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Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 2024; 32:181-190.e9. [PMID: 38228143 PMCID: PMC10922750 DOI: 10.1016/j.chom.2023.12.014] [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: 08/03/2023] [Revised: 11/14/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The early microbial colonization of the gastrointestinal tract can have long-term impacts on development and health. Keystone species, including Bacteroides spp., are prominent in early life and play crucial roles in maintaining the structure of the intestinal ecosystem. However, the process by which a resilient community is curated during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa in early life and regulates a commensal colonization program. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. NanH is required for vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and microbiota mediated through host-derived glycans to promote stable colonization.
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Affiliation(s)
- Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristija Sejane
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiaqi Zhao
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic M McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA 92093, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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2
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Buzun E, Hsu CY, Sejane K, Oles RE, Ayala AV, Loomis LR, Zhao J, Rossitto LA, McGrosso D, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early life colonization by a pioneering gut commensal. bioRxiv 2023:2023.08.08.552477. [PMID: 37609270 PMCID: PMC10441351 DOI: 10.1101/2023.08.08.552477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversity, and function of the intestinal ecosystem. However, the process by which a defined and resilient community is curated and maintained during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa and regulates the commensal colonization program during the first weeks of life. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. After examining the dynamics between pioneer gut Bacteroides species in the murine gut, we discovered that NanH enables vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, we demonstrate that NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and the microbiota mediated through host-derived glycans to promote stable intestinal colonization.
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3
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Elsaid K, Merriman TR, Rossitto LA, Liu-Bryan R, Karsh J, Phipps-Green A, Jay GD, Elsayed S, Qadri M, Miner M, Cadzow M, Dambruoso TJ, Schmidt TA, Dalbeth N, Chhana A, Höglund J, Ghassemian M, Campeau A, Maltez N, Karlsson NG, Gonzalez DJ, Terkeltaub R. Amplification of Inflammation by Lubricin Deficiency Implicated in Incident, Erosive Gout Independent of Hyperuricemia. Arthritis Rheumatol 2023; 75:794-805. [PMID: 36457235 PMCID: PMC10191887 DOI: 10.1002/art.42413] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 07/05/2022] [Revised: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022]
Abstract
OBJECTIVE In gout, hyperuricemia promotes urate crystal deposition, which stimulates the NLRP3 inflammasome and interleukin-1β (IL-1β)-mediated arthritis. Incident gout without background hyperuricemia is rarely reported. To identify hyperuricemia-independent mechanisms driving gout incidence and progression, we characterized erosive urate crystalline inflammatory arthritis in a young female patient with normouricemia diagnosed as having sufficient and weighted classification criteria for gout according to the American College of Rheumatology (ACR)/EULAR gout classification criteria (the proband). METHODS We conducted whole-genome sequencing, quantitative proteomics, whole-blood RNA-sequencing analysis using serum samples from the proband. We used a mouse model of IL-1β-induced knee synovitis to characterize proband candidate genes, biomarkers, and pathogenic mechanisms of gout. RESULTS Lubricin level was attenuated in human proband serum and associated with elevated acute-phase reactants and inflammatory whole-blood transcripts and transcriptional pathways. The proband had predicted damaging gene variants of NLRP3 and of inter-α trypsin inhibitor heavy chain 3, an inhibitor of lubricin-degrading cathepsin G. Changes in the proband's serum protein interactome network supported enhanced lubricin degradation, with cathepsin G activity increased relative to its inhibitors, SERPINB6 and thrombospondin 1. Activation of Toll-like receptor 2 (TLR-2) suppressed levels of lubricin mRNA and lubricin release in cultured human synovial fibroblasts (P < 0.01). Lubricin blunted urate crystal precipitation and IL-1β induction of xanthine oxidase and urate in cultured macrophages (P < 0.001). In lubricin-deficient mice, injection of IL-1β in knees increased xanthine oxidase-positive synovial resident M1 macrophages (P < 0.05). CONCLUSION Our findings linked normouricemic erosive gout to attenuated lubricin, with impaired control of cathepsin G activity, compounded by deleterious NLRP3 variants. Lubricin suppressed monosodium urate crystallization and blunted IL-1β-induced increases in xanthine oxidase and urate in macrophages. The collective activities of articular lubricin that could limit incident and erosive gouty arthritis independently of hyperuricemia are subject to disruption by inflammation, activated cathepsin G, and synovial fibroblast TLR-2 signaling.
