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Sargsian S, Mondragón-Palomino O, Lejeune A, Ercelen D, Jin WB, Varghese A, Lim YAL, Guo CJ, Loke P, Cadwell K. Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation. Microbiome 2024; 12:86. [PMID: 38730492 PMCID: PMC11084060 DOI: 10.1186/s40168-024-01793-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/10/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Parasitic helminths influence the composition of the gut microbiome. However, the microbiomes of individuals living in helminth-endemic regions are understudied. The Orang Asli, an indigenous population in Malaysia with high burdens of the helminth Trichuris trichiura, display microbiotas enriched in Clostridiales, an order of spore-forming obligate anaerobes with immunogenic properties. We previously isolated novel Clostridiales that were enriched in these individuals and found that a subset promoted the Trichuris life cycle. In this study, we aimed to further characterize the functional properties of these bacteria. RESULTS Clostridiales isolates were profiled for their ability to perform 57 enzymatic reactions and produce short-chain fatty acids (SCFAs) and hydrogen sulfide, revealing that these bacteria were capable of a range of activities associated with metabolism and host response. Consistent with this finding, monocolonization of mice with individual isolates identified bacteria that were potent inducers of regulatory T-cell (Treg) differentiation in the colon. Comparisons between variables revealed by these studies identified enzymatic properties correlated with Treg induction and Trichuris egg hatching. CONCLUSION We identified Clostridiales species that are sufficient to induce high levels of Tregs. We also identified a set of metabolic activities linked with Treg differentiation and Trichuris egg hatching mediated by these newly isolated bacteria. Altogether, this study provides functional insights into the microbiotas of individuals residing in a helminth-endemic region. Video Abstract.
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Affiliation(s)
- Shushan Sargsian
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Octavio Mondragón-Palomino
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Defne Ercelen
- Department of Medicine, Division of Gastroenterology and Hepatology, New York University Langone Health, New York, NY, 10016, USA
| | - Wen-Bing Jin
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - Alan Varghese
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Yvonne A L Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Chun-Jun Guo
- Weill Cornell Medicine, Jill Roberts Institute for Research in Inflammatory Bowel Disease, Cornell University, New York, NY, 10021, USA
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Ken Cadwell
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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2
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Arifuzzaman M, Won TH, Yano H, Uddin J, Emanuel ER, Hu E, Zhang W, Li TT, Jin WB, Grier A, Kashyap S, Guo CJ, Schroeder FC, Artis D. Dietary fiber is a critical determinant of pathologic ILC2 responses and intestinal inflammation. J Exp Med 2024; 221:e20232148. [PMID: 38506708 PMCID: PMC10955042 DOI: 10.1084/jem.20232148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/18/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
Innate lymphoid cells (ILCs) can promote host defense, chronic inflammation, or tissue protection and are regulated by cytokines and neuropeptides. However, their regulation by diet and microbiota-derived signals remains unclear. We show that an inulin fiber diet promotes Tph1-expressing inflammatory ILC2s (ILC2INFLAM) in the colon, which produce IL-5 but not tissue-protective amphiregulin (AREG), resulting in the accumulation of eosinophils. This exacerbates inflammation in a murine model of intestinal damage and inflammation in an ILC2- and eosinophil-dependent manner. Mechanistically, the inulin fiber diet elevated microbiota-derived bile acids, including cholic acid (CA) that induced expression of ILC2-activating IL-33. In IBD patients, bile acids, their receptor farnesoid X receptor (FXR), IL-33, and eosinophils were all upregulated compared with controls, implicating this diet-microbiota-ILC2 axis in human IBD pathogenesis. Together, these data reveal that dietary fiber-induced changes in microbial metabolites operate as a rheostat that governs protective versus pathologic ILC2 responses with relevance to precision nutrition for inflammatory diseases.
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Affiliation(s)
- Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Tae Hyung Won
- Department of Chemistry and Chemical Biology, Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Hiroshi Yano
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jazib Uddin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Elizabeth R. Emanuel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Elin Hu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Wen Zhang
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ting-Ting Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alex Grier
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sanchita Kashyap
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Frank C. Schroeder
- Department of Chemistry and Chemical Biology, Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Allen Discovery Center for Neuroimmune Interactions, New York, NY, USA
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3
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Bonazzi E, Bretin A, Vigué L, Hao F, Patterson AD, Gewirtz AT, Chassaing B. Individualized microbiotas dictate the impact of dietary fiber on colitis sensitivity. Microbiome 2024; 12:5. [PMID: 38178260 PMCID: PMC10768099 DOI: 10.1186/s40168-023-01724-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/17/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND The observation that the intestinal microbiota is central in the development of IBD suggests that dietary fiber, the microbiota's primary source of nourishment, could play a central role in these diseases. Accordingly, enriching diets with specific soluble fibers remodels microbiota and modulates colitis sensitivity. In humans, a recent study suggests that the microbiota of select IBD patients might influence the impacts they would experience upon fiber exposure. We sought here to define the extent to which individual microbiotas varied in their responsiveness to purified soluble fiber inulin and psyllium. Moreover, the extent to which such variance might impact proneness to colitis. RESULTS We observed a high level of inter-individual variation in microbiota responsiveness to fiber inulin and psyllium: while microbiotas from select donors exhibited stark fiber-induced modulation in composition, pro-inflammatory potential, and metabolomic profile, others were only minimally impacted. Mice transplanted with fiber-sensitive microbiomes exhibited colitis highly modulated by soluble fiber consumption, while mice receiving fiber-resistant microbiotas displayed colitis severity irrespective of fiber exposure. CONCLUSION The extent to which select soluble fibers alter proneness to colitis is highly influenced by an individual's microbiota composition and further investigation of individual microbiota responsiveness toward specific dietary fiber could pave the way to personalized fiber-based intervention, both in IBD patients and healthy individuals. Video Abstract.
