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Aly R, Darwish S, Bala N, Ebrahim A, Shoemaker LR, McCray J, Garrett TJ, Alli AA. Functional and metabolomic analysis of urinary extracellular vesicles from juvenile mice with renal compensatory hypertrophy. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167096. [PMID: 38499276 DOI: 10.1016/j.bbadis.2024.167096] [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: 11/22/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/20/2024]
Abstract
Unilateral nephrectomy, a procedure reducing kidney mass, triggers a compensatory response in the remaining kidney, increasing its size and function to maintain a normal glomerular filtration rate (GFR). Recent research has highlighted the role of extracellular vesicles (EVs) in renal physiology and disease, although their involvement in unilateral nephrectomy has been underexplored. In this study, unilateral nephrectomy was performed on young mice, and urinary extracellular vesicles (uEVs) characterization and cargo were analyzed. Kidney volume increased significantly post-nephrectomy, demonstrating compensatory hypertrophy. Serum creatinine, cystatin C, and urinary electrolytes concentrations were similar in both nephrectomized and control groups. Western blot analysis revealed upregulation of sodium-glucose cotransporter 2 (SGLT2) and sodium chloride cotransporter (NCC), and downregulation of sodium‑potassium-chloride co-transporter (NKCC2) and epithelial sodium channel (ENaC) in the nephrectomized group. Metabolomic analysis of uEVs showed an enrichment of certain metabolites, including citrate and stachydrine. Interestingly, uEVs from the nephrectomized group demonstrated a protective effect, downregulating signal transducer and activator of transcription 3 (STAT3) and reducing reactive oxygen species (ROS) in renal proximal cells, compared to uEVs from the control group. This study suggests that uEVs contain bioactive components capable of inducing protective, anti-inflammatory, anti-fibrinolytic, and antioxidative effects in renal cells. These findings contribute to our understanding of uEVs' role in renal compensatory mechanisms after unilateral nephrectomy and may hold promise for future therapeutic interventions in renal diseases.
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Affiliation(s)
- Rasha Aly
- Departement of Pediatrics, Division of Pediatric Nephrology, University of Florida, 32610, United States of America
| | - Sara Darwish
- Department of Physiology and Aging, College of Medicine, University of Florida, 32610, United States of America
| | - Niharika Bala
- Department of Physiology and Aging, College of Medicine, University of Florida, 32610, United States of America
| | - Areej Ebrahim
- Department of Physiology and Aging, College of Medicine, University of Florida, 32610, United States of America
| | - Lawrence R Shoemaker
- Departement of Pediatrics, Division of Pediatric Nephrology, University of Florida, 32610, United States of America
| | - Joel McCray
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL 32610, United States of America
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL 32610, United States of America
| | - Abdel A Alli
- Department of Physiology and Aging, College of Medicine, University of Florida, 32610, United States of America; Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, College of Medicine, University of Florida, 32610, United States of America.
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Shabnaz S, Nguyen TN, Williams R, Rubinstein SM, Garrett TJ, Tantawy M, Fradley MG, Alomar ME, Shain KH, Baz RC, Lenihan D, Cornell RF, Lu Q, Gong Y. Metabolomic signatures of carfilzomib-related cardiotoxicity in patients with multiple myeloma. Clin Transl Sci 2024; 17:e13828. [PMID: 38783568 DOI: 10.1111/cts.13828] [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: 01/12/2024] [Revised: 04/12/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
As a treatment for relapsed or refractory multiple myeloma (MM), carfilzomib has been associated with a significant risk of cardiovascular adverse events (CVAE). The goals of our study were to evaluate the metabolomic profile of MM patients to identify those at high risk prior to carfilzomib treatment and to explore the mechanisms of carfilzomib-CVAE to inform potential strategies to protect patients from this cardiotoxicity. Global metabolomic profiling was performed on the baseline and post-baseline plasma samples of 60 MM patients treated with carfilzomib-based therapy, including 31 who experienced CVAE, in a prospective cohort study. Baseline metabolites and post-baseline/baseline metabolite ratios that differ between the CVAE and no-CVAE patients were identified using unadjusted and adjusted methods. A baseline metabolomic risk score was created to stratify patients. We observed a lower abundance of tauroursodeoxycholic acid (T-UDCA) in CVAE patients at baseline (odds ratio [OR] = 0.47, 95% confidence interval [CI] = 0.21-0.94, p = 0.044) compared with the no-CVAE patients. A metabolite risk score was able to stratify patients into three risk groups. The area under the receiver-operating curve of the model with clinical predictors and metabolite risk score was 0.93. Glycochenodeoxycholic acid (OR = 0.56, 95% CI = 0.31-0.87, p = 0.023) was significantly lower in post-baseline/baseline ratios of CVAE patients compared with no-CVAE patients. Following metabolomic analysis, we created a baseline metabolite risk score that can stratify MM patients into different risk groups. The result also provided intriguing clues about the mechanism of carfilzomib-CVAE and potential cardioprotective strategies.
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Affiliation(s)
- Samia Shabnaz
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Trang N Nguyen
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Roy Williams
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Samuel M Rubinstein
- Department of Medicine, Division of Hematology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marwa Tantawy
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Michael G Fradley
- Cardio-Oncology Center of Excellence, Division of Cardiology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mohammed E Alomar
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Kenneth H Shain
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Rachid C Baz
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Daniel Lenihan
- Cape Cardiology Group, Saint Francis Medical Center, Cape Girardeau, Missouri, USA
| | - Robert F Cornell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Qing Lu
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics and Precision Medicine, College of Pharmacy, University of Florida, Gainesville, Florida, USA
- Cardio-Oncology Working Group, UF Health Cancer Center, Gainesville, Florida, USA
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Kollareth DJM, Leroy V, Tu Z, Woolet-Stockton MJ, Kamat M, Garrett TJ, Atkinson C, Cai G, Upchurch GR, Sharma AK. Lipoxin A 4 /FPR2 signaling mitigates ferroptosis of alveolar epithelial cells via NRF2-dependent pathway during lung ischemia-reperfusion injury. bioRxiv 2024:2024.04.22.590127. [PMID: 38712069 PMCID: PMC11071405 DOI: 10.1101/2024.04.22.590127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
BACKGROUND Post-lung transplantation (LTx) injury can involve sterile inflammation due to ischemia-reperfusion injury (IRI). We investigated the cell-specific role of ferroptosis (excessive iron-mediated cell death) in mediating lung IRI and determined if specialized pro-resolving mediators such as Lipoxin A4 (LxA 4 ) can protect against ferroptosis in lung IRI. METHODS Single-cell RNA sequencing of lung tissue from post-LTx patients was analyzed. Lung IRI was evaluated in C57BL/6 (WT), formyl peptide receptor 2 knockout ( Fpr2 -/- ) and nuclear factor erythroid 2-related factor 2 knockout ( Nrf2 -/- ) mice using a hilar-ligation model with or without LxA 4 administration. Furthermore, the protective efficacy of LxA 4 was evaluated employing a murine orthotopic LTx model and in vitro studies using alveolar type II epithelial (ATII) cells. RESULTS Differential expression of ferroptosis-related genes was observed in post-LTx patient samples compared to healthy controls. A significant increase in the levels of oxidized lipids and reduction in the levels of intact lipids were observed in mice subjected to IRI compared to shams. Furthermore, pharmacological inhibition of ferroptosis with liproxstatin-1 mitigated lung IRI and lung dysfunction. Importantly, LxA 4 treatment attenuated pulmonary dysfunction, ferroptosis and inflammation in WT mice subjected to lung IRI, but not in Fpr2 -/- or Nrf2 -/- mice, after IRI. In the murine LTx model, LxA 4 treatment increased PaO 2 levels and attenuated lung IRI. Mechanistically, LxA 4 -mediated protection involves increase in NRF2 activation and glutathione concentration as well as decrease in MDA levels in ATII cells. CONCLUSIONS LxA 4 /FPR2 signaling on ATII cells mitigates ferroptosis via NRF2 activation and protects against lung IRI.
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Ahrens AP, Hyötyläinen T, Petrone JR, Igelström K, George CD, Garrett TJ, Orešič M, Triplett EW, Ludvigsson J. Infant microbes and metabolites point to childhood neurodevelopmental disorders. Cell 2024; 187:1853-1873.e15. [PMID: 38574728 DOI: 10.1016/j.cell.2024.02.035] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 11/22/2023] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
This study has followed a birth cohort for over 20 years to find factors associated with neurodevelopmental disorder (ND) diagnosis. Detailed, early-life longitudinal questionnaires captured infection and antibiotic events, stress, prenatal factors, family history, and more. Biomarkers including cord serum metabolome and lipidome, human leukocyte antigen (HLA) genotype, infant microbiota, and stool metabolome were assessed. Among the 16,440 Swedish children followed across time, 1,197 developed an ND. Significant associations emerged for future ND diagnosis in general and for specific ND subtypes, spanning intellectual disability, speech disorder, attention-deficit/hyperactivity disorder, and autism. This investigation revealed microbiome connections to future diagnosis as well as early emerging mood and gastrointestinal problems. The findings suggest links to immunodysregulation and metabolism, compounded by stress, early-life infection, and antibiotics. The convergence of infant biomarkers and risk factors in this prospective, longitudinal study on a large-scale population establishes a foundation for early-life prediction and intervention in neurodevelopment.
