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357 results on '"Abdala‐Valencia, Hiam"'

1. Profibrotic monocyte-derived alveolar macrophages are expanded in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19

Author

Bailey, Joseph I., Puritz, Connor H., Senkow, Karolina J., Markov, Nikolay S., Diaz, Estefani, Jonasson, Emmy, Yu, Zhan, Swaminathan, Suchitra, Lu, Ziyan, Fenske, Samuel, Grant, Rogan A., Abdala-Valencia, Hiam, Mylvaganam, Ruben J., Ludwig, Amy, Miller, Janet, Cumming, R. Ian, Tighe, Robert M., Gowdy, Kymberly M., Kalhan, Ravi, Jain, Manu, Bharat, Ankit, Kurihara, Chitaru, San Jose Estepar, Ruben, San Jose Estepar, Raul, Washko, George R., Shilatifard, Ali, Sznajder, Jacob I., Ridge, Karen M., Budinger, G. R. Scott, Braun, Rosemary, Misharin, Alexander V., and Sala, Marc A.

Published
2024
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2. Distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia

Author

Markov, Nikolay S., Ren, Ziyou, Senkow, Karolina J., Grant, Rogan A., Gao, Catherine A., Malsin, Elizabeth S., Sichizya, Lango, Kihshen, Hermon, Helmin, Kathryn A., Jovisic, Milica, Arnold, Jason M., Pérez-Leonor, Xóchitl G., Abdala-Valencia, Hiam, Swaminathan, Suchitra, Nwaezeapu, Julu, Kang, Mengjia, Rasmussen, Luke, Ozer, Egon A., Lorenzo-Redondo, Ramon, Hultquist, Judd F., Simons, Lacy M., Rios-Guzman, Estefany, Misharin, Alexander V., Wunderink, Richard G., Budinger, G. R. Scott, Singer, Benjamin D., and Morales-Nebreda, Luisa

Published
2024
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3. Mitochondria regulate proliferation in adult cardiac myocytes

Author

Waypa, Gregory B., Smith, Kimberly A., Mungai, Paul T., Dudley, Vincent J., Helmin, Kathryn A., Singer, Benjamin D., Peek, Clara Bien, Bass, Joseph, Nelson, Lauren, Shah, Sanjiv J., Ofman, Gaston, Wasserstrom, J. Andrew, Muller, William A., Misharin, Alexander V., Budinger, G.R. Scott, Abdala-Valencia, Hiam, Chandel, Navdeep S., Dokic, Danijela, Bartom, Elizabeth, Zhang, Shuang, Tatekoshi, Yuki, Mahmoodzadeh, Amir, Ardehali, Hossein, Thorp, Edward B., and Schumacker, Paul T.

Subjects
Oxidative phosphorylation -- Health aspects, RNA sequencing -- Analysis, Ischemia -- Complications and side effects -- Care and treatment, Epigenetic inheritance -- Analysis, Mitochondrial DNA -- Analysis, Health care industry, Care and treatment, Analysis, Complications and side effects, Health aspects
Abstract