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Affiliation(s)
- Erica Bonazzi
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR10 8104, Université Paris Cité, Paris, France
| | - Alexis Bretin
- Institute for Biomedical Sciences, Centre for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, GA, USA
| | - Lucile Vigué
- INSERM U1016, Team "Robustness and Evolvability of Life", CNRS UMR10 8104, Université Paris Cité, Paris, France
| | - Fuhua Hao
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, Pennsylvania State University, University Park, PA, USA
| | - Andrew D Patterson
- INSERM U1016, Team "Robustness and Evolvability of Life", CNRS UMR10 8104, Université Paris Cité, Paris, France
| | - Andrew T Gewirtz
- Institute for Biomedical Sciences, Centre for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, GA, USA
| | - Benoit Chassaing
- INSERM U1016, Team "Mucosal Microbiota in Chronic Inflammatory Diseases", CNRS UMR10 8104, Université Paris Cité, Paris, France.
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4
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Zhu YP, Speir M, Tan Z, Lee JC, Nowell CJ, Chen AA, Amatullah H, Salinger AJ, Huang CJ, Wu G, Peng W, Askari K, Griffis E, Ghassemian M, Santini J, Gerlic M, Kiosses WB, Catz SD, Hoffman HM, Greco KF, Weller E, Thompson PR, Wong LP, Sadreyev R, Jeffrey KL, Croker BA. NET formation is a default epigenetic program controlled by PAD4 in apoptotic neutrophils. Sci Adv 2023; 9:eadj1397. [PMID: 38117877 PMCID: PMC10732518 DOI: 10.1126/sciadv.adj1397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Neutrophil extracellular traps (NETs) not only counteract bacterial and fungal pathogens but can also promote thrombosis, autoimmunity, and sterile inflammation. The presence of citrullinated histones, generated by the peptidylarginine deiminase 4 (PAD4), is synonymous with NETosis and is considered independent of apoptosis. Mitochondrial- and death receptor-mediated apoptosis promote gasdermin E (GSDME)-dependent calcium mobilization and membrane permeabilization leading to histone H3 citrullination (H3Cit), nuclear DNA extrusion, and cytoplast formation. H3Cit is concentrated at the promoter in bone marrow neutrophils and redistributes in a coordinated process from promoter to intergenic and intronic regions during apoptosis. Loss of GSDME prevents nuclear and plasma membrane disruption of apoptotic neutrophils but prolongs early apoptosis-induced cellular changes to the chromatin and cytoplasmic granules. Apoptotic signaling engages PAD4 in neutrophils, establishing a cellular state that is primed for NETosis, but that occurs only upon membrane disruption by GSDME, thereby redefining the end of life for neutrophils.
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Affiliation(s)
- Yanfang Peipei Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Mary Speir
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - ZheHao Tan
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jamie Casey Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
| | - Alyce A. Chen
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ari J. Salinger
- Program in Chemical Biology and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Carolyn J. Huang
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Gio Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiqi Peng
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kasra Askari
- Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric Griffis
- Nikon Imaging Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Santini
- UCSD School of Medicine Microscopy Core, University of California San Diego, La Jolla 92093, CA, USA
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | - Hal M. Hoffman
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kimberly F. Greco
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, 02115, USA
| | - Edie Weller
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, 02115, USA
| | - Paul R. Thompson
- Program in Chemical Biology and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kate L. Jeffrey
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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5
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Kordahi MC, Delaroque C, Bredèche MF, Gewirtz AT, Chassaing B. Vaccination against microbiota motility protects mice from the detrimental impact of dietary emulsifier consumption. PLoS Biol 2023; 21:e3002289. [PMID: 37725584 PMCID: PMC10508614 DOI: 10.1371/journal.pbio.3002289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
Dietary emulsifiers, including carboxymethylcellulose (CMC) and polysorbate 80 (P80), perturb gut microbiota composition and gene expression, resulting in a microbiota with enhanced capacity to activate host pro-inflammatory gene expression and invade the intestine's inner mucus layer. Such microbiota alterations promote intestinal inflammation, which can have a variety of phenotypic consequences including increased adiposity. Bacterial flagellin is a key mediator of emulsifiers' impact in that this molecule enables motility and is itself a pro-inflammatory agonist. Hence, we reasoned that training the adaptive mucosal immune system to exclude microbes that express flagellin might protect against emulsifiers. Investigating this notion found that immunizing mice with flagellin elicited an increase in mucosal anti-flagellin IgA and IgA-coated microbiota that would have otherwise developed in response to CMC and P80 consumption. Yet, eliciting these responses in advance via flagellin immunization prevented CMC/P80-induced increases in microbiota expression of pro-inflammatory agonists including LPS and flagellin. Furthermore, such immunization prevented CMC/P80-induced microbiota encroachment and deleterious pro-inflammatory consequences associated therewith, including colon shortening and increased adiposity. Hence, eliciting mucosal immune responses to pathobiont surface components, including flagellin, may be a means of combatting the array of inflammatory diseases that are promoted by emulsifiers and perhaps other modern microbiota stressors.