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Affiliation(s)
- Angelica P Ahrens
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Tuulia Hyötyläinen
- School of Science and Technology, Örebro University, Örebro 702 81, Sweden
| | - Joseph R Petrone
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Kajsa Igelström
- Department of Biomedical and Clinical Sciences, Division of Neurobiology, Linköping University, Linköping 58185, Sweden
| | - Christian D George
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Matej Orešič
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro 702 81, Sweden; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; Department of Life Technologies, University of Turku, Turku 20014, Finland
| | - Eric W Triplett
- Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32603, USA.
| | - Johnny Ludvigsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58185, Sweden
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Garrett TJ, Jones JW. Review of the 2023 Fall Workshop on Lipidomics─The Essentials to the Cutting Edge. J Am Soc Mass Spectrom 2024; 35:653-654. [PMID: 38566574 DOI: 10.1021/jasms.4c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
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6
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Kim J, Stechmiller J, Weaver M, Lyon D, Garrett TJ, Yi F, Park J, Rezende de Carvalho M, Kelly DL. Association of Tryptophan: Kynurenine Metabolites with Healing in Chronic Venous Leg Ulcers. Adv Wound Care (New Rochelle) 2024. [PMID: 38511520 DOI: 10.1089/wound.2023.0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
OBJECTIVE Chronic wound healing is a complex process that is still not well understood. The tryptophan (TRP)-L-Kynurenine (KYN) pathway has recently been under increased scrutiny in regards to wound healing. The study applied metabolomics to elucidate the TRP-L- KYN pathway associated with wound healing in chronic venous leg ulcers (CVLUs). APPROACH This study used a longitudinal comparative design of 60 serum samples collected from 30 older adult patients with CVLUs, receiving weekly sharp debridement at a wound clinic. The serum samples were collected at baseline and week 4 (healed wounds) or week 8 (non-healed wounds). Liquid chromatography-mass spectrometry (LC-MS) metabolomics was used to analyze targeted metabolites. A Bayesian approach was employed to examine robust correlations between changes in metabolite values and linear healing slope and to compare by group. RESULTS The mean age was 71.13 (±9.46). Half of the sample were female and the minority (17%) were Black. The mean values of evaluated metabolites for the non-healed group were consistently lower than those for the healed group. The healed group (n=12) had higher KYN values; Those on a healing trajectory (n=23) had lower KYN levels and higher TRP levels at baseline and over time. There was moderate support (Bayes Factor = 3.70) for a negative association between change in Kynurenic Acid and linear healing slope (r = -0.35, CrI = -0.62, -0.04, PD= 98%). Results suggest KYN and TRP may be markers for healing in individuals with CVLUs. INNOVATION AND CONCLUSION Gaining a better understanding of the associations between the TRP-L- KYN pathway and the healing of CVLUs may help to clarify the links of inflammation with the rate and success of wound healing. Biomarker development focused on the TRP-L- KYN pathway could be pursued, if the associations are further supported by focused research studies.
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Affiliation(s)
- Junglyun Kim
- Chungnam National University, 26715, College of Nursing, Yuseong, Daejeon, Korea (the Republic of), 305764;
| | - Joyce Stechmiller
- University of Florida College of Nursing, 16096, Gainesville, Florida, United States;
| | - Michael Weaver
- University of Florida, 3463, Gainesville, Florida, United States;
| | - Debra Lyon
- University of Florida College of Nursing, 16096, Gainesville, Florida, United States;
| | - Timothy J Garrett
- University of Florida College of Medicine, 12233, Gainesville, Florida, United States;
| | - Fan Yi
- University of Idaho College of Science, 123393, Moscow, Idaho, United States;
| | - Jungmin Park
- University of Florida College of Nursing, Gainesville, Florida, United States;
| | - Magali Rezende de Carvalho
- University of Florida College of Nursing, 16096, 1225 Center Dr, Gainesville, Florida, United States, 32603;
| | - Debra Lynch Kelly
- University of Florida College of Nursing, 16096, Gainesville, Florida, United States;
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Smith AB, Specker JT, Hewlett KK, Scoggins TR, Knight M, Lustig AM, Li Y, Evans KM, Guo Y, She Q, Christopher MW, Garrett TJ, Moustafa AM, Van Tyne D, Prentice BM, Zackular JP. Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection. mBio 2024; 15:e0165623. [PMID: 38078767 PMCID: PMC10790701 DOI: 10.1128/mbio.01656-23] [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: 06/28/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.
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Affiliation(s)
- Alexander B. Smith
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Katharine K. Hewlett
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Troy R. Scoggins
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Montana Knight
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail M. Lustig
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yanhong Li
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Tsinghua University School of Medicine, Beijing, China
| | - Kirsten M. Evans
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingchan Guo
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Qianxuan She
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Timothy J. Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Ahmed M. Moustafa
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Boone M. Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Joseph P. Zackular
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Mody H, Nair S, Rump A, Vaidya TR, Garrett TJ, Lesko L, Ait-Oudhia S. Identification of Novel and Early Biomarkers for Cisplatin-induced Nephrotoxicity and the Nephroprotective Role of Cimetidine using a Pharmacometabolomic-based Approach Coupled with In Vitro Toxicodynamic Modeling and Simulation. J Pharm Sci 2024; 113:268-277. [PMID: 37992870 DOI: 10.1016/j.xphs.2023.11.018] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023]
Abstract
Cisplatin is widely used for the treatment of various types of cancer. However, cisplatin-induced nephrotoxicity (CIN) is frequently observed in patients receiving cisplatin therapy which poses a challenge in its clinical utility. Currently used clinical biomarkers for CIN are not adequate for early detection of nephrotoxicity, hence there is a need to identify potential early biomarkers in predicting CIN. In the current study, a combination of in vitro toxicodynamic (TD) modeling and untargeted global metabolomics approach was used to identify novel potential metabolite biomarkers for early detection of CIN. In addition, we investigated the protective role of cimetidine (CIM), an inhibitor of the organic cation transporter 2 (OCT2), in suppressing CIN. We first characterized the time-course of nephrotoxic effects of cisplatin (CIS) and the protective effects of CIM in a human pseudo-immortalized renal proximal tubule epithelial cell line (RPTEC), SA7K cell line. Secondly, we used a mathematical cell-level, in vitro TD modeling approach to quantitatively characterize the time-course effects of CIS and CIM as single agents and combination in SA7K cells. Based on the experimental and modeling results, we selected relevant concentrations of CIS and CIM for our metabolomics study. With the help of PCA (Principal Component Analysis) and PLS-DA (Projection to Latent Structure - Discriminate Analysis) analyses, we confirmed global metabolome changes for different groups (CIS, CIM, CIS+CIM vs control) in SA7K cells. Based on the criterion of a p-value ≤ 0.05 and a fold change ≥ 2 or ≤ 0.5, we identified 20 top metabolites that were significantly changed during the early phase i.e. within first 12 h of CIS treatment. Finally, pathway analysis was conducted that revealed the key metabolic pathways that were most impacted in CIN.
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Affiliation(s)
- Hardik Mody
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, FL, USA
| | - Sreenath Nair
- Pharmaceutical Sciences Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adrian Rump
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, FL, USA
| | - Tanaya R Vaidya
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, FL, USA
| | - Timothy J Garrett
- Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL, USA
| | - Lawrence Lesko
- Center for Pharmacometrics and Systems Pharmacology, Department of Pharmaceutics, College of Pharmacy, University of Florida, FL, USA
| | - Sihem Ait-Oudhia
- Quantitative Pharmacology and Pharmacometrics (QP2), Merck & Co., Inc, Rahway, NJ, USA.
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Farage G, Zhao C, Choi HY, Garrett TJ, Kechris K, Elam MB, Sen Ś. Matrix Linear Models for connecting metabolite composition to individual characteristics. bioRxiv 2023:2023.12.19.572450. [PMID: 38187579 PMCID: PMC10769268 DOI: 10.1101/2023.12.19.572450] [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] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
High-throughput metabolomics data provide a detailed molecular window into biological processes. We consider the problem of assessing how the association of metabolite levels with individual (sample) characteristics such as sex or treatment may depend on metabolite characteristics such as pathway. Typically this is one in a two-step process: In the first step we assess the association of each metabolite with individual characteristics. In the second step an enrichment analysis is performed by metabolite characteristics among significant associations. We combine the two steps using a bilinear model based on the matrix linear model (MLM) framework we have previously developed for high-throughput genetic screens. Our framework can estimate relationships in metabolites sharing known characteristics, whether categorical (such as type of lipid or pathway) or numerical (such as number of double bonds in triglycerides). We demonstrate how MLM offers flexibility and interpretability by applying our method to three metabolomic studies. We show that our approach can separate the contribution of the overlapping triglycerides characteristics, such as the number of double bonds and the number of carbon atoms. The proposed method have been implemented in the open-source Julia package, MatrixLM. Data analysis scripts with example data analyses are also available.