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Affiliation(s)
- Khaled Elsaid
- Chapman University School of Pharmacy, Irvine, California
| | - Tony R Merriman
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Leigh-Ana Rossitto
- Department of Pharmacology, School of Medicine, and Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, California
| | - Ru Liu-Bryan
- VA San Diego Healthcare System, San Diego, and Department of Medicine, UC San Diego, La Jolla, California
| | - Jacob Karsh
- The Ottawa Hospital, Division of Rheumatology, University of Ottawa, Canada
| | | | - Gregory D Jay
- Department of Emergency Medicine, Alpert School of Medicine, and Division of Biomedical Engineering, School of Engineering, Brown University, Rhode, Island
| | - Sandy Elsayed
- Chapman University School of Pharmacy, Irvine, California
| | | | - Marin Miner
- VA San Diego Healthcare System, San Diego, California
| | - Murray Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Talia J Dambruoso
- Division of Biomedical Engineering, School of Engineering, Brown University, Rhode, Island
| | - Tannin A Schmidt
- Biomedical Engineering Department, School of Dental Medicine, UConn Health, Farmington, Connecticut
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Ashika Chhana
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Jennifer Höglund
- Department of Medical Biochemistry, Institute for Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, Department of Chemistry/Biochemistry, UC San Diego
| | - Anaamika Campeau
- Department of Pharmacology, School of Medicine, and Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, California
| | - Nancy Maltez
- The Ottawa Hospital, Division of Rheumatology, University of Ottawa, Canada
| | - Niclas G Karlsson
- Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway, and Department of Medical Biochemistry, Institute for Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - David J Gonzalez
- Department of Pharmacology, School of Medicine, and Skaggs School of Pharmacy and Pharmaceutical Sciences, Collaborative Center for Multiplexed Proteomics, Program for Integrative Omics and Data Science in Disease Prevention and Therapeutics, UC San Diego, La Jolla, California
| | - Robert Terkeltaub
- VA San Diego Healthcare System and Department of Medicine, UC San Diego
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Podvin S, Mosier C, Poon W, Wei E, Rossitto LA, Hook V. Dysregulation of Human Juvenile Huntington's Disease Brain Proteomes in Cortex and Putamen Involves Mitochondrial and Neuropeptide Systems. J Huntingtons Dis 2023; 12:315-333. [PMID: 38108356 DOI: 10.3233/jhd-230577] [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] [Indexed: 12/19/2023]
Abstract
BACKGROUND Huntington's disease (HD) is a genetic neurodegenerative disease caused by trinucleotide repeat CAG expansions in the human HTT gene. Early onset juvenile HD (JHD) in children is the most severe form of the disease caused by high CAG repeat numbers of the HTT gene. OBJECTIVE To gain understanding of human HD mechanisms hypothesized to involve dysregulated proteomes of brain regions that regulate motor and cognitive functions, this study analyzed the proteomes of human JHD cortex and putamen brain regions compared to age-matched controls. METHODS JHD and age-matched control brain tissues were assessed for CAG repeat numbers of HTT by PCR. Human brain JHD brain cortex regions of BA4 and BA6 with the putamen region (n = 5) were analyzed by global proteomics, compared to age-matched controls (n = 7). Protein interaction pathways were assessed by gene ontology (GO), STRING-db, and KEGG bioinformatics. RESULTS JHD brain tissues were heterozygous for one mutant HTT allele containing 60 to 120 CAG repeats, and one normal HTT allele with 10 to 19 CAG repeats. Proteomics data for JHD brain regions showed dysregulated mitochondrial energy pathways and changes in synaptic systems including peptide neurotransmitters. JHD compared to control proteomes of cortex and putamen displayed (a) proteins present only in JHD, (b) proteins absent in JHD, and (c) proteins that were downregulated or upregulated. CONCLUSIONS Human JHD brain cortex and putamen regions display significant dysregulation of proteomes representing deficits in mitochondrial and synaptic neurotransmission functions. These findings advance understanding of JHD brain molecular mechanisms associated with HD disabilities.