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Affiliation(s)
- Melissa C. Kordahi
- INSERM U1016, Team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université Paris Cité, Paris, France
| | - Clara Delaroque
- INSERM U1016, Team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université Paris Cité, Paris, France
| | - Marie-Florence Bredèche
- INSERM U1016, Team “Robustness and evolvability of life”, CNRS UMR 8104, Université Paris Cité, Paris, France
| | - Andrew T. Gewirtz
- Institute for Biomedical Sciences, Centre for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, Georgia, United States of America
| | - Benoit Chassaing
- INSERM U1016, Team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université Paris Cité, Paris, France
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Robertson A, Sall J, Venzon M, Olivas JJ, Zheng X, Cammer M, Antao N, Zhou C, Devlin JC, Saes Thur R, Bethony J, Nejsum P, Shopsin B, Torres VJ, Liang FX, Cadwell K. Bacterial contact induces polar plug disintegration to mediate whipworm egg hatching. PLoS Pathog 2023; 19:e1011647. [PMID: 37738244 PMCID: PMC10550136 DOI: 10.1371/journal.ppat.1011647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/04/2023] [Accepted: 08/30/2023] [Indexed: 09/24/2023] Open
Abstract
The bacterial microbiota promotes the life cycle of the intestine-dwelling whipworm Trichuris by mediating hatching of parasite eggs ingested by the mammalian host. Despite the enormous disease burden associated with Trichuris colonization, the mechanisms underlying this transkingdom interaction have been obscure. Here, we used a multiscale microscopy approach to define the structural events associated with bacteria-mediated hatching of eggs for the murine model parasite Trichuris muris. Through the combination of scanning electron microscopy (SEM) and serial block face SEM (SBFSEM), we visualized the outer surface morphology of the shell and generated 3D structures of the egg and larva during the hatching process. These images revealed that exposure to hatching-inducing bacteria catalyzed asymmetric degradation of the polar plugs prior to exit by the larva. Unrelated bacteria induced similar loss of electron density and dissolution of the structural integrity of the plugs. Egg hatching was most efficient when high densities of bacteria were bound to the poles. Consistent with the ability of taxonomically distant bacteria to induce hatching, additional results suggest chitinase released from larva within the eggs degrade the plugs from the inside instead of enzymes produced by bacteria in the external environment. These findings define at ultrastructure resolution the evolutionary adaptation of a parasite for the microbe-rich environment of the mammalian gut.
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Affiliation(s)
- Amicha Robertson
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Joseph Sall
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Mericien Venzon
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Janet J. Olivas
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Xuhui Zheng
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Michael Cammer
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Noelle Antao
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Chunyi Zhou
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Joseph C. Devlin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Rafaela Saes Thur
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC, United States of America
| | - Jeffrey Bethony
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC, United States of America
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, United States of America
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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7
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Smith KE, Graf E, Faig KE, Dimitroff SJ, Rockwood F, Hernandez MW, Norman GJ. Perceived control, loneliness, early-life stress, and parents' perceptions of stress. Sci Rep 2023; 13:13037. [PMID: 37563259 PMCID: PMC10415274 DOI: 10.1038/s41598-023-39572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
The COVID-19 pandemic has highlighted the importance of understanding what contributes to individual variability in experiences of stress. Increases in stress related to the pandemic have been especially pronounced in parents, indicating a need for research examining what factors contribute to parents' perceptions of stress. Here, we assessed the relationship between parents' perceptions of stress, control, loneliness, and experiences of childhood trauma in two populations of caregivers. In Study 1, we examined the relationship between perceptions of stress, control, loneliness, and history of early stress, along with indices of socioeconomic risk and resting parasympathetic nervous systema activity, which has been linked to variability in perceptions of stress, in caregivers of young children. Perceived control, loneliness, childhood stress, and resting parasympathetic nervous system activity predicted caregivers' stress. In Study 2, we replicated these initial findings in a second sample of caregivers. Additionally, we examined how these processes change over time. Caregivers demonstrated significant changes in perceptions of control, loneliness, and stress, and changes in control and childhood trauma history were associated with changes in perceptions of stress. Together these results indicate the importance of assessing how caregivers perceive their environment when examining what contributes to increased risk for stress. Additionally, they suggest that caregivers' stress-related processes are malleable and provide insight into potential targets for interventions aimed at reducing parents' stress.