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Affiliation(s)
- Gregory Farage
- Department of Preventive Medicine, Division of Biostatistics, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Chenhao Zhao
- Department of Preventive Medicine, Division of Biostatistics, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Hyo Young Choi
- Department of Preventive Medicine, Division of Biostatistics, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610
| | - Katerina Kechris
- Department of Biostatistics & Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marshall B Elam
- Department of Pharmacology and of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Śaunak Sen
- Department of Preventive Medicine, Division of Biostatistics, University of Tennessee Health Science Center Memphis, TN 38163
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Yuan M, Mahmud I, Katsushima K, Joshi K, Saulnier O, Pokhrel R, Lee B, Liyanage W, Kunhiraman H, Stapleton S, Gonzalez-Gomez I, Kannan RM, Eisemann T, Kolanthai E, Seal S, Garrett TJ, Abbasi S, Bockley K, Hanes J, Chapagain P, Jallo G, Wechsler-Reya RJ, Taylor MD, Eberhart CG, Ray A, Perera RJ. miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4. Acta Neuropathol Commun 2023; 11:203. [PMID: 38115140 PMCID: PMC10729563 DOI: 10.1186/s40478-023-01684-w] [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: 10/07/2023] [Accepted: 11/05/2023] [Indexed: 12/21/2023] Open
Abstract
The prognosis of childhood medulloblastoma (MB) is often poor, and it usually requires aggressive therapy that adversely affects quality of life. microRNA-211 (miR-211) was previously identified as an important regulator of cells that descend from neural cells. Since medulloblastomas primarily affect cells with similar ontogeny, we investigated the role and mechanism of miR-211 in MB. Here we showed that miR-211 expression was highly downregulated in cell lines, PDXs, and clinical samples of different MB subgroups (SHH, Group 3, and Group 4) compared to normal cerebellum. miR-211 gene was ectopically expressed in transgenic cells from MB subgroups, and they were subjected to molecular and phenotypic investigations. Monoclonal cells stably expressing miR-211 were injected into the mouse cerebellum. miR-211 forced expression acts as a tumor suppressor in MB both in vitro and in vivo, attenuating growth, promoting apoptosis, and inhibiting invasion. In support of emerging regulatory roles of metabolism in various forms of cancer, we identified the acyl-CoA synthetase long-chain family member (ACSL4) as a direct miR-211 target. Furthermore, lipid nanoparticle-coated, dendrimer-coated, and cerium oxide-coated miR-211 nanoparticles were applied to deliver synthetic miR-211 into MB cell lines and cellular responses were assayed. Synthesizing nanoparticle-miR-211 conjugates can suppress MB cell viability and invasion in vitro. Our findings reveal miR-211 as a tumor suppressor and a potential therapeutic agent in MB. This proof-of-concept paves the way for further pre-clinical and clinical development.
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Affiliation(s)
- Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Kandarp Joshi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rudramani Pokhrel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Bongyong Lee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Wathsala Liyanage
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Haritha Kunhiraman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Ignacio Gonzalez-Gomez
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Rangaramanujam M Kannan
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tanja Eisemann
- National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Elayaraja Kolanthai
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL, 32826, USA
| | - Sudipta Seal
- Advanced Materials Processing and Analysis Centre, Nanoscience Technology Center, Materials Science and Engineering, College of Medicine, University of Central Florida, Orlando, FL, 32826, USA
| | - Timothy J Garrett
- Department Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Saed Abbasi
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Kimberly Bockley
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Justin Hanes
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, 33199, USA
| | - George Jallo
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA
| | - Robert J Wechsler-Reya
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Texas Children's Cancer Center, Hematology-Oncology Section, Houston, TX, 77030, USA
- Department of Pediatrics-Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD, 21231, USA.
- Johns Hopkins All Children's Hospital, 600 5th St. South, St. Petersburg, FL, 33701, USA.
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11
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Garrett TJ, Puchowicz MA, Park EA, Dong Q, Farage G, Childress R, Guingab J, Simpson CL, Sen S, Brogdon EC, Buchanan LM, Raghow R, Elam MB. Effect of statin treatment on metabolites, lipids and prostanoids in patients with Statin Associated Muscle Symptoms (SAMS). PLoS One 2023; 18:e0294498. [PMID: 38100464 PMCID: PMC10723679 DOI: 10.1371/journal.pone.0294498] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Between 5-10% of patients discontinue statin therapy due to statin-associated adverse reactions, primarily statin associated muscle symptoms (SAMS). The absence of a clear clinical phenotype or of biomarkers poses a challenge for diagnosis and management of SAMS. Similarly, our incomplete understanding of the pathogenesis of SAMS hinders the identification of treatments for SAMS. Metabolomics, the profiling of metabolites in biofluids, cells and tissues is an important tool for biomarker discovery and provides important insight into the origins of symptomatology. In order to better understand the pathophysiology of this common disorder and to identify biomarkers, we undertook comprehensive metabolomic and lipidomic profiling of plasma samples from patients with SAMS who were undergoing statin rechallenge as part of their clinical care. METHODS AND FINDINGS We report our findings in 67 patients, 28 with SAMS (cases) and 39 statin-tolerant controls. SAMS patients were studied during statin rechallenge and statin tolerant controls were studied while on statin. Plasma samples were analyzed using untargeted LC-MS metabolomics and lipidomics to detect differences between cases and controls. Differences in lipid species in plasma were observed between cases and controls. These included higher levels of linoleic acid containing phospholipids and lower ether lipids and sphingolipids. Reduced levels of acylcarnitines and altered amino acid profile (tryptophan, tyrosine, proline, arginine, and taurine) were observed in cases relative to controls. Pathway analysis identified significant increase of urea cycle metabolites and arginine and proline metabolites among cases along with downregulation of pathways mediating oxidation of branched chain fatty acids, carnitine synthesis, and transfer of acetyl groups into mitochondria. CONCLUSIONS The plasma metabolome of patients with SAMS exhibited reduced content of long chain fatty acids and increased levels of linoleic acid (18:2) in phospholipids, altered energy production pathways (β-oxidation, citric acid cycle and urea cycles) as well as reduced levels of carnitine, an essential mediator of mitochondrial energy production. Our findings support the hypothesis that alterations in pro-inflammatory lipids (arachidonic acid pathway) and impaired mitochondrial energy metabolism underlie the muscle symptoms of patients with statin associated muscle symptoms (SAMS).
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Affiliation(s)
- Timothy J. Garrett
- Southeast Center for Integrated Metabolomics (SECIM), Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Michelle A. Puchowicz
- Pediatrics-Obesity, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Edwards A. Park
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Qingming Dong
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Gregory Farage
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Richard Childress
- Endocrine Section, Memphis Veteran’s Affairs Medical Center, Memphis, Tennessee, United States of America
| | - Joy Guingab
- Southeast Center for Integrated Metabolomics (SECIM), Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Claire L. Simpson
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Elizabeth C. Brogdon
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Logan M. Buchanan
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Rajendra Raghow
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
| | - Marshall B. Elam
- Department of Pharmacology, University of Tennessee Health Sciences Center, Memphis, Tennessee, United States of America
- Cardiology Section, Memphis Veteran’s Affairs Medical Center, Memphis, Tennessee, United States of America
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12
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Du X, Dastmalchi F, Diller MA, Brochhausen M, Garrett TJ, Hogan WR, Lemas DJ. An Automated Workflow Composition System for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing. J Am Soc Mass Spectrom 2023; 34:2857-2863. [PMID: 37874901 DOI: 10.1021/jasms.3c00248] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) metabolomics studies produce high-dimensional data that must be processed by a complex network of informatics tools to generate analysis-ready data sets. As the first computational step in metabolomics, data processing is increasingly becoming a challenge for researchers to develop customized computational workflows that are applicable for LC-MS metabolomics analysis. Ontology-based automated workflow composition (AWC) systems provide a feasible approach for developing computational workflows that consume high-dimensional molecular data. We used the Automated Pipeline Explorer (APE) to create an AWC for LC-MS metabolomics data processing across three use cases. Our results show that APE predicted 145 data processing workflows across all the three use cases. We identified six traditional workflows and six novel workflows. Through manual review, we found that one-third of novel workflows were executable whereby the data processing function could be completed without obtaining an error. When selecting the top six workflows from each use case, the computational viable rate of our predicted workflows reached 45%. Collectively, our study demonstrates the feasibility of developing an AWC system for LC-MS metabolomics data processing.
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Affiliation(s)
- Xinsong Du
- Division of General Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Farhad Dastmalchi
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew A Diller
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - William R Hogan
- Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
- Department of Obstetrics and Gynecology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
- Center for Perinatal Outcomes Research, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
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13
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Rody WJ, Reuter NG, Brooks SE, Hammadi LI, Martin ML, Cagmat JG, Garrett TJ, Holliday LS. Metabolomic signatures distinguish extracellular vesicles from osteoclasts and odontoclasts. Orthod Craniofac Res 2023; 26:632-641. [PMID: 36997279 PMCID: PMC10542960 DOI: 10.1111/ocr.12658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 11/16/2022] [Revised: 02/15/2023] [Accepted: 03/19/2023] [Indexed: 04/01/2023]
Abstract
AIMS Pathological dental root resorption and alveolar bone loss are often detected only after irreversible damage. Biomarkers in the gingival crevicular fluid or saliva could provide a means for early detection; however, such biomarkers have proven elusive. We hypothesize that a multiomic approach might yield reliable diagnostic signatures for root resorption and alveolar bone loss. Previously, we showed that extracellular vesicles (EVs) from osteoclasts and odontoclasts differ in their protein composition. In this study, we investigated the metabolome of EVs from osteoclasts, odontoclasts and clasts (non-resorbing clastic cells). MATERIALS AND METHODS Mouse haematopoietic precursors were cultured on dentine, bone or plastic, in the presence of recombinant RANKL and CSF-1 to trigger differentiation along the clastic line. On Day 7, the cells were fixed and the differentiation state and resorptive status of the clastic cells were confirmed. EVs were isolated from the conditioned media on Day 7 and characterized by nanoparticle tracking and electron microscopy to ensure quality. Global metabolomic profiling was performed using a Thermo Q-Exactive Orbitrap mass spectrometer with a Dionex UHPLC and autosampler. RESULTS We identified 978 metabolites in clastic EVs. Of those, 79 are potential biomarkers with Variable Interdependent Parameters scores of 2 or greater. Known metabolites cytidine, isocytosine, thymine, succinate and citrulline were found at statistically higher levels in EVs from odontoclasts compared with osteoclasts. CONCLUSION We conclude that numerous metabolites found in odontoclast EVs differ from those in osteoclast EVs, and thus represent potential biomarkers for root resorption and periodontal tissue destruction.