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Affiliation(s)
- Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Charles Mosier
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - William Poon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Enlin Wei
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Leigh-Ana Rossitto
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Neuroscience and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Neuroscience and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
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5
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Pilo CA, Baffi TR, Kornev AP, Kunkel MT, Malfavon M, Chen DH, Rossitto LA, Chen DX, Huang LC, Longman C, Kannan N, Raskind WH, Gonzalez DJ, Taylor SS, Gorrie G, Newton AC. Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition. Sci Signal 2022; 15:eabk1147. [PMID: 36166510 PMCID: PMC9810342 DOI: 10.1126/scisignal.abk1147] [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: 01/07/2023]
Abstract
Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca2+-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. Most of the identified mutations cluster in the DAG-sensing C1 domains. Here, we found with a FRET-based activity reporter that SCA14-associated PKCγ mutations, including a previously undescribed variant, D115Y, enhanced the basal activity of the kinase by compromising its autoinhibition. Unlike other mutations in PKC that impair its autoinhibition but lead to its degradation, the C1 domain mutations protected PKCγ from such down-regulation. This enhanced basal signaling rewired the brain phosphoproteome, as revealed by phosphoproteomic analysis of cerebella from mice expressing a human SCA14-associated H101Y mutant PKCγ transgene. Mutations that induced a high basal activity in vitro were associated with earlier average age of onset in patients. Furthermore, the extent of disrupted autoinhibition, but not agonist-stimulated activity, correlated with disease severity. Molecular modeling indicated that almost all SCA14 variants not within the C1 domain were located at interfaces with the C1B domain, suggesting that mutations in and proximal to the C1B domain are a susceptibility for SCA14 because they uniquely enhance PKCγ basal activity while protecting the enzyme from down-regulation. These results provide insight into how PKCγ activation is modulated and how deregulation of the cerebellar phosphoproteome by SCA14-associated mutations affects disease progression.
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Affiliation(s)
- Caila A. Pilo
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92037, USA
| | - Timothy R. Baffi
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Maya T. Kunkel
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mario Malfavon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Dong-Hui Chen
- Department of Neurology, University of Washington Seattle, WA 98195, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
- Biomedical Sciences Graduate Program, University of California, La Jolla, CA 92037, USA
| | - Daniel X. Chen
- Department of Neurology, University of Washington Seattle, WA 98195, USA
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Cheryl Longman
- Queen Elizabeth University Hospital, Glasgow, Scotland G51 4TF, United Kingdom
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wendy H. Raskind
- Department of Medicine/Medical Genetics, University of Washington Seattle, WA 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA 98195, USA
- Mental Illness Research, Education and Clinical Center, Department of Veterans Affairs, Seattle, WA 98108, USA
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
| | - George Gorrie
- Queen Elizabeth University Hospital, Glasgow, Scotland G51 4TF, United Kingdom
| | - Alexandra C. Newton
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92037, USA
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Yuskaitis CJ, Modasia JB, Schrötter S, Rossitto LA, Groff KJ, Morici C, Mithal DS, Chakrabarty RP, Chandel NS, Manning BD, Sahin M. DEPDC5-dependent mTORC1 signaling mechanisms are critical for the anti-seizure effects of acute fasting. Cell Rep 2022; 40:111278. [PMID: 36044864 PMCID: PMC9508617 DOI: 10.1016/j.celrep.2022.111278] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 04/05/2022] [Revised: 06/11/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022] Open
Abstract
Caloric restriction and acute fasting are known to reduce seizures but through unclear mechanisms. mTOR signaling has been suggested as a potential mechanism for seizure protection from fasting. We demonstrate that brain mTORC1 signaling is reduced after acute fasting of mice and that neuronal mTORC1 integrates GATOR1 complex-mediated amino acid and tuberous sclerosis complex (TSC)-mediated growth factor signaling. Neuronal mTORC1 is most sensitive to withdrawal of leucine, arginine, and glutamine, which are dependent on DEPDC5, a component of the GATOR1 complex. Metabolomic analysis reveals that Depdc5 neuronal-specific knockout mice are resistant to sensing significant fluctuations in brain amino acid levels after fasting. Depdc5 neuronal-specific knockout mice are resistant to the protective effects of fasting on seizures or seizure-induced death. These results establish that acute fasting reduces seizure susceptibility in a DEPDC5-dependent manner. Modulation of nutrients upstream of GATOR1 and mTORC1 could offer a rational therapeutic strategy for epilepsy treatment.