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Affiliation(s)
- Karen E Smith
- University of Chicago, Chicago, Illinois, 60637, USA.
- Rutgers University-Newark, Smith Hall Rm 341, 101 Warren St, Newark, NJ, 07102, USA.
| | - Eileen Graf
- NORC at the University of Chicago, Chicago, Illinois, USA
| | - Kelly E Faig
- University of Chicago, Chicago, Illinois, 60637, USA
| | | | | | | | - Greg J Norman
- University of Chicago, Chicago, Illinois, 60637, USA
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8
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Wong P, Foltz JA, Chang L, Neal CC, Yao T, Cubitt CC, Tran J, Kersting-Schadek S, Palakurty S, Jaeger N, Russler-Germain DA, Marin ND, Gang M, Wagner JA, Zhou AY, Jacobs MT, Foster M, Schappe T, Marsala L, McClain E, Pence P, Becker-Hapak M, Fisk B, Petti AA, Griffith OL, Griffith M, Berrien-Elliott MM, Fehniger TA. T-BET and EOMES sustain mature human NK cell identity and antitumor function. J Clin Invest 2023; 133:e162530. [PMID: 37279078 PMCID: PMC10313375 DOI: 10.1172/jci162530] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Since the T-box transcription factors (TFs) T-BET and EOMES are necessary for initiation of NK cell development, their ongoing requirement for mature NK cell homeostasis, function, and molecular programming remains unclear. To address this, T-BET and EOMES were deleted in unexpanded primary human NK cells using CRISPR/Cas9. Deleting these TFs compromised in vivo antitumor response of human NK cells. Mechanistically, T-BET and EOMES were required for normal NK cell proliferation and persistence in vivo. NK cells lacking T-BET and EOMES also exhibited defective responses to cytokine stimulation. Single-cell RNA-Seq revealed a specific T-box transcriptional program in human NK cells, which was rapidly lost following T-BET and EOMES deletion. Further, T-BET- and EOMES-deleted CD56bright NK cells acquired an innate lymphoid cell precursor-like (ILCP-like) profile with increased expression of the ILC-3-associated TFs RORC and AHR, revealing a role for T-box TFs in maintaining mature NK cell phenotypes and an unexpected role of suppressing alternative ILC lineages. Our study reveals the critical importance of sustained EOMES and T-BET expression to orchestrate mature NK cell function and identity.
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Affiliation(s)
- Pamela Wong
- Department of Medicine, Division of Oncology
| | | | - Lily Chang
- Department of Medicine, Division of Oncology
| | | | - Tony Yao
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | | | | | | | | | | | | | - Mark Foster
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | - Bryan Fisk
- Department of Medicine, Division of Oncology
| | | | | | | | | | - Todd A. Fehniger
- Department of Medicine, Division of Oncology
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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9
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Rothlin CV, Ghosh S. When aging gets on the way of disposal: Senescent cell suppression of efferocytosis. J Cell Biol 2023; 222:e202212023. [PMID: 36602762 PMCID: PMC9827511 DOI: 10.1083/jcb.202212023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chronic senescence can trigger pathological inflammation. In this issue, Schloesser et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202207097) demonstrate that senescent cells employ "don't eat me" signals that inhibit the ability of macrophages to engulf them and additionally prevent macrophages from removing neighboring corpses, revealing a new mechanism by which senescence may contribute to triggering inflammation.
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Affiliation(s)
- Carla V. Rothlin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Sourav Ghosh
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
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10
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Smyth DJ, White MPJ, Johnston CJC, Donachie AM, Campillo Poveda M, McSorley HJ, Maizels RM. Protection from T cell-dependent colitis by the helminth-derived immunomodulatory mimic of transforming growth factor-β, Hp-TGM. Discov Immunol 2023; 2:kyad001. [PMID: 36855464 PMCID: PMC9958376 DOI: 10.1093/discim/kyad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/07/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
In animal models of inflammatory colitis, pathology can be ameliorated by several intestinal helminth parasites, including the mouse nematode Heligmosomoides polygyrus. To identify parasite products that may exert anti-inflammatory effects in vivo, we tested H. polygyrus excretory-secretory (HES) products, as well as a recombinantly expressed parasite protein, transforming growth factor mimic (TGM), that functionally mimics the mammalian immunomodulatory cytokine TGF-β. HES and TGM showed a degree of protection in dextran sodium sulphate-induced colitis, with a reduction in inflammatory cytokines, but did not fully block the development of pathology. HES also showed little benefit in a similar acute trinitrobenzene sulphonic acid-induced model. However, in a T cell transfer-mediated model with recombination activation gene (RAG)-deficient mice, HES-reduced disease scores if administered throughout the first 2 or 4 weeks following transfer but was less effective if treatment was delayed until 14 days after T cell transfer. Recombinant TGM similarly dampened colitis in RAG-deficient recipients of effector T cells, and was effective even if introduced only once symptoms had begun to be manifest. These results are a promising indication that TGM may replicate, and even surpass, the modulatory properties of native parasite HES.