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Affiliation(s)
- Wellington J Rody
- Department of Orthodontics and Dentofacial Orthopedics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, Pennsylvania, 15261, USA
| | - Nathan G Reuter
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, Florida, 32610, USA
| | - Shannen E Brooks
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, Florida, 32610, USA
| | - Lina I Hammadi
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, Florida, 32610, USA
| | - Macey L Martin
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, Florida, 32610, USA
| | - Joy G Cagmat
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, 32610, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, 32610, USA
| | - L Shannon Holliday
- Department of Orthodontics, University of Florida College of Dentistry, Gainesville, Florida, 32610, USA
- Department of Anatomy & Cell Biology, University of Florida, Gainesville, Florida, 32610, USA
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14
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Koelmel JP, Kummer M, Chevallier O, Hindle R, Hunt K, Camacho CG, Abril N, Gill EL, Beecher CWW, Garrett TJ, Yost RA, Townsend TG, Klein C, Rennie EE, Bowden JA, Godri Pollitt KJ. Expanding Per- and Polyfluoroalkyl Substances Coverage in Nontargeted Analysis Using Data-Independent Analysis and IonDecon. J Am Soc Mass Spectrom 2023; 34:2525-2537. [PMID: 37751518 DOI: 10.1021/jasms.3c00244] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are widespread, persistent environmental contaminants that have been linked to various health issues. Comprehensive PFAS analysis often relies on ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC HRMS) and molecular fragmentation (MS/MS). However, the selection and fragmentation of ions for MS/MS analysis using data-dependent analysis results in only the topmost abundant ions being selected. To overcome these limitations, All Ions fragmentation (AIF) can be used alongside data-dependent analysis. In AIF, ions across the entire m/z range are simultaneously fragmented; hence, precursor-fragment relationships are lost, leading to a high false positive rate. We introduce IonDecon, which filters All Ions data to only those fragments correlating with precursor ions. This software can be used to deconvolute any All Ions files and generates an open source DDA formatted file, which can be used in any downstream nontargeted analysis workflow. In a neat solution, annotation of PFAS standards using IonDecon and All Ions had the exact same false positive rate as when using DDA; this suggests accurate annotation using All Ions and IonDecon. Furthermore, deconvoluted All Ions spectra retained the most abundant peaks also observed in DDA, while filtering out much of the artifact peaks. In complex samples, incorporating AIF and IonDecon into workflows can enhance the MS/MS coverage of PFAS (more than tripling the number of annotations in domestic sewage). Deconvolution in complex samples of All Ions data using IonDecon did retain some false fragments (fragments not observed when using ion selection, which were not isotopes or multimers), and therefore DDA and intelligent acquisition methods should still be acquired when possible alongside All Ions to decrease the false positive rate. Increased coverage of PFAS can inform on the development of regulations to address the entire PFAS problem, including both legacy and newly discovered PFAS.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Environmental Health Science, Yale School of Public Health, New Haven, Connecticut 06520, United States
| | - Michael Kummer
- Innovative Omics, Inc., Sarasota, Florida 34235, United States
| | - Olivier Chevallier
- Agilent Technologies, Inc., Santa Clara, California 95051, United States
| | - Ralph Hindle
- Vogon Laboratory Services Ltd., Cochrane, Alberta T4C 0A3, Canada
| | - Kathy Hunt
- Vogon Laboratory Services Ltd., Cochrane, Alberta T4C 0A3, Canada
| | - Camden G Camacho
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Nandarani Abril
- Innovative Omics, Inc., Sarasota, Florida 34235, United States
| | - Emily L Gill
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | | | - Timothy J Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Timothy G Townsend
- Department of Environmental Engineering Sciences, University of Florida, P. O. Box 116450, Gainesville, Florida 32611-6450, United States
| | - Christian Klein
- Agilent Technologies, Inc., Santa Clara, California 95051, United States
| | - Emma E Rennie
- Agilent Technologies, Inc., Santa Clara, California 95051, United States
| | - John A Bowden
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida 32610, United States
| | - Krystal J Godri Pollitt
- Department of Environmental Health Science, Yale School of Public Health, New Haven, Connecticut 06520, United States
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15
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Garrett TJ, Coatsworth H, Mahmud I, Hamerly T, Stephenson CJ, Ayers JB, Yazd HS, Miller MR, Lednicky JA, Dinglasan RR. Niclosamide as a chemical probe for analyzing SARS-CoV-2 modulation of host cell lipid metabolism. Front Microbiol 2023; 14:1251065. [PMID: 37901834 PMCID: PMC10603251 DOI: 10.3389/fmicb.2023.1251065] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/15/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction SARS-CoV-2 subverts host cell processes to facilitate rapid replication and dissemination, and this leads to pathological inflammation. Methods We used niclosamide (NIC), a poorly soluble anti-helminth drug identified initially for repurposed treatment of COVID-19, which activates the cells' autophagic and lipophagic processes as a chemical probe to determine if it can modulate the host cell's total lipid profile that would otherwise be either amplified or reduced during SARS-CoV-2 infection. Results Through parallel lipidomic and transcriptomic analyses we observed massive reorganization of lipid profiles of SARS-CoV-2 infected Vero E6 cells, especially with triglycerides, which were elevated early during virus replication, but decreased thereafter, as well as plasmalogens, which were elevated at later timepoints during virus replication, but were also elevated under normal cell growth. These findings suggested a complex interplay of lipid profile reorganization involving plasmalogen metabolism. We also observed that NIC treatment of both low and high viral loads does not affect virus entry. Instead, NIC treatment reduced the abundance of plasmalogens, diacylglycerides, and ceramides, which we found elevated during virus infection in the absence of NIC, resulting in a significant reduction in the production of infectious virions. Unexpectedly, at higher viral loads, NIC treatment also resulted in elevated triglyceride levels, and induced significant changes in phospholipid metabolism. Discussion We posit that future screens of approved or new partner drugs should prioritize compounds that effectively counter SARS-CoV-2 subversion of lipid metabolism, thereby reducing virus replication, egress, and the subsequent regulation of key lipid mediators of pathological inflammation.
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Affiliation(s)
- Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, FL, United States
| | - Heather Coatsworth
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Iqbal Mahmud
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, FL, United States
| | - Timothy Hamerly
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Caroline J. Stephenson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
| | - Jasmine B. Ayers
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Hoda S. Yazd
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Megan R. Miller
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - John A. Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
| | - Rhoel R. Dinglasan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
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16
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Safari Yazd H, Bazargani SF, Fitzpatrick G, Yost RA, Kresak J, Garrett TJ. Metabolomic and Lipidomic Characterization of Meningioma Grades Using LC-HRMS and Machine Learning. J Am Soc Mass Spectrom 2023; 34:2187-2198. [PMID: 37708056 DOI: 10.1021/jasms.3c00158] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Meningiomas are among the most common brain tumors that arise from the leptomeningeal cover of the brain and spinal cord and account for around 37% of all central nervous system tumors. According to the World Health Organization, meningiomas are classified into three histological subtypes: benign, atypical, and anaplastic. Sometimes, meningiomas with a histological diagnosis of benign tumors show clinical characteristics and behavior of aggressive tumors. In this study, we examined the metabolomic and lipidomic profiles of meningioma tumors, focusing on comparing low-grade and high-grade tumors and identifying potential markers that can discriminate between benign and malignant tumors. High-resolution mass spectrometry coupled to liquid chromatography was used for untargeted metabolomics and lipidomics analyses of 85 tumor biopsy samples with different meningioma grades. We then applied feature selection and machine learning techniques to find the features with the highest information to aid in the diagnosis of meningioma grades. Three biomarkers were identified to differentiate low- and high-grade meningioma brain tumors. The use of mass-spectrometry-based metabolomics and lipidomics combined with machine learning analyses to prospect and characterize biomarkers associated with meningioma grades may pave the way for elucidating potential therapeutic and prognostic targets.