Newborn mammalian cardiomyocytes quickly transition from a fetal to an adult phenotype that utilizes mitochondrial oxidative phosphorylation but loses mitotic capacity. We tested whether forced reversal of adult cardiomyocytes back to a fetal glycolytic phenotype would restore proliferative capacity. We deleted Uqcrfsl (mitochondrial Rieske iron- sulfur protein, RISP) in hearts of adult mice. As RISP protein decreased, heart mitochondrial function declined, and glucose utilization increased. Simultaneously, the hearts underwent hyperplastic remodeling during which cardiomyocyte number doubled without cellular hypertrophy. Cellular energy supply was preserved, AMPK activation was absent, and mTOR activation was evident. In ischemic hearts with RISP deletion, new cardiomyocytes migrated into the infarcted region, suggesting the potential for therapeutic cardiac regeneration. RNA sequencing revealed upregulation of genes associated with cardiac development and proliferation. Metabolomic analysis revealed a decrease in a-ketoglutarate (required for TET-mediated demethylation) and an increase in 5-adenosylmethionine (required for methyltransferase activity). Analysis revealed an increase in methylated CpGs near gene transcriptional start sites. Genes that were both differentially expressed and differentially methylated were linked to upregulated cardiac developmental pathways. We conclude that decreased mitochondrial function and increased glucose utilization can restore mitotic capacity in adult cardiomyocytes, resulting in the generation of new heart cells, potentially through the modification of substrates that regulate epigenetic modification of genes required for proliferation., Introduction Mitochondria generate ATP through oxidative phosphorylation (OXPHOS), but they also participate in diverse biological functions that include redox signaling (1), metabolite signaling (2), calcium signaling (3), and the generation [...]

Published
2024
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5. Author Correction: Fibroblast A20 governs fibrosis susceptibility and its repression by DREAM promotes fibrosis in multiple organs

Author

Wang, Wenxia, Bale, Swarna, Wei, Jun, Yalavarthi, Bharath, Bhattacharyya, Dibyendu, Yan, Jing Jing, Abdala-Valencia, Hiam, Xu, Dan, Sun, Hanshi, Marangoni, Roberta G., Herzog, Erica, Berdnikovs, Sergejs, Miller, Stephen D., Sawalha, Amr H., Tsou, Pei-Suen, Awaji, Kentaro, Yamashita, Takashi, Sato, Shinichi, Asano, Yoshihide, Tiruppathi, Chinnaswamy, Yeldandi, Anjana, Schock, Bettina C., Bhattacharyya, Swati, and Varga, John

Published
2023
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6. Aging is associated with a systemic length-associated transcriptome imbalance

Author

Stoeger, Thomas, Grant, Rogan A., McQuattie-Pimentel, Alexandra C., Anekalla, Kishore R., Liu, Sophia S., Tejedor-Navarro, Heliodoro, Singer, Benjamin D., Abdala-Valencia, Hiam, Schwake, Michael, Tetreault, Marie-Pier, Perlman, Harris, Balch, William E., Chandel, Navdeep S., Ridge, Karen M., Sznajder, Jacob I., Morimoto, Richard I., Misharin, Alexander V., Budinger, G. R. Scott, and Nunes Amaral, Luis A.

Published
2022
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7. scRNA-seq profiling of human granulocytes reveals expansion of developmentally flexible neutrophil precursors with mixed neutrophil and eosinophil properties in asthma.

Author

Haruna, Nana-Fatima, Politanska, Yuliya, Connelly, Andrew R, O'Connor, Kathrine, Bhattacharya, Sourav, Miklaszewski, Grace E, Pérez-Leonor, Xóchitl G, Rerko, Geddy, Hentenaar, Ian T, Nguyen, Doan C, Molina, Pedro Alberto Lamothe, Bochner, Bruce S, Abdala-Valencia, Hiam, Gill, Michelle A, Lee, F Eun-Hyung, and Berdnikovs, Sergejs

Subjects
BONE marrow, EOSINOPHILS, HEMATOPOIESIS, GRANULOCYTES, NEUTROPHILS
Abstract

