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Shen X, Wang C, Zhou X, Zhou W, Hornburg D, Wu S, Snyder MP. Nonlinear dynamics of multi-omics profiles during human aging. NATURE AGING 2024:10.1038/s43587-024-00692-2. [PMID: 39143318 DOI: 10.1038/s43587-024-00692-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 07/22/2024] [Indexed: 08/16/2024]
Abstract
Aging is a complex process associated with nearly all diseases. Understanding the molecular changes underlying aging and identifying therapeutic targets for aging-related diseases are crucial for increasing healthspan. Although many studies have explored linear changes during aging, the prevalence of aging-related diseases and mortality risk accelerates after specific time points, indicating the importance of studying nonlinear molecular changes. In this study, we performed comprehensive multi-omics profiling on a longitudinal human cohort of 108 participants, aged between 25 years and 75 years. The participants resided in California, United States, and were tracked for a median period of 1.7 years, with a maximum follow-up duration of 6.8 years. The analysis revealed consistent nonlinear patterns in molecular markers of aging, with substantial dysregulation occurring at two major periods occurring at approximately 44 years and 60 years of chronological age. Distinct molecules and functional pathways associated with these periods were also identified, such as immune regulation and carbohydrate metabolism that shifted during the 60-year transition and cardiovascular disease, lipid and alcohol metabolism changes at the 40-year transition. Overall, this research demonstrates that functions and risks of aging-related diseases change nonlinearly across the human lifespan and provides insights into the molecular and biological pathways involved in these changes.
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Affiliation(s)
- Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Singapore, Singapore
| | - Chuchu Wang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Center for Genomics and Personalized Medicine, Stanford, CA, USA.
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2
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Francis KL, Zheng HB, Suskind DL, Murphree TA, Phan BA, Quah E, Hendrickson AS, Zhou X, Nuding M, Hudson AS, Guttman M, Morton GJ, Schwartz MW, Alonge KM, Scarlett JM. Characterizing the human intestinal chondroitin sulfate glycosaminoglycan sulfation signature in inflammatory bowel disease. Sci Rep 2024; 14:11839. [PMID: 38782973 PMCID: PMC11116513 DOI: 10.1038/s41598-024-60959-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
The intestinal extracellular matrix (ECM) helps maintain appropriate tissue barrier function and regulate host-microbial interactions. Chondroitin sulfate- and dermatan sulfate-glycosaminoglycans (CS/DS-GAGs) are integral components of the intestinal ECM, and alterations in CS/DS-GAGs have been shown to significantly influence biological functions. Although pathologic ECM remodeling is implicated in inflammatory bowel disease (IBD), it is unknown whether changes in the intestinal CS/DS-GAG composition are also linked to IBD in humans. Our aim was to characterize changes in the intestinal ECM CS/DS-GAG composition in intestinal biopsy samples from patients with IBD using mass spectrometry. We characterized intestinal CS/DS-GAGs in 69 pediatric and young adult patients (n = 13 control, n = 32 active IBD, n = 24 IBD in remission) and 6 adult patients. Here, we report that patients with active IBD exhibit a significant decrease in the relative abundance of CS/DS isomers associated with matrix stability (CS-A and DS) compared to controls, while isomers implicated in matrix instability and inflammation (CS-C and CS-E) were significantly increased. This imbalance of intestinal CS/DS isomers was restored among patients in clinical remission. Moreover, the abundance of pro-stabilizing CS/DS isomers negatively correlated with clinical disease activity scores, whereas both pro-inflammatory CS-C and CS-E content positively correlated with disease activity scores. Thus, pediatric patients with active IBD exhibited increased pro-inflammatory and decreased pro-stabilizing CS/DS isomer composition, and future studies are needed to determine whether changes in the CS/DS-GAG composition play a pathogenic role in IBD.
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Affiliation(s)
- Kendra L Francis
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Hengqi B Zheng
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - David L Suskind
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Bao Anh Phan
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Emily Quah
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Aarun S Hendrickson
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Xisheng Zhou
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Mason Nuding
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - Alexandra S Hudson
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Gregory J Morton
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Michael W Schwartz
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
| | - Kimberly M Alonge
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Jarrad M Scarlett
- Department of Pediatric Gastroenterology and Hepatology, Seattle Children's Hospital, Seattle, WA, USA.
- Department of Medicine, University of Washington Medicine Diabetes Institute, 750 Republican St, Box 358062, Seattle, WA, 98195, USA.