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Affiliation(s)
- Hoda Safari Yazd
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | | | - Garrett Fitzpatrick
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | - Jesse Kresak
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
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17
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Li W, Chace DH, Garrett TJ. Quantitation of phenylalanine and tyrosine from dried Blood/Plasma spots with impregnated stable isotope internal standards (SIIS) by FIA-SRM. Clin Chim Acta 2023; 549:117551. [PMID: 37683717 DOI: 10.1016/j.cca.2023.117551] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/18/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND Dried Blood Spot (DBS) analysis has been used for identification and quantification of diseases and disorders in large populations. Simply collecting blood or plasma samples on cotton paper, followed with an organic solvent extraction, many small molecules can be detected and quantified. In a typical procedure of DBS analysis in newborn screening, stable isotope internal standards (SIIS) are added to extraction solvent as a reference. However, this way of employing SIIS does not reflect extraction efficiency, or protein binding issues, nor does it reflect potential degradation that could occur. In addition, punched-out discs from larger DBS are known to have imprecision typically ≥ 15%. METHODS We developed and tested an approach, internal quantitative DBS (iqDBS), which delivers an exact volume of whole blood or plasma to a paper disc that is impregnated with a dried concentration of SIIS for quantitation. Amino acids were derivatized to make butyl esters and measured using Flow Injection Analysis with Selected Reaction Monitoring (FIA-SRM). RESULTS We demonstrated with phenylalanine and tyrosine improved sensitivity and accuracy by applying iqDBS. CONCLUSIONS We established a new method for quantitative analysis of small molecules from dried blood spots that incorporates stable isotope internal standard at the time of blood collection.
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Affiliation(s)
- Wenqian Li
- University of Florida, Department of Chemistry, Gainesville, FL, United States
| | | | - Timothy J Garrett
- University of Florida, Department of Pathology, Immunology and Laboratory Medicine, Gainesville, FL, United States.
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18
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Lemas DJ, Du X, Dado-Senn B, Xu K, Dobrowolski A, Magalhães M, Aristizabal-Henao JJ, Young BE, Francois M, Thompson LA, Parker LA, Neu J, Laporta J, Misra BB, Wane I, Samaan S, Garrett TJ. Untargeted Metabolomic Analysis of Lactation-Stage-Matched Human and Bovine Milk Samples at 2 Weeks Postnatal. Nutrients 2023; 15:3768. [PMID: 37686800 PMCID: PMC10490210 DOI: 10.3390/nu15173768] [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: 07/26/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Epidemiological data demonstrate that bovine whole milk is often substituted for human milk during the first 12 months of life and may be associated with adverse infant outcomes. The objective of this study is to interrogate the human and bovine milk metabolome at 2 weeks of life to identify unique metabolites that may impact infant health outcomes. Human milk (n = 10) was collected at 2 weeks postpartum from normal-weight mothers (pre-pregnant BMI < 25 kg/m2) that vaginally delivered term infants and were exclusively breastfeeding their infant for at least 2 months. Similarly, bovine milk (n = 10) was collected 2 weeks postpartum from normal-weight primiparous Holstein dairy cows. Untargeted data were acquired on all milk samples using high-resolution liquid chromatography-high-resolution tandem mass spectrometry (HR LC-MS/MS). MS data pre-processing from feature calling to metabolite annotation was performed using MS-DIAL and MS-FLO. Our results revealed that more than 80% of the milk metabolome is shared between human and bovine milk samples during early lactation. Unbiased analysis of identified metabolites revealed that nearly 80% of milk metabolites may contribute to microbial metabolism and microbe-host interactions. Collectively, these results highlight untargeted metabolomics as a potential strategy to identify unique and shared metabolites in bovine and human milk that may relate to and impact infant health outcomes.
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Affiliation(s)
- Dominick J. Lemas
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
- Department of Obstetrics and Gynecology, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
- Center for Perinatal Outcomes Research, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Bethany Dado-Senn
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Ke Xu
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Amanda Dobrowolski
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Marina Magalhães
- Department of Behavioral Nursing Science, College of Nursing, University of Florida, Gainesville, FL 32603, USA;
| | - Juan J. Aristizabal-Henao
- Department of Physiological Science, Center for Environmental and Human Toxicology, College of Veterinary Science, University of Florida, Gainesville, FL 32608, USA;
| | - Bridget E. Young
- Division of Breastfeeding and Lactation Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Magda Francois
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Lindsay A. Thompson
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Leslie A. Parker
- Center for Perinatal Outcomes Research, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Josef Neu
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | - Jimena Laporta
- Department of Obstetrics and Gynecology, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
| | | | - Ismael Wane
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Samih Samaan
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32608, USA; (X.D.); (K.X.); (A.D.); (M.F.); (L.A.T.); (I.W.); (S.S.)
| | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32608, USA;
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19
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Elshikha AS, Ge Y, Brown J, Kanda N, Zadeh M, Abboud G, Choi SC, Silverman G, Garrett TJ, Clapp WL, Mohamadzadeh M, Morel L. Pharmacologic inhibition of glycolysis prevents the development of lupus by altering the gut microbiome in mice. iScience 2023; 26:107122. [PMID: 37416482 PMCID: PMC10320500 DOI: 10.1016/j.isci.2023.107122] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/21/2023] [Accepted: 06/09/2023] [Indexed: 07/08/2023] Open
Abstract
Gut dysbiosis has been associated with lupus pathogenesis, and fecal microbiota transfers (FMT) from lupus-prone mice shown to induce autoimmune activation into healthy mice. The immune cells of lupus patients exhibit an increased glucose metabolism and treatments with 2-deoxy-D-glucose (2DG), a glycolysis inhibitor, are therapeutic in lupus-prone mice. Here, we showed in two models of lupus with different etiologies that 2DG altered the composition of the fecal microbiome and associated metabolites. In both models, FMT from 2DG-treated mice protected lupus-prone mice of the same strain from the development of glomerulonephritis, reduced autoantibody production as well as the activation of CD4+ T cells and myeloid cells as compared to FMT from control mice. Thus, we demonstrated that the protective effect of glucose inhibition in lupus is transferable through the gut microbiota, directly linking alterations in immunometabolism to gut dysbiosis in the hosts.
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Affiliation(s)
- Ahmed S. Elshikha
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
- The Laboratory of B Cell Immunobiology and the Division of Rheumatology, NYU School of Medicine, New York, NY 10016, USA
| | - Yong Ge
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health, San Antonio, TX 78229, USA
- The Laboratory of B Cell Immunobiology and the Division of Rheumatology, NYU School of Medicine, New York, NY 10016, USA
| | - Josephine Brown
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nathalie Kanda
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health, San Antonio, TX 78229, USA
| | - Mojgan Zadeh
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health, San Antonio, TX 78229, USA
| | - Georges Abboud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Seung-Chul Choi
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health, San Antonio, TX 78229, USA
| | - Gregg Silverman
- The Laboratory of B Cell Immunobiology and the Division of Rheumatology, NYU School of Medicine, New York, NY 10016, USA
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - William L. Clapp
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mansour Mohamadzadeh
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health, San Antonio, TX 78229, USA
| | - Laurence Morel
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health, San Antonio, TX 78229, USA
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20
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Filiberto AC, Leroy V, Ladd Z, Su G, Elder CT, Pruitt EY, Lu G, Hartman J, Zarrinpar A, Garrett TJ, Sharma AK, Upchurch GR. Sex differences in specialized pro-resolving lipid mediators and their receptors in abdominal aortic aneurysms. JVS Vasc Sci 2023; 4:100107. [PMID: 37292185 PMCID: PMC10245328 DOI: 10.1016/j.jvssci.2023.100107] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/08/2023] [Indexed: 06/10/2023] Open
Abstract
Objective In this study, we tested the hypothesis that endogenous expression of specialized pro-resolving lipid mediators (SPMs) that facilitate the resolution of inflammation, specifically Resolvin D1and -D2, as well as Maresin1 (MaR1), can impact abdominal aortic aneurysm (AAA) formation and progression in a sex-specific manner. Methods SPM expression was quantified in aortic tissue from human AAA samples and from a murine in vivo AAA model via liquid chromatography-tandem mass spectrometry. mRNA expression for SPM receptors FPR2, LGR6, and GPR18 were quantified by real-time polymerase chain reaction. A Student t test with nonparametric Mann-Whitney or Wilcoxon test was used for pair-wise comparisons of groups. One-way analysis of variance after post hoc Tukey test was used to determine the differences among multiple comparative groups. Results Human aortic tissue analysis revealed a significant decrease in RvD1 levels in male AAAs compared with controls, whereas FPR2 and LGR6 receptor expressions were downregulated in male AAAs compared with male controls. In vivo studies of elastase-treated mice showed higher levels of RvD2 and MaR1 as well as the SPM precursors, omega-3 fatty acids DHA and EPA, in aortic tissue from males compared with females. FPR2 expression was increased in elastase-treated females compared with males. Conclusions Our findings demonstrate that specific differences in SPMs and their associated G-protein coupled receptors exist between sexes. These results indicate the relevance of SPM-mediated signaling pathways in sex differences impacting the pathogenesis of AAAs.