Neutrophils and eosinophils share common hematopoietic precursors and usually diverge into distinct lineages with unique markers before being released from their hematopoietic site, which is the bone marrow (BM). However, previous studies identified an immature Ly6g(+) Il-5Rα(+) neutrophil population in mouse BM, expressing both neutrophil and eosinophil markers suggesting hematopoietic flexibility. Moreover, others have reported neutrophil populations expressing eosinophil-specific cell surface markers in tissues and altered disease states, confusing the field regarding eosinophil origins, function, and classification. Despite these reports, it is still unclear whether hematopoietic flexibility exists in human granulocytes. To answer this, we utilized single-cell RNA sequencing and cellular indexing of transcriptomes and epitopes by sequencing to profile human BM and circulating neutrophils and eosinophils at different stages of differentiation and determine whether neutrophil plasticity plays role in asthmatic inflammation. We show that immature metamyelocyte neutrophils in humans expand during severe asthmatic inflammation and express both neutrophil and eosinophil markers. We also show an increase in trilobed eosinophils with mixed neutrophil and eosinophil markers in allergic asthma and that interleukin-5 promotes differentiation of immature blood neutrophils into trilobed eosinophilic phenotypes, suggesting a mechanism of emergency granulopoiesis to promote myeloid inflammatory or remodeling response in patients with chronic asthma. By providing insights into unexpectedly flexible granulocyte biology and demonstrating emergency hematopoiesis in asthma, our results highlight the importance of granulocyte plasticity in eosinophil development and allergic diseases. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Fibroblast A20 governs fibrosis susceptibility and its repression by DREAM promotes fibrosis in multiple organs

Author

Wang, Wenxia, Bale, Swarna, Wei, Jun, Yalavarthi, Bharath, Bhattacharyya, Dibyendu, Yan, Jing Jing, Abdala-Valencia, Hiam, Xu, Dan, Sun, Hanshi, Marangoni, Roberta G., Herzog, Erica, Berdnikovs, Sergejs, Miller, Stephen D., Sawalha, Amr H., Tsou, Pei-Suen, Awaji, Kentaro, Yamashita, Takashi, Sato, Shinichi, Asano, Yoshihide, Tiruppathi, Chinnaswamy, Yeldandi, Anjana, Schock, Bettina C., Bhattacharyya, Swati, and Varga, John

Published
2022
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9. Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs

Author

Liu, Qianli, primary, Helmin, Kathryn A, additional, Dortzbach, Zachary D, additional, Reyes Flores, Carla P, additional, Torres Acosta, Manuel A, additional, Gurkan, Jonathan K, additional, Joudi, Anthony M, additional, Mambetsariev, Nurbek, additional, Morales-Nebreda, Luisa, additional, Perez-Leonor, Xochitl G, additional, Abdala-Valencia, Hiam, additional, and Singer, Benjamin D, additional

Published
2024
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10. Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span

Author

Misharin, Alexander V, Morales-Nebreda, Luisa, Reyfman, Paul A, Cuda, Carla M, Walter, James M, McQuattie-Pimentel, Alexandra C, Chen, Ching-I, Anekalla, Kishore R, Joshi, Nikita, Williams, Kinola JN, Abdala-Valencia, Hiam, Yacoub, Tyrone J, Chi, Monica, Chiu, Stephen, Gonzalez-Gonzalez, Francisco J, Gates, Khalilah, Lam, Anna P, Nicholson, Trevor T, Homan, Philip J, Soberanes, Saul, Dominguez, Salina, Morgan, Vince K, Saber, Rana, Shaffer, Alexander, Hinchcliff, Monique, Marshall, Stacy A, Bharat, Ankit, Berdnikovs, Sergejs, Bhorade, Sangeeta M, Bartom, Elizabeth T, Morimoto, Richard I, Balch, William E, Sznajder, Jacob I, Chandel, Navdeep S, Mutlu, Gökhan M, Jain, Manu, Gottardi, Cara J, Singer, Benjamin D, Ridge, Karen M, Bagheri, Neda, Shilatifard, Ali, Budinger, GR Scott, and Perlman, Harris

Subjects
Biomedical and Clinical Sciences, Lung, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Respiratory, Animals, Cell Differentiation, Fibrosis, Humans, Macrophages, Alveolar, Mice, Monocytes, Medical and Health Sciences, Immunology, Biomedical and clinical sciences, Health sciences
Abstract