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Affiliation(s)
- Danielle J Smyth
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Division of Cell Signalling and Immunology, University of Dundee, Dundee, UK
| | - Madeleine P J White
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | | | - Anne-Marie Donachie
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Marta Campillo Poveda
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Henry J McSorley
- Division of Cell Signalling and Immunology, University of Dundee, Dundee, UK
| | - Rick M Maizels
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, Glasgow, UK
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11
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Sinha A, Li Y, Mirzaei MK, Shamash M, Samadfam R, King IL, Maurice CF. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. Microbiome 2022; 10:105. [PMID: 35799219 PMCID: PMC9264660 DOI: 10.1186/s40168-022-01275-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. RESULTS Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. CONCLUSIONS Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.
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Affiliation(s)
- Anshul Sinha
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Yue Li
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, Guangdong, China
| | - Mohammadali Khan Mirzaei
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
- Institute of Virology, Helmholtz Center Munich and Technical University of Munich, 85764, Neuherberg, Bavaria, Germany
| | - Michael Shamash
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Rana Samadfam
- Charles River Laboratories, 22022 Transcanadienne, Senneville, QC, H9X 3R3, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, QC, Canada.
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12
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Wymore Brand M, Proctor AL, Hostetter JM, Zhou N, Friedberg I, Jergens AE, Phillips GJ, Wannemuehler MJ. Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life. PLoS One 2022; 17:e0266005. [PMID: 35381031 PMCID: PMC8982877 DOI: 10.1371/journal.pone.0266005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
The gastrointestinal microbiota begins to be acquired at birth and continually matures through early adolescence. Despite the relevance for gut health, few studies have evaluated the impact of pathobiont colonization of neonates on the severity of colitis later in life. LF82 is an adherent invasive E. coli strain associated with ileal Crohn’s disease. The aim of this study was to evaluate the severity of dextran sodium sulfate (DSS)-induced colitis in mice following E. coli LF82 colonization. Gnotobiotic mice harboring the altered Schaedler flora (ASF) were used as the model. While E. coli LF82 is neither adherent nor invasive, it was been demonstrated that adult ASF mice colonized with E. coli LF82 develop more severe DSS-induced colitis compared to control ASF mice treated with DSS. Therefore, we hypothesized that E. coli LF82 colonization of neonatal ASF mice would reduce the severity of DSS-induced inflammation compared to adult ASF mice colonized with E. coli LF82. To test this hypothesis, adult ASF mice were colonized with E. coli LF82 and bred to produce offspring (LF82N) that were vertically colonized with LF82. LF82N and adult-colonized (LF82A) mice were given 2.0% DSS in drinking water for seven days to trigger colitis. More severe inflammatory lesions were observed in the LF82N + DSS mice when compared to LF82A + DSS mice, and were characterized as transmural in most of the LF82N + DSS mice. Colitis was accompanied by secretion of proinflammatory cytokines (IFNγ, IL-17) and specific mRNA transcripts within the colonic mucosa. Using 16S rRNA gene amplicon sequencing, LF82 colonization did not induce significant changes in the ASF community; however, minimal changes in spatial redistribution by fluorescent in situ hybridization were observed. These results suggest that the age at which mice were colonized with E. coli LF82 pathobiont differentially impacted severity of subsequent colitic events.