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Affiliation(s)
| | - Victoria Leroy
- Department of Surgery, University of Florida, Gainesville, FL
| | - Zachary Ladd
- Department of Surgery, University of Florida, Gainesville, FL
| | - Gang Su
- Department of Surgery, University of Florida, Gainesville, FL
| | - Craig T. Elder
- Department of Surgery, University of Florida, Gainesville, FL
| | - Eric Y. Pruitt
- Department of Surgery, University of Florida, Gainesville, FL
| | - Guanyi Lu
- Department of Surgery, University of Florida, Gainesville, FL
| | - Joseph Hartman
- Department of Surgery, University of Florida, Gainesville, FL
| | - Ali Zarrinpar
- Department of Surgery, University of Florida, Gainesville, FL
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Ashish K. Sharma
- Department of Surgery, University of Florida, Gainesville, FL
- Aortic Disease Center, University of Florida, Gainesville, FL
| | - Gilbert R. Upchurch
- Department of Surgery, University of Florida, Gainesville, FL
- Aortic Disease Center, University of Florida, Gainesville, FL
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21
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Mahmud I, Tian G, Wang J, Hutchinson TE, Kim BJ, Awasthee N, Hale S, Meng C, Moore A, Zhao L, Lewis JE, Waddell A, Wu S, Steger JM, Lydon ML, Chait A, Zhao LY, Ding H, Li JL, Purayil HT, Huo Z, Daaka Y, Garrett TJ, Liao D. DAXX drives de novo lipogenesis and contributes to tumorigenesis. Nat Commun 2023; 14:1927. [PMID: 37045819 PMCID: PMC10097704 DOI: 10.1038/s41467-023-37501-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 02/03/2019] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Cancer cells exhibit elevated lipid synthesis. In breast and other cancer types, genes involved in lipid production are highly upregulated, but the mechanisms that control their expression remain poorly understood. Using integrated transcriptomic, lipidomic, and molecular studies, here we report that DAXX is a regulator of oncogenic lipogenesis. DAXX depletion attenuates, while its overexpression enhances, lipogenic gene expression, lipogenesis, and tumor growth. Mechanistically, DAXX interacts with SREBP1 and SREBP2 and activates SREBP-mediated transcription. DAXX associates with lipogenic gene promoters through SREBPs. Underscoring the critical roles for the DAXX-SREBP interaction for lipogenesis, SREBP2 knockdown attenuates tumor growth in cells with DAXX overexpression, and DAXX mutants unable to bind SREBP1/2 have weakened activity in promoting lipogenesis and tumor growth. Remarkably, a DAXX mutant deficient of SUMO-binding fails to activate SREBP1/2 and lipogenesis due to impaired SREBP binding and chromatin recruitment and is defective of stimulating tumorigenesis. Hence, DAXX's SUMO-binding activity is critical to oncogenic lipogenesis. Notably, a peptide corresponding to DAXX's C-terminal SUMO-interacting motif (SIM2) is cell-membrane permeable, disrupts the DAXX-SREBP1/2 interactions, and inhibits lipogenesis and tumor growth. These results establish DAXX as a regulator of lipogenesis and a potential therapeutic target for cancer therapy.
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Affiliation(s)
- Iqbal Mahmud
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guimei Tian
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jia Wang
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, 450008, Zhengzhou, Henan, China
| | - Tarun E Hutchinson
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Brandon J Kim
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Nikee Awasthee
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Seth Hale
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Chengcheng Meng
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Allison Moore
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Liming Zhao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jessica E Lewis
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Aaron Waddell
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Shangtao Wu
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Julia M Steger
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - McKenzie L Lydon
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Aaron Chait
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Lisa Y Zhao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
- Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Haocheng Ding
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Hamsa Thayele Purayil
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Yehia Daaka
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA
| | - Timothy J Garrett
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida College of Medicine, Gainesville, FL, USA.
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22
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Rischke S, Hahnefeld L, Burla B, Behrens F, Gurke R, Garrett TJ. Small molecule biomarker discovery: Proposed workflow for LC-MS-based clinical research projects. J Mass Spectrom Adv Clin Lab 2023; 28:47-55. [PMID: 36872952 PMCID: PMC9982001 DOI: 10.1016/j.jmsacl.2023.02.003] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Mass spectrometry focusing on small endogenous molecules has become an integral part of biomarker discovery in the pursuit of an in-depth understanding of the pathophysiology of various diseases, ultimately enabling the application of personalized medicine. While LC-MS methods allow researchers to gather vast amounts of data from hundreds or thousands of samples, the successful execution of a study as part of clinical research also requires knowledge transfer with clinicians, involvement of data scientists, and interactions with various stakeholders. The initial planning phase of a clinical research project involves specifying the scope and design, and engaging relevant experts from different fields. Enrolling subjects and designing trials rely largely on the overall objective of the study and epidemiological considerations, while proper pre-analytical sample handling has immediate implications on the quality of analytical data. Subsequent LC-MS measurements may be conducted in a targeted, semi-targeted, or non-targeted manner, resulting in datasets of varying size and accuracy. Data processing further enhances the quality of data and is a prerequisite for in-silico analysis. Nowadays, the evaluation of such complex datasets relies on a mix of classical statistics and machine learning applications, in combination with other tools, such as pathway analysis and gene set enrichment. Finally, results must be validated before biomarkers can be used as prognostic or diagnostic decision-making tools. Throughout the study, quality control measures should be employed to enhance the reliability of data and increase confidence in the results. The aim of this graphical review is to provide an overview of the steps to be taken when conducting an LC-MS-based clinical research project to search for small molecule biomarkers.
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Key Words
- (U)HPLC (Ultra-), High pressure liquid chromatography
- Biomarker Discovery Study
- HILIC, Hydrophilic interaction liquid chromatography
- HRMS, High resolution mass spectrometry
- LC-MS, Liquid chromatography – mass spectrometry
- LC-MS-Based Clinical Research
- Lipidomics
- MRM, Multiple reaction monitoring
- Metabolomics
- PCA, Principal component analysis
- QA, Quality assurance
- QC, Quality control
- RF, Random Forest
- RP, Reversed phase
- SVA, Support vector machine
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Affiliation(s)
- S Rischke
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - L Hahnefeld
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - B Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - F Behrens
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.,Division of Rheumatology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - R Gurke
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Johann Wolfgang Goethe University, Theodor Stern-Kai 7, 60590 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, and Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - T J Garrett
- Department of Pathology, Immunology and Laboratory Medicine and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, FL 32611, USA
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23
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Pendsey S, James S, Garrett TJ, Nord AB, Pendsey S, Malmodin D, Karlsson G, Maniam J, Atkinson MA, Forsander G, Ogle GD. Insulin thermostability in a real-world setting. Lancet Diabetes Endocrinol 2023; 11:310-312. [PMID: 37003280 DOI: 10.1016/s2213-8587(23)00028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 04/03/2023]
Affiliation(s)
- Sanket Pendsey
- Diabetes Research Education and Management Trust, Nagpur, India
| | - Steven James
- Life for a Child, Diabetes NSW & ACT, Sydney, NSW 2037, Australia; University of the Sunshine Coast, Petrie, QLD, Australia
| | | | | | - Sharad Pendsey
- Diabetes Research Education and Management Trust, Nagpur, India
| | | | - Göran Karlsson
- University of Gothenburg, Gothenburg, Sweden; Science for Life Laboratory, Gothenburg, Sweden
| | - Jayanthi Maniam
- Life for a Child, Diabetes NSW & ACT, Sydney, NSW 2037, Australia
| | | | - Gun Forsander
- University of Gothenburg, Gothenburg, Sweden; Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Graham D Ogle
- Life for a Child, Diabetes NSW & ACT, Sydney, NSW 2037, Australia.
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24
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Richter S, Garrett TJ, Bechmann N, Clifton-Bligh RJ, Ghayee HK. Metabolomics in paraganglioma: applications and perspectives from genetics to therapy. Endocr Relat Cancer 2023; 30:ERC-22-0376. [PMID: 36897220 DOI: 10.1530/erc-22-0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/10/2023] [Indexed: 03/11/2023]
Abstract
Metabolites represent the highest layer of biological information. Their diverse chemical nature enables networks of chemical reactions that are critical for maintaining life by providing energy and building blocks. Quantification by targeted and untargeted analytical methods using either mass spectrometry or nuclear magnetic resonance spectroscopy has been applied to pheochromocytoma/paraganglioma (PPGL) with the long-term goal to improve diagnosis and therapy. PPGLs have unique features that provide useful biomarkers and clues for targeted treatments. Firstly, high production rates of catecholamines and metanephrines allow for specific and sensitive detection of the disease in plasma or urine. Secondly, PPGLs are associated with heritable pathogenic variants (PV) in around 40% of cases, many of which occur in genes encoding enzymes, such as succinate dehydrogenase (SDH) and fumarate hydratase (FH). These genetic aberrations lead to overproduction of oncometabolites succinate or fumarate, respectively, and are detectable in tumors and blood. Such metabolic dysregulation can be exploited diagnostically, with the aim to ensure appropriate interpretation of gene variants, especially those with unknown significance, and facilitate early tumor detection through regular patient follow-up. Furthermore, SDHx and FH PV alter cellular pathways, including DNA hypermethylation, hypoxia signaling, redox homeostasis, DNA repair, calcium signaling, kinase cascades, and central carbon metabolism. Pharmacological interventions targeted towards such features have the potential to uncover treatments against metastatic PPGL, around 50% of which are associated with germline PV in SDHx. With the availability of omics technologies for all layers of biological information personalized diagnostics and treatment is in close reach.