Little is known about the relative importance of monocyte and tissue-resident macrophages in the development of lung fibrosis. We show that specific genetic deletion of monocyte-derived alveolar macrophages after their recruitment to the lung ameliorated lung fibrosis, whereas tissue-resident alveolar macrophages did not contribute to fibrosis. Using transcriptomic profiling of flow-sorted cells, we found that monocyte to alveolar macrophage differentiation unfolds continuously over the course of fibrosis and its resolution. During the fibrotic phase, monocyte-derived alveolar macrophages differ significantly from tissue-resident alveolar macrophages in their expression of profibrotic genes. A population of monocyte-derived alveolar macrophages persisted in the lung for one year after the resolution of fibrosis, where they became increasingly similar to tissue-resident alveolar macrophages. Human homologues of profibrotic genes expressed by mouse monocyte-derived alveolar macrophages during fibrosis were up-regulated in human alveolar macrophages from fibrotic compared with normal lungs. Our findings suggest that selectively targeting alveolar macrophage differentiation within the lung may ameliorate fibrosis without the adverse consequences associated with global monocyte or tissue-resident alveolar macrophage depletion.

Published
2017

12. Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19

Author

Grant, Rogan A., primary, Poor, Taylor A., additional, Sichizya, Lango, additional, Diaz, Estefani, additional, Bailey, Joseph I., additional, Soni, Sahil, additional, Senkow, Karolina J., additional, Pérez-Leonor, Xóchitl G., additional, Abdala-Valencia, Hiam, additional, Lu, Ziyan, additional, Donnelly, Helen K., additional, Simons, Lacy M., additional, Ozer, Egon A., additional, Tighe, Robert M., additional, Lomasney, Jon W., additional, Wunderink, Richard G., additional, Singer, Benjamin D., additional, Misharin, Alexander V., additional, and Budinger, G.R. Scott, additional

Published
2024
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14. Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

Author

Grant, Rogan A., Morales-Nebreda, Luisa, Markov, Nikolay S., Swaminathan, Suchitra, Querrey, Melissa, Guzman, Estefany R., Abbott, Darryl A., Donnelly, Helen K., Donayre, Alvaro, Goldberg, Isaac A., Klug, Zasu M., Borkowski, Nicole, Lu, Ziyan, Kihshen, Hermon, Politanska, Yuliya, Sichizya, Lango, Kang, Mengjia, Shilatifard, Ali, Qi, Chao, Lomasney, Jon W., Argento, A. Christine, Kruser, Jacqueline M., Malsin, Elizabeth S., Pickens, Chiagozie O., Smith, Sean B., Walter, James M., Pawlowski, Anna E., Schneider, Daniel, Nannapaneni, Prasanth, Abdala-Valencia, Hiam, Bharat, Ankit, Gottardi, Cara J., Budinger, G. R. Scott, Misharin, Alexander V., Singer, Benjamin D., and Wunderink, Richard G.

Published
2021
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15. Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function

Author

Helmin, Kathryn A., Morales-Nebreda, Luisa, Acosta, Manuel A. Torres, Anekalla, Kishore R., Chen, Shang-Yang, Abdala-Valencia, Hiam, Politanska, Yuliya, Cheresh, Paul, Akbarpour, Mahzad, Steinert, Elizabeth M., Weinberg, Samuel E., and Singer, Benjamin D.

Subjects
Genetic research, Gene expression -- Health aspects, Transcription factors -- Health aspects, Health care industry
Abstract

