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3. Profiling the human intestinal environment under physiological conditions

Author

Shalon, Dari, Culver, Rebecca Neal, Grembi, Jessica A, Folz, Jacob, Treit, Peter V, Shi, Handuo, Rosenberger, Florian A, Dethlefsen, Les, Meng, Xiandong, Yaffe, Eitan, Aranda-Díaz, Andrés, Geyer, Philipp E, Mueller-Reif, Johannes B, Spencer, Sean, Patterson, Andrew D, Triadafilopoulos, George, Holmes, Susan P, Mann, Matthias, Fiehn, Oliver, Relman, David A, and Huang, Kerwyn Casey

Subjects
Clinical Research, Digestive Diseases, Underpinning research, 1.1 Normal biological development and functioning, Oral and gastrointestinal, Humans, Bile Acids and Salts, Gastrointestinal Microbiome, Metabolome, Proteome, Bacteria, Bacteriophages, Feces, Intestines, Digestion, General Science & Technology
Abstract

The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.

Published
2023

4. Cell types of origin of the cell-free transcriptome

Author

Jones, Robert C, Karkanias, Jim, Krasnow, Mark, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D’Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin, Weinstein, Hannah NW, Winkler, Juliane, Wu, Timothy TH, Xie, Jamie, and Yung, Andrea R

Subjects
Human Genome, Genetics, Cell-Free Nucleic Acids, Humans, Transcriptome, Tabula Sapiens Consortium
Abstract

Cell-free RNA from liquid biopsies can be analyzed to determine disease tissue of origin. We extend this concept to identify cell types of origin using the Tabula Sapiens transcriptomic cell atlas as well as individual tissue transcriptomic cell atlases in combination with the Human Protein Atlas RNA consensus dataset. We define cell type signature scores, which allow the inference of cell types that contribute to cell-free RNA for a variety of diseases.

Published
2022

5. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Author

Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Vorperian, Sevahn K, Wang, Wanxin, Weinstein, Hannah NW, Winkler, Juliane, Wu, Timothy TH, Xie, Jamie, Yung, Andrea R, Zhang, Yue, and Detweiler, Angela M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Atlases as Topic, B-Lymphocytes, Cells, Humans, Organ Specificity, RNA Splicing, Single-Cell Analysis, T-Lymphocytes, Transcriptome, Tabula Sapiens Consortium*, General Science & Technology
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

10. Pursuing Human-Relevant Gut Microbiota-Immune Interactions.

Author

Spencer, Sean, Fragiadakis, Gabriela, and Sonnenburg, Justin

Subjects
Animals, Gastrointestinal Microbiome, Homeostasis, Host-Pathogen Interactions, Humans, Immune System, Immunity, Patient-Centered Care
Abstract

The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant map of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this fields current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.