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Affiliation(s)
- Christopher J Yuskaitis
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jinita B Modasia
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandra Schrötter
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Leigh-Ana Rossitto
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Karenna J Groff
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher Morici
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Divakar S Mithal
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Section of Neurology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Ram P Chakrabarty
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Navdeep S Chandel
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Brendan D Manning
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mustafa Sahin
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA.
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7
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Russell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell 2022; 185:3263-3277.e15. [PMID: 35931082 PMCID: PMC9464905 DOI: 10.1016/j.cell.2022.06.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/15/2022] [Accepted: 06/25/2022] [Indexed: 12/26/2022]
Abstract
Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to “knock in” specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent. Native E. coli strains isolated from mouse stool are genetically engineered for long-term engraftment in the conventional mouse gut and enable long-term systemic effects on the host, such as improvements in insulin sensitivity in mouse models of type 2 diabetes.
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Affiliation(s)
- Baylee J Russell
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steven D Brown
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole Siguenza
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irene Mai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand R Saran
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica S Maissy
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ana C Dantas Machado
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Concepcion Sanchez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yukiko Miyamoto
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel B Ho
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA
| | - Lars Eckmann
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Podvin S, Jiang Z, Boyarko B, Rossitto LA, O'Donoghue A, Rissman RA, Hook V. Dysregulation of Neuropeptide and Tau Peptide Signatures in Human Alzheimer's Disease Brain. ACS Chem Neurosci 2022; 13:1992-2005. [PMID: 35758417 PMCID: PMC9264367 DOI: 10.1021/acschemneuro.2c00222] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Synaptic dysfunction and loss occur in Alzheimer's disease (AD) brains, which results in cognitive deficits and brain neurodegeneration. Neuropeptides comprise the major group of synaptic neurotransmitters in the nervous system. This study evaluated neuropeptide signatures that are hypothesized to differ in human AD brain compared to age-matched controls, achieved by global neuropeptidomics analysis of human brain cortex synaptosomes. Neuropeptidomics demonstrated distinct profiles of neuropeptides in AD compared to controls consisting of neuropeptides derived from chromogranin A (CHGA) and granins, VGF (nerve growth factor inducible), cholecystokinin, and others. The differential neuropeptide signatures indicated differences in proteolytic processing of their proneuropeptides. Analysis of cleavage sites showed that dibasic residues at the N-termini and C-termini of neuropeptides were the main sites for proneuropeptide processing, and data also showed that the AD group displayed differences in preferred residues adjacent to the cleavage sites. Notably, tau peptide signatures differed in the AD compared to age-matched control human brain cortex synaptosomes. Unique tau peptides were derived from the tau protein through proteolysis using similar and differential cleavage sites in the AD brain cortex compared to the control. Protease profiles differed in the AD compared to control, indicated by proteomics data. Overall, these results demonstrate that dysregulation of neuropeptides and tau peptides occurs in AD brain cortex synaptosomes compared to age-matched controls, involving differential cleavage site properties for proteolytic processing of precursor proteins. These dynamic changes in neuropeptides and tau peptide signatures may be associated with the severe cognitive deficits of AD.