Tregs require Foxp3 expression and induction of a specific DNA hypomethylation signature during development, after which Tregs persist as a self-renewing population that regulates immune system activation. Whether maintenance DNA methylation is required for Treg lineage development and stability and how methylation patterns are maintained during lineage self-renewal remain unclear. Here, we demonstrate that the epigenetic regulator ubiquitin-like with plant homeodomain and RING finger domains 1 (Uhrf1) is essential for maintenance of methyl-DNA marks that stabilize Treg cellular identity by repressing effector T cell transcriptional programs. Constitutive and induced deficiency of Uhrf1 within [Foxp3.sup.+] cells resulted in global yet nonuniform loss of DNA methylation, derepression of inflammatory transcriptional programs, destabilization of the Treg lineage, and spontaneous inflammation. These findings support a paradigm in which maintenance DNA methylation is required in distinct regions of the Treg genome for both lineage establishment and stability of identity and suppressive function., Introduction [CD4.sup.+][Foxp3.sup.+] Tregs prevent catastrophic inflammation by suppressing immune system activation and promoting self tolerance (1-3). The Foxp3 transcription factor serves as the Treg lineage-specifying marker, and Tregs require constitutive [...]

Published
2020
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16. Metformin Targets Mitochondrial Electron Transport to Reduce Air-Pollution-Induced Thrombosis

Author

Soberanes, Saul, Misharin, Alexander V., Jairaman, Amit, Morales-Nebreda, Luisa, McQuattie-Pimentel, Alexandra C., Cho, Takugo, Hamanaka, Robert B., Meliton, Angelo Y., Reyfman, Paul A., Walter, James M., Chen, Ching-I, Chi, Monica, Chiu, Stephen, Gonzalez-Gonzalez, Francisco J., Antalek, Matthew, Abdala-Valencia, Hiam, Chiarella, Sergio E., Sun, Kaitlyn A., Woods, Parker S., Ghio, Andrew J., Jain, Manu, Perlman, Harris, Ridge, Karen M., Morimoto, Richard I., Sznajder, Jacob I., Balch, William E., Bhorade, Sangeeta M., Bharat, Ankit, Prakriya, Murali, Chandel, Navdeep S., Mutlu, Gökhan M., and Budinger, G.R. Scott

Published
2019
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21. Data from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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22. Supplementary Table 10 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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23. Supplementary Table 8 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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24. Supplementary Table 7 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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25. Supplementary Table 2 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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26. Supplementary Table 6 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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27. Supplementary Table 9 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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28. Supplementary Table 4 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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29. Supplementary Table 5 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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30. Supplementary Figures S1-15 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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31. Supplementary Table 3 from Posttranslational Regulation of the Exon Skipping Machinery Controls Aberrant Splicing in Leukemia

Author

Zhou, Yalu, primary, Han, Cuijuan, primary, Wang, Eric, primary, Lorch, Adam H., primary, Serafin, Valentina, primary, Cho, Byoung-Kyu, primary, Gutierrez Diaz, Blanca T., primary, Calvo, Julien, primary, Fang, Celestia, primary, Khodadadi-Jamayran, Alireza, primary, Tabaglio, Tommaso, primary, Marier, Christian, primary, Kuchmiy, Anna, primary, Sun, Limin, primary, Yacu, George, primary, Filip, Szymon K., primary, Jin, Qi, primary, Takahashi, Yoh-Hei, primary, Amici, David R., primary, Rendleman, Emily J., primary, Rawat, Radhika, primary, Bresolin, Silvia, primary, Paganin, Maddalena, primary, Zhang, Cheng, primary, Li, Hu, primary, Kandela, Irawati, primary, Politanska, Yuliya, primary, Abdala-Valencia, Hiam, primary, Mendillo, Marc L., primary, Zhu, Ping, primary, Palhais, Bruno, primary, Van Vlierberghe, Pieter, primary, Taghon, Tom, primary, Aifantis, Iannis, primary, Goo, Young Ah, primary, Guccione, Ernesto, primary, Heguy, Adriana, primary, Tsirigos, Aristotelis, primary, Wee, Keng Boon, primary, Mishra, Rama K., primary, Pflumio, Francoise, primary, Accordi, Benedetta, primary, Basso, Giuseppe, primary, and Ntziachristos, Panagiotis, primary

Published
2023
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32. Expression of vimentin alters cell mechanics, cell-cell adhesion, and gene expression profiles suggesting the induction of a hybrid EMT in human mammary epithelial cells

