MH, primary, Kumasaka, Natsuhiko, additional, Calvert, Fiona, additional, Hammond, Timothy R., additional, Knights, Andrew, additional, Panousis, Nikolaos, additional, Schwartzentruber, Jeremy, additional, Liu, Jimmy, additional, Kundu, Kousik, additional, Segel, Michael, additional, Murphy, Natalia, additional, McMurran, Christopher E, additional, Bulstrode, Harry, additional, Correia, Jason, additional, Budohoski, Karol P, additional, Joannides, Alexis, additional, Guilfoyle, Mathew R, additional, Trivedi, Rikin, additional, Kirollos, Ramez, additional, Morris, Robert, additional, Garnett, Matthew R, additional, Fernandes, Helen, additional, Timofeev, Ivan, additional, Jalloh, Ibrahim, additional, Holland, Katherine, additional, Mannion, Richard, additional, Mair, Richard, additional, Watts, Colin, additional, Price, Stephen J, additional, Kirkpatrick, Peter J, additional, Santarius, Thomas, additional, Soranzo, Nicole, additional, Stevens, Beth, additional, Hutchinson, Peter J, additional, Franklin, Robin JM, additional, and Gaffney, Daniel J, additional

Published
2019
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48. Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells

Author

Kumasaka, Natsuhiko and Rouhani, Foad

Abstract

Human iPS cells have been generated using a diverse range of tissues from a variety of donors using different reprogramming vectors. However, these cell lines are heterogeneous, which presents a limitation for their use in disease modeling and personalized medicine. To explore the basis of this heterogeneity we generated 25 iPS cell lines under normalised conditions from the same set of somatic tissues across a number of donors. RNA-seq data sets from each cell line were compared to identify the majority contributors to transcriptional heterogeneity. We found that genetic differences between individual donors were the major cause of transcriptional variation between lines. In contrast, residual signatures from the somatic cell of origin, so called epigenetic memory, contributed relatively little to transcriptional variation. Thus, underlying genetic variation is responsible for most heterogeneity between human iPS cell lines. We conclude that epigenetic effects in hIPSCs are minimal, and that hIPSCs are a stable, robust and powerful platform for large-scale studies of the function of genetic differences between individuals. Our data also suggest that future studies using hIPSCs as a model system should focus most effort on collection of large numbers of donors, rather than generating large numbers of lines from the same donor.

Published
2014

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