Published
2019

11. A Decorative Defence : Apotropaic magic in Roman baths

Author

Spencer, Sean and Spencer, Sean

Abstract

The aim of this study is to explore the relationship between apotropaic decorations, here termed as apotropaic devices, and the architectural layout of an average Roman bathhouse. Moreover, to argue for the hypothesis that there was an apotropaic decorative program, i.e. an intentional plan for the placement of apotropaic devices within a Roman bathhouse. A sample of decorations are analysed, specifically 16 mosaics which constitute the main material, which is divided into three categories, namely, labyrinth, geometric/grid and Gorgon mosaics. Along with these there is supplementary material, namely, three freestanding sculptures (one hunchback and two herms) and two mosaics with inscriptions (One Greek and one Latin, both with a phallus symbol). The material is analysed with a modified phenomenological framework in mind, focusing on the experience which a bather might have had of the decoration itself and the room/space in which it was placed. Moreover, in order to argue for this hypothetical decorative program, this study constructs a hypothetical plan/map of an average Roman bathhouse based on the analysed material. The results gained from the analysis reveal patterns that seem to indicate a deeper intentionality than mere aesthetic appeal, and in turn these patterns seem to indicate, when viewed via our conceptual plan/map, some sort of apotropaic defence of Roman bathhouses. Thus, these results seem to lend credence to the hypothesis of an apotropaic decorative program., Syftet med denna studie är att undersöka förhållandet mellan apotropeiska dekorationer, här kallade apotropeiska anordningar, och den arkitektoniska utformningen av ett genomsnittligt romerskt badhus. Vidare syftar studien till att argumentera för hypotesen att det fanns ett apotropaiskt dekorativt program, det vill säga en avsiktlig plan för placeringen av apotropeiska anordningar i ett romerskt badhus. Ett urval av dekorationer analyseras i studien, närmare bestämt 16 mosaiker som utgör huvudmaterialet, som är indelat i tre kategorier, nämligen labyrint, geometrisk/rutnät och Gorgon mosaik. Utöver dessa analyseras kompletterande material såsom tre fristående skulpturer (en puckelrygg och två hermer) och två mosaiker med inskriptioner (en grekisk och en latinsk, båda med fallossymbol). Materialet analyseras med en modifierad fenomenologisk ram i åtanke, med fokus på den upplevelse som en badgäst kan ha haft av själva utsmyckningen och rummet/utrymmet där den placerades. I syfte att argumentera för detta hypotetiska dekorativa program konstruerar denna studie en hypotetisk plan/karta över ett genomsnittligt romerskt badhus baserat på det analyserade materialet. Resultaten från analysen avslöjar mönster som tycks indikera en djupare intentionalitet än enbart estetiskt tilltalande. I sin tur verkar dessa mönster indikera, när de ses via studiens konceptuella plan/karta, något slags apotropeiskt försvar av romerska badhus. Således verkar dessa resultat ge trovärdighet åt hypotesen om ett apotropeiskt dekorativt program.

Published
2024

14. The long noncoding RNA Morrbid regulates CD8 T cells in response to viral infection

Author

Kotzin, Jonathan J., Iseka, Fany, Wright, Jasmine, Basavappa, Megha G., Clark, Megan L., Ali, Mohammed-Alkhatim, Robertson, Tanner F., Mowel, Walter K., Joannas, Leonel, Neal, Vanessa D., Spencer, Sean P., Syrett, Camille M., Anguera, Montserrat C., Williams, Adam, Wherry, E. John, and Henao-Mejia, Jorge

Published
2019

17. Retinoic acid controls the homeostasis of pre-cDC-derived splenic and intestinal dendritic cells.

Author

Klebanoff, Christopher, Spencer, Sean, Torabi-Parizi, Parizad, Grainger, John, Roychoudhuri, Rahul, Ji, Yun, Sukumar, Madhusudhanan, Muranski, Pawel, Scott, Christopher, Hall, Jason, Ferreyra, Gabriela, Leonardi, Anthony, Borman, Zachary, Wang, Jinshan, Palmer, Douglas, Wilhelm, Christoph, Cai, Rongman, Sun, Junfeng, Danner, Robert, Gattinoni, Luca, Belkaid, Yasmine, Restifo, Nicholas, and Napoli, Joseph

Subjects
Animals, Cell Differentiation, Cell Proliferation, Cell Survival, Dendritic Cells, Female, Histocompatibility Antigens Class II, Homeostasis, Humans, Immunophenotyping, Intestinal Mucosa, Intestines, Mice, Neoplasms, Organ Specificity, Phenotype, Receptors, Retinoic Acid, Signal Transduction, Spleen, Tretinoin, Vitamin A, Whole-Body Irradiation
Abstract

Dendritic cells (DCs) comprise distinct populations with specialized immune-regulatory functions. However, the environmental factors that determine the differentiation of these subsets remain poorly defined. Here, we report that retinoic acid (RA), a vitamin A derivative, controls the homeostasis of pre-DC (precursor of DC)-derived splenic CD11b(+)CD8α(-)Esam(high) DCs and the developmentally related CD11b(+)CD103(+) subset within the gut. Whereas mice deprived of RA signaling significantly lost both of these populations, neither pre-DC-derived CD11b(-)CD8α(+) and CD11b(-)CD103(+) nor monocyte-derived CD11b(+)CD8α(-)Esam(low) or CD11b(+)CD103(-) DC populations were deficient. In fate-tracking experiments, transfer of pre-DCs into RA-supplemented hosts resulted in near complete conversion of these cells into the CD11b(+)CD8α(-) subset, whereas transfer into vitamin A-deficient (VAD) hosts caused diversion to the CD11b(-)CD8α(+) lineage. As vitamin A is an essential nutrient, we evaluated retinoid levels in mice and humans after radiation-induced mucosal injury and found this conditioning led to an acute VAD state. Consequently, radiation led to a selective loss of both RA-dependent DC subsets and impaired class II-restricted auto and antitumor immunity that could be rescued by supplemental RA. These findings establish a critical role for RA in regulating the homeostasis of pre-DC-derived DC subsets and have implications for the management of patients with immune deficiencies resulting from malnutrition and irradiation.