Author

Massachusetts Institute of Technology. Department of Mechanical Engineering, Sivagurunathan, Suganya, Vahabikashi, Amir, Yang, Haiqian, Zhang, Jun, Vazquez, Kelly, Rajasundaram, Dhivyaa, Politanska, Yuliya, Abdala-Valencia, Hiam, Notbohm, Jacob, Guo, Ming, Adam, Stephen A, Goldman, Robert D, Massachusetts Institute of Technology. Department of Mechanical Engineering, Sivagurunathan, Suganya, Vahabikashi, Amir, Yang, Haiqian, Zhang, Jun, Vazquez, Kelly, Rajasundaram, Dhivyaa, Politanska, Yuliya, Abdala-Valencia, Hiam, Notbohm, Jacob, Guo, Ming, Adam, Stephen A, and Goldman, Robert D

Abstract

Vimentin is a Type III intermediate filament (VIF) cytoskeletal protein that regulates the mechanical and migratory behavior of cells. Its expression is considered to be a marker for the epithelial to mesenchymal transition (EMT) that takes place in tumor metastasis. However, the molecular mechanisms regulated by the expression of vimentin in the EMT remain largely unexplored. We created MCF7 epithelial cell lines expressing vimentin from a cumate-inducible promoter to address this question. When vimentin expression was induced in these cells, extensive cytoplasmic VIF networks were assembled accompanied by changes in the organization of the endogenous keratin intermediate filament networks and disruption of desmosomes. Significant reductions in intercellular forces by the cells expressing VIFs were measured by quantitative monolayer traction force and stress microscopy. In contrast, laser trapping micro-rheology revealed that the cytoplasm of MCF7 cells expressing VIFs was stiffer than the uninduced cells. Vimentin expression activated transcription of genes involved in pathways responsible for cell migration and locomotion. Importantly, the EMT related transcription factor TWIST1 was upregulated only in wild type vimentin expressing cells and not in cells expressing a mutant non-polymerized form of vimentin, which only formed unit length filaments (ULF). Taken together, our results suggest that vimentin expression induces a hybrid EMT correlated with the upregulation of genes involved in cell migration.

Published
2023

33. The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging

Author

McQuattie-Pimentel, Alexandra C., Ren, Ziyou, Joshi, Nikita, Watanabe, Satoshi, Stoeger, Thomas, Chi, Monica, Lu, Ziyan, Sichizya, Lango, Aillon, Raul Piseaux, Chen, Ching-I, Soberanes, Saul, Chen, Zhangying, Reyfman, Paul A., Walter, James M., Anekalla, Kishore R., Davis, Jennifer M., Helmin, Kathryn A., Runyan, Constance E., Abdala-Valencia, Hiam, Nam, Kiwon, Meliton, Angelo Y., Winter, Deborah R., Morimoto, Richard I., Mutlu, Gokhan M., Bharat, Ankit, Perlman, Harris, Gottardi, Cara J., Ridge, Karen M., Chandel, Navdeep S., Sznajder, Jacob I., Balch, William E., Singer, Benjamin D., Misharin, Alexander V., and Budinger, G.R. Scott

Subjects
Lung diseases -- Genetic aspects -- Risk factors, Age factors in disease -- Genetic aspects, Macrophages -- Genetic aspects -- Health aspects, Health care industry
Abstract

Alveolar macrophages orchestrate the response to viral infections. Age-related changes in these cells may underlie the differential severity of pneumonia in older patients. We performed an integrated analysis of single-cell RNA-Seq data that revealed homogenous age-related changes in the alveolar macrophage transcriptome in humans and mice. Using genetic lineage tracing with sequential injury, heterochronic adoptive transfer, and parabiosis, we found that the lung microenvironment drove an age-related resistance of alveolar macrophages to proliferation that persisted during influenza A viral infection. Ligand-receptor pair analysis localized these changes to the extracellular matrix, where hyaluronan was increased in aged animals and altered the proliferative response of bone marrow-derived macrophages to granulocyte macrophage colony-stimulating factor (GM-CSF). Our findings suggest that strategies targeting the aging lung microenvironment will be necessary to restore alveolar macrophage function in aging., Introduction Advanced age is the most important risk factor for severe disease or death in patients with viral pneumonia, including coronavirus disease 2019 (COVID-19) (1,2). Alveolar macrophages play central roles [...]