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Affiliation(s)
- Susan Richter
- S Richter, Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Timothy J Garrett
- T Garrett, Medicine, University of Florida, Gainesville, United States
| | - Nicole Bechmann
- N Bechmann, Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Hans K Ghayee
- H Ghayee, Medicine, University of Florida College of Medicine, Gainesville, United States
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25
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Du X, Dastmalchi F, Ye H, Garrett TJ, Diller MA, Liu M, Hogan WR, Brochhausen M, Lemas DJ. Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software. Metabolomics 2023; 19:11. [PMID: 36745241 DOI: 10.1007/s11306-023-01974-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a popular approach for metabolomics data acquisition and requires many data processing software tools. The FAIR Principles - Findability, Accessibility, Interoperability, and Reusability - were proposed to promote open science and reusable data management, and to maximize the benefit obtained from contemporary and formal scholarly digital publishing. More recently, the FAIR principles were extended to include Research Software (FAIR4RS). AIM OF REVIEW This study facilitates open science in metabolomics by providing an implementation solution for adopting FAIR4RS in the LC-HRMS metabolomics data processing software. We believe our evaluation guidelines and results can help improve the FAIRness of research software. KEY SCIENTIFIC CONCEPTS OF REVIEW We evaluated 124 LC-HRMS metabolomics data processing software obtained from a systematic review and selected 61 software for detailed evaluation using FAIR4RS-related criteria, which were extracted from the literature along with internal discussions. We assigned each criterion one or more FAIR4RS categories through discussion. The minimum, median, and maximum percentages of criteria fulfillment of software were 21.6%, 47.7%, and 71.8%. Statistical analysis revealed no significant improvement in FAIRness over time. We identified four criteria covering multiple FAIR4RS categories but had a low %fulfillment: (1) No software had semantic annotation of key information; (2) only 6.3% of evaluated software were registered to Zenodo and received DOIs; (3) only 14.5% of selected software had official software containerization or virtual machine; (4) only 16.7% of evaluated software had a fully documented functions in code. According to the results, we discussed improvement strategies and future directions.
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Affiliation(s)
- Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Farhad Dastmalchi
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Hao Ye
- Health Science Center Libraries, University of Florida, Florida, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Florida, USA
| | - Matthew A Diller
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mei Liu
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - William R Hogan
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, USA
| | - Dominick J Lemas
- Department of Health Outcomes and Biomedical Informatics, University of Florida College of Medicine, Gainesville, FL, USA.
- Department of Obstetrics and Gynecology, University of Florida College of Medicine, Florida, Gainesville, United States.
- Center for Perinatal Outcomes Research, University of Florida College of Medicine, Gainesville, United States.
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Klein-Gordon JM, Guingab-Cagmat J, Minsavage GV, Meke L, Vallad GE, Goss EM, Garrett TJ, Jones JB. Strength in Numbers: Density-Dependent Volatile-Induced Antimicrobial Activity by Xanthomonas perforans. Phytopathology 2023; 113:160-169. [PMID: 36129764 DOI: 10.1094/phyto-04-22-0131-r] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
For most of the 20th century, Xanthomonas euvesicatoria was the only known bacterium associated with bacterial spot of tomato in Florida. X. perforans quickly replaced X. euvesicatoria, mainly because of production of three bacteriocins (BCNs) against X. euvesicatoria; however, X. perforans outcompeted X. euvesicatoria even when the three known BCNs were deleted. Surprisingly, we observed antimicrobial activity against X. euvesicatoria in the BCN triple mutant when the triple mutant was grown in Petri plates containing multiple spots but not in Petri plates containing only one spot. We determined that changes in the headspace composition (i.e., volatiles) rather than a diffusible signal in the agar were required for induction of the antimicrobial activity. Other Xanthomonas species also produced volatile-induced antimicrobial compounds against X. euvesicatoria and elicited antimicrobial activity by X. perforans. A wide range of plant pathogenic bacteria, including Clavibacter michiganensis subsp. michiganensis, Pantoea stewartii, and Pseudomonas cichorii, also elicited antimicrobial activity by X. perforans when multiple spots of the species were present. To identify potential antimicrobial compounds, we performed liquid chromatography with high-resolution mass spectrometry of the agar surrounding the spot in the high cell density Petri plates where the antimicrobial activity was present compared with agar surrounding the spot in Petri plates with one spot where antimicrobial activity was not observed. Among the compounds identified in the zone of inhibition were N-butanoyl-L-homoserine lactone and N-(3-hydroxy-butanoyl)-homoserine lactone, which are known quorum-sensing metabolites in other bacteria.
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Affiliation(s)
- Jeannie M Klein-Gordon
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI
| | - Joy Guingab-Cagmat
- Southeast Center for Integrated Metabolomics (SECIM), University of Florida, Gainesville, FL
| | - Gerald V Minsavage
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL
| | - Laurel Meke
- Southeast Center for Integrated Metabolomics (SECIM), University of Florida, Gainesville, FL
| | - Gary E Vallad
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL
- Gulf Coast Research and Education Center, IFAS, University of Florida, Balm, FL
| | - Erica M Goss
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL
- Emerging Pathogens Institute, University of Florida, Gainesville, FL
| | - Timothy J Garrett
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Jeffrey B Jones
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL
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Lei J, Mahar R, Chang MC, Collins J, Merritt ME, Garrett TJ, Yost RA. Segmented Flow Strategies for Integrating Liquid Chromatography-Mass Spectrometry with Nuclear Magnetic Resonance for Lipidomics. Anal Chem 2023; 95:10.1021/acs.analchem.2c03974. [PMID: 36630396 PMCID: PMC10870252 DOI: 10.1021/acs.analchem.2c03974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Building an accurate lipid inventory relies on coordinated information from orthogonal analytical capabilities. Integrating the familiar workflow of liquid chromatography (LC), high-resolution mass spectrometry (HRMS), and tandem mass spectrometry (MS/MS) with proton nuclear magnetic resonance spectroscopy (1H NMR) would be ideal for building that inventory. For absolute lipid structural elucidation, LC-HRMS/MS can provide lower-level structural information with superior sensitivity, while 1H NMR can provide invaluable higher-order structural information for the disambiguation of isomers with absolute chemical specificity. Digitization of the LC eluent followed by splitting the microfractions into two flow paths in a defined ratio for HRMS/MS and NMR would be the ideal strategy to permit correlation of the MS and NMR data as a function of chromatographic retention time. Here, we report an active segmentation platform to transform analytical flow rate LC eluent into parallel microliter segmented flow queues for high confidence correlation of the MS, MS/MS, and NMR data. The practical details in implementing this strategy to achieve an integrated LC-MS-NMR platform are presented, including the development of an active segmentation technology using a four-port two-way valve to transform the LC eluent into parallel segmented flows for online MS analysis followed by offline segment-specific 1H NMR and optimization of the detector response toward segmented flow. To demonstrate the practicality of this novel platform, it was tested using lipid mixture samples.
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Affiliation(s)
- Jiajun Lei
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
| | - Rohit Mahar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida32610, United States
| | - Mario C Chang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida32610, United States
| | - James Collins
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida32610, United States
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida32610, United States
| | - Timothy J Garrett
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida32611, United States
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida32610, United States
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Thompson SC, Ford AL, Moothedan EJ, Stafford LS, Garrett TJ, Dahl WJ, Conesa A, Gonzalez CF, Lorca GL. Identification of food and nutrient components as predictors of Lactobacillus colonization. Front Nutr 2023; 10:1118679. [PMID: 37153913 PMCID: PMC10160632 DOI: 10.3389/fnut.2023.1118679] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/31/2023] [Indexed: 05/10/2023] Open
Abstract
A previous double-blind, randomized clinical trial of 42 healthy individuals conducted with Lactobacillus johnsonii N6.2 found that the probiotic's mechanistic tryptophan pathway was significantly modified when the data was stratified based on the individuals' lactic acid bacteria (LAB) stool content. These results suggest that confounding factors such as dietary intake which impact stool LAB content may affect the response to the probiotic treatment. Using dietary intake, serum metabolite, and stool LAB colony forming unit (CFU) data from a previous clinical trial, the relationships between diet, metabolic response, and fecal LAB were assessed. The diets of subject groups with high vs. low CFUs of LAB/g of wet stool differed in their intakes of monounsaturated fatty acids, vegetables, proteins, and dairy. Individuals with high LAB consumed greater amounts of cheese, fermented meats, soy, nuts and seeds, alcoholic beverages, and oils whereas individuals with low LAB consumed higher amounts of tomatoes, starchy vegetables, and poultry. Several dietary variables correlated with LAB counts; positive correlations were determined for nuts and seeds, fish high in N-3 fatty acids, soy, and processed meats, and negative correlations to consumption of vegetables including tomatoes. Using machine learning, predictors of LAB count included cheese, nuts and seeds, fish high in N-3 fatty acids, and erucic acid. Erucic acid alone accurately predicted LAB categorization, and was shown to be utilized as a sole fatty acid source by several Lactobacillus species regardless of their mode of fermentation. Several metabolites were significantly upregulated in each group based on LAB titers, notably polypropylene glycol, caproic acid, pyrazine, and chondroitin sulfate; however, none were correlated with the dietary intake variables. These findings suggest that dietary variables may drive the presence of LAB in the human gastrointestinal tract and potentially impact response to probiotic interventions.