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Heavey MK, Hazelton A, Wang Y, Garner M, Anselmo AC, Arthur JC, Nguyen J. Targeted delivery of the probiotic Saccharomyces boulardii to the extracellular matrix enhances gut residence time and recovery in murine colitis. Nat Commun 2024; 15:3784. [PMID: 38710716 DOI: 10.1038/s41467-024-48128-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
Probiotic and engineered microbe-based therapeutics are an emerging class of pharmaceutical agents. They represent a promising strategy for treating various chronic and inflammatory conditions by interacting with the host immune system and/or delivering therapeutic molecules. Here, we engineered a targeted probiotic yeast platform wherein Saccharomyces boulardii is designed to bind to abundant extracellular matrix proteins found within inflammatory lesions of the gastrointestinal tract through tunable antibody surface display. This approach enabled an additional 24-48 h of probiotic gut residence time compared to controls and 100-fold increased probiotic concentrations within the colon in preclinical models of ulcerative colitis in female mice. As a result, pharmacodynamic parameters including colon length, colonic cytokine expression profiles, and histological inflammation scores were robustly improved and restored back to healthy levels. Overall, these studies highlight the potential for targeted microbial therapeutics as a potential oral dosage form for the treatment of inflammatory bowel diseases.
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Affiliation(s)
- Mairead K Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anthony Hazelton
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yuyan Wang
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mitzy Garner
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Aaron C Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- VitaKey Incorporation, Durham, NC, 27701, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology and Disease, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Juliane Nguyen
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Jensen LJ, Loch FN, Kamphues C, Shahryari M, Marticorena Garcia SR, Siegmund B, Weidinger C, Kühl AA, Hamm B, Braun J, Sack I, Asbach P, Reiter R. Feasibility of in vivo magnetic resonance elastography of mesenteric adipose tissue in Crohn's disease. Quant Imaging Med Surg 2023; 13:4792-4805. [PMID: 37581033 PMCID: PMC10423387 DOI: 10.21037/qims-23-41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/22/2023] [Indexed: 08/16/2023]
Abstract
Background Although there is growing evidence that functional involvement and structural changes of mesenteric adipose tissue (MAT) influence the course of Crohn's disease (CD), its viscoelastic properties remain elusive. Therefore, we aimed to investigate the viscoelastic properties of MAT in CD using magnetic resonance elastography (MRE), providing reference values for CD diagnosis. Methods In this prospective proof-of-concept study, 31 subjects (CD: n=11; healthy controls: n=20) were consecutively enrolled in a specialized care center for inflammatory bowel diseases (tertiary/quaternary care). Inclusion criteria for the CD patients were a clinically and endoscopically established diagnosis of CD based on the clinical record, absence of other concurrent bowel diseases, scheduled surgery for the following day, and age of at least 18 years. Diagnoses were confirmed by histological analysis of the resected bowel the day after MRE. Subjects were investigated using MRE at 1.5-T with frequencies of 40-70 Hz. To retrieve shear wave speed (SWS), volumes of interest (VOIs) in MAT were drawn adjacent to CD lesions (MATCD) and on the opposite side without adjacent bowel lesions in patients (MATCD_Opp) and controls (MATCTRL). The presented study is not registered in the clinical trial platform. Results A statistically significant decrease in mean SWS of 7% was found for MATCD_Opp vs. MATCTRL (0.76±0.05 vs. 0.82±0.04 m/s, P=0.012), whereas there was a nonsignificant trend with an 8% increase for MATCD vs. MATCD_Opp (0.82±0.07 vs. 0.76±0.05 m/s, P=0.098) and no difference for MATCD vs. MATCTRL. Preliminary area under the receiver operating characteristic curve (AUC) analysis showed diagnostic accuracy in detecting CD to be excellent for SWS of MATCD_Opp [AUC =0.82; 95% confidence interval (CI): 0.64-0.96] but poor for SWS of MATCD (AUC =0.52; 95% CI: 0.34-0.73). Conclusions This study demonstrates the feasibility of MRE of MAT and presents preliminary reference values for CD patients and healthy controls. Our results motivate further studies for the biophysical characterization of MAT in inflammatory bowel disease.