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Affiliation(s)
- Meghan Wymore Brand
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Alexandra L. Proctor
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Jesse M. Hostetter
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Naihui Zhou
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Gregory J. Phillips
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Michael J. Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
- * E-mail:
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13
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Peterson ND, Icso JD, Salisbury JE, Rodríguez T, Thompson PR, Pukkila-Worley R. Pathogen infection and cholesterol deficiency activate the C. elegans p38 immune pathway through a TIR-1/SARM1 phase transition. eLife 2022; 11:e74206. [PMID: 35098926 PMCID: PMC8923663 DOI: 10.7554/elife.74206] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Intracellular signaling regulators can be concentrated into membrane-free, higher ordered protein assemblies to initiate protective responses during stress - a process known as phase transition. Here, we show that a phase transition of the Caenorhabditis elegans Toll/interleukin-1 receptor domain protein (TIR-1), an NAD+ glycohydrolase homologous to mammalian sterile alpha and TIR motif-containing 1 (SARM1), underlies p38 PMK-1 immune pathway activation in C. elegans intestinal epithelial cells. Through visualization of fluorescently labeled TIR-1/SARM1 protein, we demonstrate that physiologic stresses, both pathogen and non-pathogen, induce multimerization of TIR-1/SARM1 into visible puncta within intestinal epithelial cells. In vitro enzyme kinetic analyses revealed that, like mammalian SARM1, the NAD+ glycohydrolase activity of C. elegans TIR-1 is dramatically potentiated by protein oligomerization and a phase transition. Accordingly, C. elegans with genetic mutations that specifically block either multimerization or the NAD+ glycohydrolase activity of TIR-1/SARM1 fail to induce p38 PMK phosphorylation, are unable to increase immune effector expression, and are dramatically susceptible to bacterial infection. Finally, we demonstrate that a loss-of-function mutation in nhr-8, which alters cholesterol metabolism and is used to study conditions of sterol deficiency, causes TIR-1/SARM1 to oligomerize into puncta in intestinal epithelial cells. Cholesterol scarcity increases p38 PMK-1 phosphorylation, primes immune effector induction in a manner that requires TIR-1/SARM1 oligomerization and its intrinsic NAD+ glycohydrolase activity, and reduces pathogen accumulation in the intestine during a subsequent infection. These data reveal a new adaptive response that allows a metazoan host to anticipate pathogen threats during cholesterol deprivation, a time of relative susceptibility to infection. Thus, a phase transition of TIR-1/SARM1 as a prerequisite for its NAD+ glycohydrolase activity is strongly conserved across millions of years of evolution and is essential for diverse physiological processes in multiple cell types.
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Affiliation(s)
- Nicholas D Peterson
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Janneke D Icso
- Program in Chemical Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - J Elizabeth Salisbury
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Tomás Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Paul R Thompson
- Program in Chemical Biology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Read Pukkila-Worley
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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14
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Lee MY, Bedia JS, Bhate SS, Barlow GL, Phillips D, Fantl WJ, Nolan GP, Schürch CM. CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images. BMC Bioinformatics 2022; 23:46. [PMID: 35042474 PMCID: PMC8767664 DOI: 10.1186/s12859-022-04570-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Algorithmic cellular segmentation is an essential step for the quantitative analysis of highly multiplexed tissue images. Current segmentation pipelines often require manual dataset annotation and additional training, significant parameter tuning, or a sophisticated understanding of programming to adapt the software to the researcher's need. Here, we present CellSeg, an open-source, pre-trained nucleus segmentation and signal quantification software based on the Mask region-convolutional neural network (R-CNN) architecture. CellSeg is accessible to users with a wide range of programming skills. RESULTS CellSeg performs at the level of top segmentation algorithms in the 2018 Kaggle Data Challenge both qualitatively and quantitatively and generalizes well to a diverse set of multiplexed imaged cancer tissues compared to established state-of-the-art segmentation algorithms. Automated segmentation post-processing steps in the CellSeg pipeline improve the resolution of immune cell populations for downstream single-cell analysis. Finally, an application of CellSeg to a highly multiplexed colorectal cancer dataset acquired on the CO-Detection by indEXing (CODEX) platform demonstrates that CellSeg can be integrated into a multiplexed tissue imaging pipeline and lead to accurate identification of validated cell populations. CONCLUSION CellSeg is a robust cell segmentation software for analyzing highly multiplexed tissue images, accessible to biology researchers of any programming skill level.
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Affiliation(s)
- Michael Y Lee
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Computer Science, Stanford, CA, 94305, USA
| | - Jacob S Bedia
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Salil S Bhate
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Graham L Barlow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Darci Phillips
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christian M Schürch
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
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15
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Morosi LG, Cutine AM, Cagnoni AJ, Manselle-Cocco MN, Croci DO, Merlo JP, Morales RM, May M, Pérez-Sáez JM, Girotti MR, Méndez-Huergo SP, Pucci B, Gil AH, Huernos SP, Docena GH, Sambuelli AM, Toscano MA, Rabinovich GA, Mariño KV. Control of intestinal inflammation by glycosylation-dependent lectin-driven immunoregulatory circuits. Sci Adv 2021; 7:7/25/eabf8630. [PMID: 34144987 PMCID: PMC8213219 DOI: 10.1126/sciadv.abf8630] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 05/14/2023]
Abstract
Diverse immunoregulatory circuits operate to preserve intestinal homeostasis and prevent inflammation. Galectin-1 (Gal1), a β-galactoside-binding protein, promotes homeostasis by reprogramming innate and adaptive immunity. Here, we identify a glycosylation-dependent "on-off" circuit driven by Gal1 and its glycosylated ligands that controls intestinal immunopathology by targeting activated CD8+ T cells and shaping the cytokine profile. In patients with inflammatory bowel disease (IBD), augmented Gal1 was associated with dysregulated expression of core 2 β6-N-acetylglucosaminyltransferase 1 (C2GNT1) and α(2,6)-sialyltransferase 1 (ST6GAL1), glycosyltransferases responsible for creating or masking Gal1 ligands. Mice lacking Gal1 exhibited exacerbated colitis and augmented mucosal CD8+ T cell activation in response to 2,4,6-trinitrobenzenesulfonic acid; this phenotype was partially ameliorated by treatment with recombinant Gal1. While C2gnt1-/- mice exhibited aggravated colitis, St6gal1-/- mice showed attenuated inflammation. These effects were associated with intrinsic T cell glycosylation. Thus, Gal1 and its glycosylated ligands act to preserve intestinal homeostasis by recalibrating T cell immunity.