Published
2013

21. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

Author

Kotzin, Jonathan J., Spencer, Sean P., McCright, Sam J., Kumar, Dinesh B. Uthaya, Collet, Magalie A., Mowel, Walter K., Elliott, Ellen N., Uyar, Asli, Makiya, Michelle A., Dunagin, Margaret C., Harman, Christian C. D., Virtue, Anthony T., Zhu, Stella, Bailis, Will, Stein, Judith, Hughes, Cynthia, Raj, Arjun, Wherry, E. John, Goff, Loyal A., Klion, Amy D., Rinn, John L., Williams, Adam, Flavell, Richard A., and Henao-Mejia, Jorge

Subjects
Cell regulation -- Methods, Granulocytes -- Physiological aspects, RNA -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Jonathan J. Kotzin [1, 2]; Sean P. Spencer [1, 2]; Sam J. McCright [1, 2]; Dinesh B. Uthaya Kumar [3, 4]; Magalie A. Collet [3]; Walter K. Mowel [1, [...]

Published
2016
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23. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Author

Tabula Sapiens Consortium, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, and Vo, Kim Chi

Subjects
B-Lymphocytes, General Science & Technology, Cells, T-Lymphocytes, RNA Splicing, Human Genome, Tabula Sapiens Consortium, Atlases as Topic, Organ Specificity, Genetics, Humans, Generic health relevance, Single-Cell Analysis, Transcriptome, Biotechnology
Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

24. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

Author

Tabula Sapiens Consortium*, Tabula Sapiens Consortium*, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, Vo, Kim Chi, Tabula Sapiens Consortium*, Tabula Sapiens Consortium*, Jones, Robert C, Karkanias, Jim, Krasnow, Mark A, Pisco, Angela Oliveira, Quake, Stephen R, Salzman, Julia, Yosef, Nir, Bulthaup, Bryan, Brown, Phillip, Harper, William, Hemenez, Marisa, Ponnusamy, Ravikumar, Salehi, Ahmad, Sanagavarapu, Bhavani A, Spallino, Eileen, Aaron, Ksenia A, Concepcion, Waldo, Gardner, James M, Kelly, Burnett, Neidlinger, Nikole, Wang, Zifa, Crasta, Sheela, Kolluru, Saroja, Morri, Maurizio, Tan, Serena Y, Travaglini, Kyle J, Xu, Chenling, Alcántara-Hernández, Marcela, Almanzar, Nicole, Antony, Jane, Beyersdorf, Benjamin, Burhan, Deviana, Calcuttawala, Kruti, Carter, Matthew M, Chan, Charles KF, Chang, Charles A, Chang, Stephen, Colville, Alex, Culver, Rebecca N, Cvijović, Ivana, D'Amato, Gaetano, Ezran, Camille, Galdos, Francisco X, Gillich, Astrid, Goodyer, William R, Hang, Yan, Hayashi, Alyssa, Houshdaran, Sahar, Huang, Xianxi, Irwin, Juan C, Jang, SoRi, Juanico, Julia Vallve, Kershner, Aaron M, Kim, Soochi, Kiss, Bernhard, Kong, William, Kumar, Maya E, Kuo, Angera H, Leylek, Rebecca, Li, Baoxiang, Loeb, Gabriel B, Lu, Wan-Jin, Mantri, Sruthi, Markovic, Maxim, McAlpine, Patrick L, de Morree, Antoine, Mrouj, Karim, Mukherjee, Shravani, Muser, Tyler, Neuhöfer, Patrick, Nguyen, Thi D, Perez, Kimberly, Phansalkar, Ragini, Puluca, Nazan, Qi, Zhen, Rao, Poorvi, Raquer-McKay, Hayley, Schaum, Nicholas, Scott, Bronwyn, Seddighzadeh, Bobak, Segal, Joe, Sen, Sushmita, Sikandar, Shaheen, Spencer, Sean P, Steffes, Lea C, Subramaniam, Varun R, Swarup, Aditi, Swift, Michael, Van Treuren, Will, Trimm, Emily, Veizades, Stefan, Vijayakumar, Sivakamasundari, and Vo, Kim Chi