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Affiliation(s)
- Laura J. Jensen
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian N. Loch
- Department of Surgery, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mehrgan Shahryari
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stephan R. Marticorena Garcia
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carl Weidinger
- Department of Gastroenterology, Infectious Diseases and Rheumatology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anja A. Kühl
- iPATH.Berlin-Immunopathology for Experimental Models, Core Facility, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bernd Hamm
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jürgen Braun
- Department of Medical Informatics, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ingolf Sack
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Patrick Asbach
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Rolf Reiter
- Department of Radiology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Berlin, Germany
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Porras AM, Zhou H, Shi Q, Xiao X, Longman R, Brito IL. Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix. mBio 2022; 13:e0220122. [PMID: 36445085 PMCID: PMC9765649 DOI: 10.1128/mbio.02201-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022] Open
Abstract
Extracellular matrix (ECM) remodeling has emerged as a key feature of inflammatory bowel disease (IBD), and ECM fragments have been proposed as markers of clinical disease severity. Recent studies report increased protease activity in the gut microbiota of IBD patients. Nonetheless, the relationship between gut microbiota and ECM remodeling has remained unexplored. We hypothesized that members of the human gut microbiome could degrade the host ECM and that bacteria-driven remodeling, in turn, could enhance colonic inflammation. Through a variety of in vitro assays, we first confirmed that multiple bacterial species found in the human gut are capable of degrading specific ECM components. Clinical stool samples obtained from ulcerative colitis patients also exhibited higher levels of proteolytic activity in vitro, compared to those of their healthy counterparts. Furthermore, culture supernatants from bacteria species that are capable of degrading human ECM accelerated inflammation in dextran sodium sulfate (DSS)-induced colitis. Finally, we identified several of the bacterial proteases and carbohydrate degrading enzymes (CAZymes) that are potentially responsible for ECM degradation in vitro. Some of these protease families and CAZymes were also found in increased abundance in a metagenomic cohort of IBD. These results demonstrate that some commensal bacteria in the gut are indeed capable of degrading components of human ECM in vitro and suggest that this proteolytic activity may be involved in the progression of IBD. A better understanding of the relationship between nonpathogenic gut microbes, host ECM, and inflammation could be crucial to elucidating some of the mechanisms underlying host-bacteria interactions in IBD and beyond. IMPORTANCE Healthy gut epithelial cells form a barrier that keeps bacteria and other substances from entering the blood or tissues of the body. Those cells sit on scaffolding that maintains the structure of the gut and informs our immune system about the integrity of this barrier. In patients with inflammatory bowel disease (IBD), breaks are formed in this cellular barrier, and bacteria gain access to the underlying tissue and scaffolding. In our study, we discovered that bacteria that normally reside in the gut can modify and disassemble the underlying scaffolding. Additionally, we discovered that changes to this scaffolding affect the onset of IBD in mouse models of colitis as well as the abilities of these mice to recover. We propose that this new information will reveal how breaks in the gut wall lead to IBD and will open up new avenues by which to treat patients with IBD.
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Affiliation(s)
- Ana Maria Porras
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA
| | - Hao Zhou
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Xieyue Xiao
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - JRI Live Cell Bank
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, New York, USA
| | - Randy Longman
- Jill Roberts Institute for IBD Research, Weill Cornell Medicine, New York, New York, USA
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
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Yang Q, Ouyang J, Pi D, Feng L, Yang J. Malassezia in Inflammatory Bowel Disease: Accomplice of Evoking Tumorigenesis. Front Immunol 2022; 13:846469. [PMID: 35309351 PMCID: PMC8931276 DOI: 10.3389/fimmu.2022.846469] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence indicates that patients with inflammatory bowel disease (IBD) have a significantly higher risk of developing different cancers, while the exact mechanism involved is not yet fully understood. Malassezia is a lipid-dependent opportunistic yeast, which colonizes on mammalian skin and internal organs. Also, dysbiosis in fungal communities accompanied by high level of Malassezia are fairly common in inflammatory diseases such as IBD and various cancers. In cancer patients, higher levels of Malassezia are associated with worse prognosis. Once it is ablated in tumor-bearing mice, their prognostic conditions will be improved. Moreover, Malassezia manifests multiple proinflammatory biological properties, such as destruction of epithelial barrier, enrichment of inflammatory factors, and degradation of extracellular matrix (ECM), all of which have been reported to contribute to tumor initiation and malignant progression. Based on these facts, we hypothesize that high levels of Malassezia together with mycobiome dysbiosis in patients with IBD, would aggravate the microecological imbalance, worsen the inflammatory response, and further promote tumorigenesis and deterioration. Herein, we will discuss the detrimental properties of Malassezia and explore the key role of this fungus in the correlation between IBD and cancer, in order to take early surveillance and intervention to minimize the cancer risk in individuals with IBD.
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Affiliation(s)
- Qiyu Yang
- Department of Radiation Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Jing Ouyang
- Chongqing Public Health Medical Center, Chongqing, China
| | - Damao Pi
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Feng
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical and Pharmaceutical College, Chongqing, China
- *Correspondence: Li Feng, ; Jiadan Yang,
| | - Jiadan Yang
- Department of Pharmacy, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Li Feng, ; Jiadan Yang,
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