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Affiliation(s)
- Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Ben Boyarko
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Leigh-Ana Rossitto
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Robert A Rissman
- Department of Neurosciences, University of California San Diego, La Jolla, California 92093, United States.,Veterans Affairs San Diego Health System, La Jolla, California 92093, United States
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States.,Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093, United States
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9
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Gonzalez CG, Mills RH, Kordahi MC, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey JC, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS. The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients. Cell Mol Gastroenterol Hepatol 2022; 14:35-53. [PMID: 35378331 PMCID: PMC9117812 DOI: 10.1016/j.jcmgh.2022.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Hyperbaric oxygen therapy (HBOT) is a promising treatment for moderate-to-severe ulcerative colitis. However, our current understanding of the host and microbial response to HBOT remains unclear. This study examined the molecular mechanisms underpinning HBOT using a multi-omic strategy. METHODS Pre- and post-intervention mucosal biopsies, tissue, and fecal samples were collected from HBOT phase 2 clinical trials. Biopsies and fecal samples were subjected to shotgun metaproteomics, metabolomics, 16s rRNA sequencing, and metagenomics. Tissue was subjected to bulk RNA sequencing and digital spatial profiling (DSP) for single-cell RNA and protein analysis, and immunohistochemistry was performed. Fecal samples were also used for colonization experiments in IL10-/- germ-free UC mouse models. RESULTS Proteomics identified negative associations between HBOT response and neutrophil azurophilic granule abundance. DSP identified an HBOT-specific reduction of neutrophil STAT3, which was confirmed by immunohistochemistry. HBOT decreased microbial diversity with a proportional increase in Firmicutes and a secondary bile acid lithocholic acid. A major source of the reduction in diversity was the loss of mucus-adherent taxa, resulting in increased MUC2 levels post-HBOT. Targeted database searching revealed strain-level associations between Akkermansia muciniphila and HBOT response status. Colonization of IL10-/- with stool obtained from HBOT responders resulted in lower colitis activity compared with non-responders, with no differences in STAT3 expression, suggesting complementary but independent host and microbial responses. CONCLUSIONS HBOT reduces host neutrophil STAT3 and azurophilic granule activity in UC patients and changes in microbial composition and metabolism in ways that improve colitis activity. Intestinal microbiota, especially strain level variations in A muciniphila, may contribute to HBOT non-response.
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Key Words
- bclxl, b-cell lymphoma-extra large
- bim, bcl-2 interacting protein
- dsp, digital spatial profiling
- fdr, false discovery rate
- hbot, hyperbaric oxygen therapy
- hif, hypoxia inducible factor
- il, interleukin
- lca, lithocholic acid
- mapk, mitogen-activated protein kinase
- ms, mass spectrometry
- nlrp3, nod-, lrr- and pyrin domain-containing protein 3
- roi, regions of interest
- ros, reactive oxygen species
- stat3, signal transducer and activator of transcription 3
- tmt, tandem mass tag
- uc, ulcerative colitis
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Affiliation(s)
- Carlos G. Gonzalez
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Pediatrics, University of California, San Diego, California
| | - Robert H. Mills
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Pediatrics, University of California, San Diego, California
| | - Melissa C. Kordahi
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université de Paris, Paris, France
| | - Marvic Carrillo-Terrazas
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California
| | - Henry Secaira-Morocho
- School of Life Sciences, Arizona State University, Tempe, Arizona,Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona
| | - Christella E. Widjaja
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Matthew S. Tsai
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Yash Mittal
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California,Institute for Genomic Medicine, University of California San Diego, San Diego, California
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California
| | - Kelly Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Computer Science and Engineering, University of California San Diego, San Diego, California
| | - Julia M. Gauglitz
- Department of Pediatrics, University of California, San Diego, California
| | - Clara Delaroque
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université de Paris, Paris, France
| | - Consuelo Sauceda
- Department of Pharmacology, University of California, San Diego, California
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, California
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, California
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, California
| | - Austin D. Swafford
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California