Abstract

Molecular characterization of cell types using single-cell transcriptome sequencing is revolutionizing cell biology and enabling new insights into the physiology of human organs. We created a human reference atlas comprising nearly 500,000 cells from 24 different tissues and organs, many from the same donor. This atlas enabled molecular characterization of more than 400 cell types, their distribution across tissues, and tissue-specific variation in gene expression. Using multiple tissues from a single donor enabled identification of the clonal distribution of T cells between tissues, identification of the tissue-specific mutation rate in B cells, and analysis of the cell cycle state and proliferative potential of shared cell types across tissues. Cell type-specific RNA splicing was discovered and analyzed across tissues within an individual.

Published
2022

25. Compartmentalized Control of Skin Immunity by Resident Commensals

Author

Naik, Shruti, Bouladoux, Nicolas, Wilhelm, Christoph, Molloy, Michael J., Salcedo, Rosalba, Kastenmuller, Wolfgang, Deming, Clayton, Quinones, Mariam, Koo, Lily, Conlan, Sean, Spencer, Sean, Hall, Jason A., Dzutsev, Amiran, Kong, Heidi, Campbell, Daniel J., Trinchieri, Giorgio, Segre, Julia A., and Belkaid, Yasmine

Published
2012
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26. Fermented foods restructure gut microbiota and promote immune regulation via microbial metabolites

Author

Spencer, Sean Paul, primary, Silva, Evelyn Giselle Lemus, additional, Caffery, Elisa Benedetti, additional, Carter, Matthew Merrill, additional, Culver, Rebecca Neal, additional, Wang, Min, additional, Gellman, Rebecca Hope, additional, Wastyk, Hannah Constance, additional, Higginbottom, Steven Kyle, additional, and Sonnenburg, Justin Laine, additional

Published
2022
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28. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

Author

Merrill, Bryan D., primary, Carter, Matthew M., additional, Olm, Matthew R., additional, Dahan, Dylan, additional, Tripathi, Surya, additional, Spencer, Sean P., additional, Yu, Brian, additional, Jain, Sunit, additional, Neff, Norma, additional, Jha, Aashish R., additional, Sonnenburg, Erica D., additional, and Sonnenburg, Justin L., additional

Published
2022
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29. Mo1729 EFFECTS OF AN INTERMITTENT REDUCED CALORIE DIET ON CROHN'S DISEASE

Author

Kulkarni, Chiraag, Fardeen, Touran, Gubatan, John Mark, Jarr, Karolin J., Temby, Michelle, Patel, Akshar, Dickson, Eliza R., Jang, Hyunsu, Singh, Gulshan, Ye, Jiayu, Keyashian, Kian, Streett, Sarah E., Ho, Edith Y., Barber, Grant E., Singh, Sundeep, Limsui, David, Anaizi, Nadine, Becker, Laren S., Spencer, Sean, Mehrish, Divya, Perelman, Dalia, Habtezion, Aida, Sonnenburg, Justin, Gardner, Christopher, and Sinha, Sidhartha R.

Published
2024
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32. Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

Author

Shalon, Dari, primary, Culver, Rebecca Neal, additional, Grembi, Jessica A., additional, Folz, Jacob, additional, Treit, Peter, additional, Dethlefsen, Les, additional, Meng, Xiandong, additional, Yaffe, Eitan, additional, Spencer, Sean, additional, Shi, Handuo, additional, Aranda-Díaz, Andrés, additional, Patterson, Andrew D., additional, Triadafilopoulos, George, additional, Holmes, Susan P., additional, Mann, Matthias, additional, Fiehn, Oliver, additional, Relman, David A., additional, and Huang, Kerwyn Casey, additional

Published
2022
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33. Towards a Reconfigurable Cyber-Physical Systems Framework for Rapid Development of Scalable Next-Generation Smart Medical Devices