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Affiliation(s)
- Luciano G Morosi
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Anabela M Cutine
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Alejandro J Cagnoni
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Montana N Manselle-Cocco
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Diego O Croci
- Instituto de Histología y Embriología de Mendoza (IHEM-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
| | - Joaquín P Merlo
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
- Laboratorio de Inmuno-oncología Translacional, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Rosa M Morales
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - María May
- Instituto de Investigaciones Farmacológicas (ININFA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1113 Ciudad de Buenos Aires, Argentina
| | - Juan M Pérez-Sáez
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - María R Girotti
- Laboratorio de Inmuno-oncología Translacional, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Santiago P Méndez-Huergo
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Betiana Pucci
- Sección de Enfermedades Inflamatorias, Hospital de Gastroenterología Carlos Bonorino Udaondo, 1264 Ciudad de Buenos Aires, Argentina
| | - Aníbal H Gil
- Sección de Enfermedades Inflamatorias, Hospital de Gastroenterología Carlos Bonorino Udaondo, 1264 Ciudad de Buenos Aires, Argentina
| | - Sergio P Huernos
- Sección de Enfermedades Inflamatorias, Hospital de Gastroenterología Carlos Bonorino Udaondo, 1264 Ciudad de Buenos Aires, Argentina
| | - Guillermo H Docena
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC), 1900 La Plata, Argentina
| | - Alicia M Sambuelli
- Sección de Enfermedades Inflamatorias, Hospital de Gastroenterología Carlos Bonorino Udaondo, 1264 Ciudad de Buenos Aires, Argentina
| | - Marta A Toscano
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Gabriel A Rabinovich
- Laboratorio de Inmunopatología, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina.
- Laboratorio de Inmuno-oncología Translacional, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires, 1428 Ciudad de Buenos Aires, Argentina
| | - Karina V Mariño
- Laboratorio de Glicómica Funcional y Molecular, Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina.
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16
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Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract. Although the precise etiology of IBD is largely unknown, it is widely thought that diet contributes to the development of IBD. Diet shapes the composition of the gut microbiota, which plays critical roles in intestinal homeostasis. In contrast, intestinal inflammation induces gut dysbiosis and may affect the use of dietary nutrients by host cells and the gut microbiota. The interaction of diet and the gut microbiota is perturbed in patients with IBD. Herein, we review the current knowledge of diet and gut microbiota interaction in intestinal homeostasis. We also discuss alterations of diet and gut microbiota interaction that influence the outcome and the nutritional treatment of IBD. Understanding the complex relationships between diet and the gut microbiota provides crucial insight into the pathogenesis of IBD and advances the development of new therapeutic approaches.
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Affiliation(s)
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA;
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17
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Naimi S, Viennois E, Gewirtz AT, Chassaing B. Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome 2021; 9:66. [PMID: 33752754 PMCID: PMC7986288 DOI: 10.1186/s40168-020-00996-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/29/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND Epidemiologic evidence and animal studies implicate dietary emulsifiers in contributing to the increased prevalence of diseases associated with intestinal inflammation, including inflammatory bowel diseases and metabolic syndrome. Two synthetic emulsifiers in particular, carboxymethylcellulose and polysorbate 80, profoundly impact intestinal microbiota in a manner that promotes gut inflammation and associated disease states. In contrast, the extent to which other food additives with emulsifying properties might impact intestinal microbiota composition and function is not yet known. METHODS To help fill this knowledge gap, we examined here the extent to which a human microbiota, maintained ex vivo in the MiniBioReactor Array model, was impacted by 20 different commonly used dietary emulsifiers. Microbiota density, composition, gene expression, and pro-inflammatory potential (bioactive lipopolysaccharide and flagellin) were measured daily. RESULTS In accordance with previous studies, both carboxymethylcellulose and polysorbate 80 induced a lasting seemingly detrimental impact on microbiota composition and function. While many of the other 18 additives tested had impacts of similar extent, some, such as lecithin, did not significantly impact microbiota in this model. Particularly stark detrimental impacts were observed in response to various carrageenans and gums, which altered microbiota density, composition, and expression of pro-inflammatory molecules. CONCLUSIONS These results indicate that numerous, but not all, commonly used emulsifiers can directly alter gut microbiota in a manner expected to promote intestinal inflammation. Moreover, these data suggest that clinical trials are needed to reduce the usage of the most detrimental compounds in favor of the use of emulsifying agents with no or low impact on the microbiota. Video abstract.