Published
2021
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38. Hypercapnia alters stroma-derived Wnt production to limit β-catenin signaling and proliferation in AT2 cells

Author

Dada, Laura A., primary, Welch, Lynn C., additional, Magnani, Natalia D., additional, Ren, Ziyou, additional, Han, Hyebin, additional, Brazee, Patricia L., additional, Celli, Diego, additional, Flozak, Annette S., additional, Weng, Anthea, additional, Herrerias, Mariana Maciel, additional, Kryvenko, Vitalii, additional, Vadász, István, additional, Runyan, Constance E., additional, Abdala-Valencia, Hiam, additional, Shigemura, Masahiko, additional, Casalino-Matsuda, S. Marina, additional, Misharin, Alexander V., additional, Budinger, G.R. Scott, additional, Gottardi, Cara J., additional, and Sznajder, Jacob I., additional

Published
2023
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40. Expression of vimentin alters cell mechanics, cell-cell adhesion, and gene expression profiles suggesting the induction of a hybrid EMT in human mammary epithelial cells

Author

Sivagurunathan, Suganya, Vahabikashi, Amir, Yang, Haiqian, Zhang, Jun, Vazquez, Kelly, Rajasundaram, Dhivyaa, Politanska, Yuliya, Abdala-Valencia, Hiam, Notbohm, Jacob, Guo, Ming, Adam, Stephen A., and Goldman, Robert D.

Subjects
Cell Biology, Developmental Biology
Abstract

Vimentin is a Type III intermediate filament (VIF) cytoskeletal protein that regulates the mechanical and migratory behavior of cells. Its expression is considered to be a marker for the epithelial to mesenchymal transition (EMT) that takes place in tumor metastasis. However, the molecular mechanisms regulated by the expression of vimentin in the EMT remain largely unexplored. We created MCF7 epithelial cell lines expressing vimentin from a cumate-inducible promoter to address this question. When vimentin expression was induced in these cells, extensive cytoplasmic VIF networks were assembled accompanied by changes in the organization of the endogenous keratin intermediate filament networks and disruption of desmosomes. Significant reductions in intercellular forces by the cells expressing VIFs were measured by quantitative monolayer traction force and stress microscopy. In contrast, laser trapping micro-rheology revealed that the cytoplasm of MCF7 cells expressing VIFs was stiffer than the uninduced cells. Vimentin expression activated transcription of genes involved in pathways responsible for cell migration and locomotion. Importantly, the EMT related transcription factor TWIST1 was upregulated only in wild type vimentin expressing cells and not in cells expressing a mutant non-polymerized form of vimentin, which only formed unit length filaments (ULF). Taken together, our results suggest that vimentin expression induces a hybrid EMT correlated with the upregulation of genes involved in cell migration.

Published
2022
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41. Cilia-related gene signature in the nasal mucosa correlates with disease severity and outcomes in critical respiratory syncytial virus bronchiolitis

Author

Koch, Clarissa M., primary, Prigge, Andrew D., additional, Setar, Leah, additional, Anekalla, Kishore R., additional, Do-Umehara, Hahn Chi, additional, Abdala-Valencia, Hiam, additional, Politanska, Yuliya, additional, Shukla, Avani, additional, Chavez, Jairo, additional, Hahn, Grant R., additional, and Coates, Bria M., additional

Published
2022
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42. Elevation of activated neutrophils in chronic rhinosinusitis with nasal polyps