Author

Cuckov, Filip, primary, Spencer, Sean, additional, Gorczynski, Piotr, additional, Lomba, Lucas, additional, Ingles, Garry, additional, Watson, Preston, additional, Kearns, Michael, additional, Harling, Joseph, additional, Yeh, Eric, additional, Khan, Shakir, additional, Hasan, Tayyaba, additional, and Celli, Jonathan P., additional

Published
2021
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37. Environmental enteric dysfunction induces regulatory T cells that inhibit local CD4+ T cell responses and impair oral vaccine efficacy

Author

Bhattacharjee, Amrita, primary, Burr, Ansen H.P., additional, Overacre-Delgoffe, Abigail E., additional, Tometich, Justin T., additional, Yang, Deyi, additional, Huckestein, Brydie R., additional, Linehan, Jonathan L., additional, Spencer, Sean P., additional, Hall, Jason A., additional, Harrison, Oliver J., additional, Morais da Fonseca, Denise, additional, Norton, Elizabeth B., additional, Belkaid, Yasmine, additional, and Hand, Timothy W., additional

Published
2021
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40. High Prevalence of Concurrent Gastrointestinal Manifestations in Patients with SARS-CoV-2: Early Experience from California

Author

Cholankeril, George, Podboy, Alexander, Aivaliotis, Vasiliki Irene, Tarlow, Branden, Pham, Edward A., Spencer, Sean, Kim, Donghee, Hsing, Ann, and Ahmed, Aijaz

Subjects
Adult, Male, Gastrointestinal Diseases, SARS-CoV-2, Pneumonia, Viral, COVID-19, Middle Aged, Article, California, Betacoronavirus, Prevalence, Humans, Female, Coronavirus Infections, Pandemics, Aged, Retrospective Studies
Published
2020

45. Enteropathy-induced regulatory T cells inhibit intestinal CD4+ T cell responses against oral vaccines

Author

Bhattacharjee, Amrita, primary, Burr, Ansen H.P., additional, Overacre-Delgoffe, Abigail E., additional, Tometich, Justin T., additional, Yang, Deyi, additional, Huckestein, Brydie R., additional, Linehan, Jonathan L., additional, Spencer, Sean P., additional, Hall, Jason A., additional, Harrison, Oliver J., additional, da Fonseca, Denise Morais, additional, Norton, Elizabeth B., additional, Belkaid, Yasmine, additional, and Hand, Timothy W., additional

Published
2020
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47. It's Home Time.

Author

Spencer, Sean and Moore, Shorna

Abstract

For most kids, home time is something to look forward to. For others, the sound of the bell at 3:30 is a stark reminder that they have nowhere safe to go and no parent to pick them up. [ABSTRACT FROM AUTHOR]

Published
2024

48. CH4, H2S, and H2O: How Do They Relate to Microbiome-Driven IBS Pathogenesis?

Author

Spencer, Sean

Subjects
*IRRITABLE colon, *FECAL microbiota transplantation, *PATHOGENESIS
Abstract

The article discusses the relationship between the human intestinal microbiome and irritable bowel syndrome (IBS). It highlights the role of microbial composition and functions in the pathogenesis of IBS and functional gastrointestinal diseases. The article presents evidence of IBS symptom improvement with antibiotic treatment and the potential of targeting microbial alterations through fecal microbiota transplant. The study also explores the impact of microorganisms producing methane and hydrogen sulfide on gastrointestinal physiology using rat models. The findings suggest that reducing methane production may alleviate constipation, while increased hydrogen sulfide production may affect stool water. The article emphasizes the need for further research to understand the mechanisms and develop targeted therapies for microbiome-driven symptoms in IBS patients. [Extracted from the article]

Published
2024
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49. The gut microbiota regulates white adipose tissue inflammation and obesity via a family of microRNAs

Author

Virtue, Anthony T., primary, McCright, Sam J., additional, Wright, Jasmine M., additional, Jimenez, Monica T., additional, Mowel, Walter K., additional, Kotzin, Jonathan J., additional, Joannas, Leonel, additional, Basavappa, Megha G., additional, Spencer, Sean P., additional, Clark, Megan L., additional, Eisennagel, Stephen H., additional, Williams, Adam, additional, Levy, Maayan, additional, Manne, Sasikanth, additional, Henrickson, Sarah E., additional, Wherry, E. John, additional, Thaiss, Christoph A., additional, Elinav, Eran, additional, and Henao-Mejia, Jorge, additional

Published
2019
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