| | - Corey A. Siegel
- Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Jay C. Buckey
- Center for Hyperbaric Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Laura E. Raffals
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Charlotte Sadler
- Division of Hyperbaric Medicine, Department of Emergency Medicine, University of California San Diego, San Diego, California
| | - Peter Lindholm
- Division of Hyperbaric Medicine, Department of Emergency Medicine, University of California San Diego, San Diego, California
| | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, San Diego, California
| | - Mark Valaseck
- Department of Pathology, University of California San Diego, San Diego, California
| | - Arief Suriawinata
- Section of Gastroenterology and Hepatology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California,Institute for Genomic Medicine, University of California San Diego, San Diego, California
| | - Pradipta Ghosh
- Division of Gastroenterology, University of California San Diego, San Diego, California,Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, California
| | - John T. Chang
- Division of Gastroenterology, University of California San Diego, San Diego, California
| | - Hiutung Chu
- Department of Pathology, University of California San Diego, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California,Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, California
| | - Pieter Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Department of Pediatrics, University of California, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, Arizona,Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona
| | - Benoit Chassaing
- INSERM U1016, team “Mucosal microbiota in chronic inflammatory diseases”, CNRS UMR 8104, Université de Paris, Paris, France
| | - Rob Knight
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California,Department of Pediatrics, University of California, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - David J. Gonzalez
- Department of Pharmacology, University of California, San Diego, California,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California,Center for Microbiome Innovation, University of California San Diego, San Diego, California
| | - Parambir S. Dulai
- Division of Gastroenterology, University of California San Diego, San Diego, California,Division of Gastroenterology, Northwestern University, Chicago, Illinois,Correspondence Address correspondence to: Parambir S. Dulai, MD, Division of Gastroenterology & Hepatology, Northwestern University Feinberg School of Medicine, Arkes Pavilion, 676 North St Clair Street, 14th Floor, Chicago, Illinois 60611. fax: (858) 657-5022.
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10
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Yuskaitis CJ, Rossitto LA, Gurnani S, Bainbridge E, Poduri A, Sahin M. Chronic mTORC1 inhibition rescues behavioral and biochemical deficits resulting from neuronal Depdc5 loss in mice. Hum Mol Genet 2020; 28:2952-2964. [PMID: 31174205 DOI: 10.1093/hmg/ddz123] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/31/2019] [Accepted: 06/04/2019] [Indexed: 01/05/2023] Open
Abstract
DEPDC5 is now recognized as one of the genes most often implicated in familial/inherited focal epilepsy and brain malformations. Individuals with pathogenic variants in DEPDC5 are at risk for epilepsy, associated neuropsychiatric comorbidities and sudden unexplained death in epilepsy. Depdc5flox/flox-Syn1Cre (Depdc5cc+) neuronal-specific Depdc5 knockout mice exhibit seizures and neuronal mTORC1 hyperactivation. It is not known if Depdc5cc+ mice have a hyperactivity/anxiety phenotype, die early from terminal seizures or whether mTOR inhibitors rescue DEPDC5-related seizures and associated comorbidities. Herein, we report that Depdc5cc+ mice were hyperactive in open-field testing but did not display anxiety-like behaviors on the elevated-plus maze. Unlike many other mTOR-related models, Depdc5cc+ mice had minimal epileptiform activity and rare seizures prior to seizure-induced death, as confirmed by video-EEG monitoring. Treatment with the mTORC1 inhibitor rapamycin starting after 3 weeks of age significantly prolonged the survival of Depdc5cc+ mice and partially rescued the behavioral hyperactivity. Rapamycin decreased the enlarged brain size of Depdc5cc+ mice with corresponding decrease in neuronal soma size. Loss of Depdc5 led to a decrease in the other GATOR1 protein levels (NPRL2 and NPRL3). Rapamycin failed to rescue GATOR1 protein levels but rather rescued downstream mTORC1 hyperactivity as measured by phosphorylation of S6. Collectively, our data provide the first evidence of behavioral alterations in mice with Depdc5 loss and support mTOR inhibition as a rational therapeutic strategy for DEPDC5-related epilepsy in humans.
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Affiliation(s)
- Christopher J Yuskaitis
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Leigh-Ana Rossitto
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Sarika Gurnani
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Elizabeth Bainbridge
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Annapurna Poduri
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Mustafa Sahin
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
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