Author

Poposki, Julie A., primary, Klingler, Aiko I., additional, Stevens, Whitney W., additional, Suh, Lydia A., additional, Tan, Bruce K., additional, Peters, Anju T., additional, Abdala-Valencia, Hiam, additional, Grammer, Leslie C., additional, Welch, Kevin C., additional, Smith, Stephanie S., additional, Conley, David B., additional, Kern, Robert C., additional, Schleimer, Robert P., additional, and Kato, Atsushi, additional

Published
2022
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46. Age-related Differences in the Nasal Mucosal Immune Response to SARS-CoV-2

Author

Koch, Clarissa M., primary, Prigge, Andrew D., additional, Anekalla, Kishore R., additional, Shukla, Avani, additional, Do Umehara, Hanh Chi, additional, Setar, Leah, additional, Chavez, Jairo, additional, Abdala-Valencia, Hiam, additional, Politanska, Yuliya, additional, Markov, Nikolay S., additional, Hahn, Grant R., additional, Heald-Sargent, Taylor, additional, Sanchez- Pinto, L. Nelson, additional, Muller, William J., additional, Singer, Benjamin D., additional, Misharin, Alexander V., additional, Ridge, Karen M., additional, and Coates, Bria M., additional

Published
2022
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47. SF3B1 homeostasis is critical for survival and therapeutic response in T cell leukemia

Author

Han, Cuijuan, primary, Khodadadi-Jamayran, Alireza, additional, Lorch, Adam H., additional, Jin, Qi, additional, Serafin, Valentina, additional, Zhu, Ping, additional, Politanska, Yuliya, additional, Sun, Limin, additional, Gutierrez-Diaz, Blanca T., additional, Pryzhkova, Marina V., additional, Abdala-Valencia, Hiam, additional, Bartom, Elizabeth Thomas, additional, Buldini, Barbara, additional, Basso, Giuseppe, additional, Velu, Sadanandan E., additional, Sarma, Kavitha, additional, Mattamana, Basil B., additional, Cho, Byoung-Kyu, additional, Obeng, Rebecca C., additional, Goo, Young Ah, additional, Jordan, Philip W., additional, Tsirigos, Aristotelis, additional, Zhou, Yalu, additional, and Ntziachristos, Panagiotis, additional

Published
2022
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48. Hypercapnia limits β-catenin-mediated alveolar type 2 cell progenitor function by altering Wnt production from adjacent fibroblasts

Author

Dada, Laura A., primary, Welch, Lynn C., additional, Magnani, Natalia D., additional, Ren, Ziyou, additional, Brazee, Patricia L., additional, Celli, Diego, additional, Flozak, Annette S., additional, Weng, Anthea, additional, Maciel-Herrerias, Mariana, additional, Kryvenko, Vitalii, additional, Vadász, István, additional, Runyan, Constance E, additional, Abdala-Valencia, Hiam, additional, Shigemura, Masahiko, additional, Casalino-Matsuda, S. Marina, additional, Misharin, Alexander V., additional, Budinger, G.R. Scott, additional, Gottardi, Cara J., additional, and Sznajder, Jacob I., additional

Published
2022
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49. Influenza-Induced Activation of Recruited Alveolar Macrophages During the Early Inflammatory Phase Drives Lung Injury and Lethality

Author

Koch, Clarissa M., primary, Anekalla, Kishore R., additional, Hu, Yuan-Shih, additional, Davis, Jennifer M., additional, Ciesielski, Mark, additional, Gadhvi, Gaurav, additional, Chen, Shang-Yang, additional, Turner, Margaret, additional, Cheng, Yuan, additional, Coates, Bria M., additional, Abdala-Valencia, Hiam, additional, Reyfman, Paul A., additional, Misharin, Alexander V., additional, Budinger, Scott, additional, Winter, Deborah R., additional, and Ridge, Karen M., additional

Published
2022
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