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Affiliation(s)
- Sabrine Naimi
- INSERM U1016, team "Mucosal microbiota in chronic inflammatory diseases", CNRS UMR 8104, Université de Paris, Paris, France
| | - Emilie Viennois
- INSERM, U1149, Center of Research on Inflammation, Université de Paris, Paris, France
| | - Andrew T Gewirtz
- Institute for Biomedical Sciences, Center for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, GA, USA
| | - Benoit Chassaing
- INSERM U1016, team "Mucosal microbiota in chronic inflammatory diseases", CNRS UMR 8104, Université de Paris, Paris, France.
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18
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Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, Aghaeepour N, Kim K, Nolan GP, McIlwain DR. Landscape of coordinated immune responses to H1N1 challenge in humans. J Clin Invest 2020; 130:5800-5816. [PMID: 33044226 PMCID: PMC7598057 DOI: 10.1172/jci137265] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza is a significant cause of morbidity and mortality worldwide. Here we show changes in the abundance and activation states of more than 50 immune cell subsets in 35 individuals over 11 time points during human A/California/2009 (H1N1) virus challenge monitored using mass cytometry along with other clinical assessments. Peak change in monocyte, B cell, and T cell subset frequencies coincided with peak virus shedding, followed by marked activation of T and NK cells. Results led to the identification of CD38 as a critical regulator of plasmacytoid dendritic cell function in response to influenza virus. Machine learning using study-derived clinical parameters and single-cell data effectively classified and predicted susceptibility to infection. The coordinated immune cell dynamics defined in this study provide a framework for identifying novel correlates of protection in the evaluation of future influenza therapeutics.
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Affiliation(s)
- Zainab Rahil
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Rebecca Leylek
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Christian M. Schürch
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Han Chen
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Zach Bjornson-Hooper
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Shannon R. Christensen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Salil S. Bhate
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | | | - Gabriela K. Fragiadakis
- UCSF Data Science CoLab and UCSF Department of Medicine, UCSF, San Francisco, California, USA
| | - Nilanjan Mukherjee
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Nelson Kim
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sizun Jiang
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer Yo
- ARK Clinical Research, Long Beach, California, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Kenneth Kim
- ARK Clinical Research, Long Beach, California, USA
| | - Garry P. Nolan
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - David R. McIlwain
- Department of Pathology and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- WCCT Global, Cypress, California, USA
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19
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Abstract
Although the microbiome is established as an important regulator of health and disease, the role of viruses that inhabit asymptomatic humans (collectively, the virome) is less defined. While we are still characterizing what constitutes a healthy or diseased virome, an exciting next step is to move beyond correlations and toward identification of specific viruses and their precise mechanisms of beneficial or harmful immunomodulation. Illuminating this will represent a first step toward developing virome-focused therapies.
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Affiliation(s)
- Fatemeh Adiliaghdam
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Kate L Jeffrey
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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20
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Zhou R, Kuang Y, Zhou J, Du X, Li J, Shi J, Haburcak R, Xu B. Nanonets Collect Cancer Secretome from Pericellular Space. PLoS One 2016; 11:e0154126. [PMID: 27100780 PMCID: PMC4839576 DOI: 10.1371/journal.pone.0154126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 04/09/2016] [Indexed: 01/08/2023] Open
Abstract
Identifying novel cancer biomarkers is important for early cancer detection as it can reduce mortality rates. The cancer secretome, the collection of all macromolecules secreted by a tumor cell, alters its composition compared to normal tissue, and this change plays an important role in the observation of cancer progression. The collection and accurate analysis of cancer secretomes could lead to the discovery of novel biomarkers, thus improving outcomes of cancer treatment. We unexpectedly discovered that enzyme-instructed self-assembly (EISA) of a D-peptide hydrogelator results in nanonets/hydrogel around cancer cells that overexpress ectophosphatases. Here we show that these nanonets are able to rapidly collect proteins in the pericellular space (i.e., near the surface) of cancer cells. Because the secretory substances are at their highest concentration near the cell surface, the use of pericellular nanonets to collect the cancer secretome maximizes the yield and quality of samples, reduces pre-analytical variations, and allows the dynamic profiling of secretome samples. Thus, this new approach has great potential in identifying the heterotypic signaling in tumor microenvironments thereby improving the understanding of tumor microenvironments and accelerating the discovery of potential biomarkers in cancer biology. Data are available via ProteomeXchange with identifier PXD003924.
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Affiliation(s)
- Rong Zhou
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yi Kuang
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jie Zhou
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Xuewen Du
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jie Li
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Richard Haburcak
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
| | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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