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Affiliation(s)
- Sharon C. Thompson
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Amanda L. Ford
- Department of Food Science and Human Nutrition, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Elijah J. Moothedan
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Lauren S. Stafford
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Wendy J. Dahl
- Department of Food Science and Human Nutrition, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Ana Conesa
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Institute for Integrative Systems Biology, Spanish National Research CouncilValencia, Spain
| | - Claudio F. Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Graciela L. Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- *Correspondence: Graciela L. Lorca,
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Garrett TJ, Feizbakhsh Bazargani S, Harmon T, Kruse J, Atkinson P, Quinlivan EP, Ang L, Hirsch IB, Laffel L, Pietropaolo M, Haller MJ, Atkinson MA. Commercially Available Insulin Products Demonstrate Consistency With Product Labeling Throughout All Seasons in the U.S. Diabetes Care 2022; 45:e166-e168. [PMID: 36102751 DOI: 10.2337/dc22-0972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/29/2022] [Indexed: 02/03/2023]
Affiliation(s)
- Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Sina Feizbakhsh Bazargani
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL
| | - Taylor Harmon
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL
| | - Jordan Kruse
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL
| | | | - Eoin P Quinlivan
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL
| | - Lynn Ang
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Irl B Hirsch
- Endocrine and Diabetes Care Center, University of Washington Medical Center-Roosevelt, Seattle, WA
| | - Lori Laffel
- Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Massimo Pietropaolo
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL.,Insulin for Life USA, Gainesville, FL.,Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL
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Lauro F, Giancotti LA, Kolar G, Harada CM, Harmon TA, Garrett TJ, Salvemini D. Role of Adenosine Kinase in Sphingosine-1-Phosphate Receptor 1-Induced Mechano-Hypersensitivities. Cell Mol Neurobiol 2022; 42:2909-2918. [PMID: 34773542 PMCID: PMC9098694 DOI: 10.1007/s10571-021-01162-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/26/2021] [Accepted: 10/22/2021] [Indexed: 12/21/2022]
Abstract
Emerging evidence implicates the sphingosine-1-phosphate receptor subtype 1 (S1PR1) in the development of neuropathic pain. Continued investigation of the signaling pathways downstream of S1PR1 are needed to support development of S1PR1 antagonists. In rodents, intrathecal (i.th.) injection of SEW2871, a selective S1PR1 agonist, activates the nod-like receptor family, pyrin domain containing 3 inflammasome, increases interleukin-1β (IL-1β) and causes behavioral hypersensitivity. I.th. injection of a IL-1β receptor antagonist blocks SEW2871-induced hypersensitivity, suggesting that IL-1β contributes to S1PR1's actions. Interestingly, previous studies have suggested that IL-1β increases the expression/activity of adenosine kinase (ADK), a key regulator of adenosine signaling at its receptors (ARs). Increased ADK expression reduces adenosine signaling whereas inhibiting ADK restores the action of adenosine. Here, we show that SEW287-induced behavioral hypersensitivity is associated with increased expression of ADK in astrocytes of the dorsal horn of the spinal cord. Moreover, the ADK inhibitor, ABT702, blocks SEW2871-induced hypersensitivity. These findings link ADK activation to S1PR1. If SEW2871-induced pain is mediated by IL-1β, which in turn activates ADK and leads to mechano-allodynia, then blocking ADK should attenuate IL-1β effects. In support of this idea, recombinant rat (rrIL-1β)-induced allodynia was blocked by at least 90% with ABT702, functionally linking ADK to IL-1β. Moreover, the selective A3AR antagonist, MRS1523, prevents the ability of ABT702 to block SEW2871 and IL-1β-induced allodynia, implicating A3AR signaling in the beneficial effects exerted by ABT702. Our findings provide novel mechanistic insight into how S1PR1 signaling in the spinal cord produces hypersensitivity through IL1-β and ADK activation.
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Affiliation(s)
- Filomena Lauro
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
| | - Luigino Antonio Giancotti
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
| | - Grant Kolar
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
- Department of Pathology, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
| | - Caron Mitsue Harada
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA
| | - Taylor A Harmon
- Department of Chemistry, University of Florida, Gainesville, FL, 32610, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Daniela Salvemini
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA.
- Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University School of Medicine, 1402 South Grand Blvd., St. Louis, MO, 63104, USA.
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Vijayakurup V, Maeng K, Lee HS, Meyer BS, Burkett S, Nawab A, Dougherty MW, Jobin C, Mahmud I, Garrett TJ, Feely M, Lee KB, Kaye FJ, Guijarro MV, Zajac-Kaye M. Thymidylate synthase accelerates Men1-mediated pancreatic tumor progression and reduces survival. JCI Insight 2022; 7:147417. [PMID: 36048542 PMCID: PMC9675466 DOI: 10.1172/jci.insight.147417] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/31/2022] [Indexed: 12/05/2022] Open
Abstract
Clinical studies of cancer patients have shown that overexpression or amplification of thymidylate synthase (TS) correlates with a worse clinical outcome. We previously showed that elevated TS exhibits properties of an oncogene and promotes pancreatic neuroendocrine tumors (PanNETs) with a long latency. To study the causal impact of elevated TS levels in PanNETs, we generated a mouse model with elevated human TS (hTS) and conditional inactivation of the Men1 gene in pancreatic islet cells (hTS/Men1–/–). We demonstrated that increased hTS expression was associated with earlier tumor onset and accelerated PanNET development in comparison with control Men1–/– and Men1+/ΔN3-8 mice. We also observed a decrease in overall survival of hTS/Men1+/– and hTS/Men1–/– mice as compared with control mice. We showed that elevated hTS in Men1-deleted tumor cells enhanced cell proliferation, deregulated cell cycle kinetics, and was associated with a higher frequency of somatic mutations, DNA damage, and genomic instability. In addition, we analyzed the survival of 88 patients with PanNETs and observed that high TS protein expression independently predicted worse clinical outcomes. In summary, elevated hTS directly participates in promoting PanNET tumorigenesis with reduced survival in Men1-mutant background. This work will refocus attention on new strategies to inhibit TS activity for PanNET treatment.
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Affiliation(s)
- Vinod Vijayakurup
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, United States of America
| | - Kyungah Maeng
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, United States of America
| | - Hye Seung Lee
- Department of Pathology, College of Medicine, Seoul National University, Seoul, Korea, Republic of
| | - Benjamin S Meyer
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, United States of America
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Insititute, Frederick, United States of America
| | - Akbar Nawab
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, United States of America
| | - Michael W Dougherty
- Department of Medicine, College of Medicine University of Florida, Gainesville, United States of America
| | - Christian Jobin
- College of Medicine University of Florida, Gainesville, United States of America
| | - Iqbal Mahmud
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, United States of America
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, United States of America
| | - Michael Feely
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, United States of America
| | - Kyoung Bun Lee
- Department of Pathology, College of Medicine, Seoul National University, Seoul, Korea, Republic of
| | - Frederic J Kaye
- Department of Medicine, University of Florida, Gainesville, United States of America
| | - Maria V Guijarro
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, United States of America
| | - Maria Zajac-Kaye
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, United States of America
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Narayan S, Raza A, Mahmud I, Koo N, Garrett TJ, Law ME, Law BK, Sharma AK. Sensitization of FOLFOX-resistant colorectal cancer cells via the modulation of a novel pathway involving protein phosphatase 2A. iScience 2022; 25:104518. [PMID: 35754740 PMCID: PMC9218363 DOI: 10.1016/j.isci.2022.104518] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
The treatment of colorectal cancer (CRC) with FOLFOX shows some efficacy, but these tumors quickly develop resistance to this treatment. We have observed increased phosphorylation of AKT1/mTOR/4EBP1 and levels of p21 in FOLFOX-resistant CRC cells. We have identified a small molecule, NSC49L, that stimulates protein phosphatase 2A (PP2A) activity, downregulates the AKT1/mTOR/4EBP1-axis, and inhibits p21 translation. We have provided evidence that NSC49L- and TRAIL-mediated sensitization is synergistically induced in p21-knockdown CRC cells, which is reversed in p21-overexpressing cells. p21 binds with procaspase 3 and prevents the activation of caspase 3. We have shown that TRAIL induces apoptosis through the activation of caspase 3 by NSC49L-mediated downregulation of p21 translation, and thereby cleavage of procaspase 3 into caspase 3. NSC49L does not affect global protein synthesis. These studies provide a mechanistic understanding of NSC49L as a PP2A agonist, and how its combination with TRAIL sensitizes FOLFOX-resistant CRC cells.
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Affiliation(s)
- Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Asif Raza
- Department of Pharmacology, Penn State University College of Medicine, Penn State Cancer Institute, Hershey, PA 17033, USA
| | - Iqbal Mahmud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nayeong Koo
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mary E. Law
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Brian K. Law
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Arun K. Sharma
- Department of Pharmacology, Penn State University College of Medicine, Penn State Cancer Institute, Hershey, PA 17033, USA
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Humes ST, Iovine N, Prins C, Garrett TJ, Lednicky JA, Coker ES, Sabo-Attwood T. Association between lipid profiles and viral respiratory infections in human sputum samples. Respir Res 2022; 23:177. [PMID: 35780155 PMCID: PMC9250719 DOI: 10.1186/s12931-022-02091-w] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
Background Respiratory infections such as influenza account for significant global mortality each year. Generating lipid profiles is a novel and emerging research approach that may provide new insights regarding the development and progression of priority respiratory infections. We hypothesized that select clusters of lipids in human sputum would be associated with specific viral infections (Influenza (H1N1, H3N2) or Rhinovirus). Methods Lipid identification and semi-quantitation was determined with liquid chromatography and high-resolution mass spectrometry in induced sputum from individuals with confirmed respiratory infections (influenza (H1N1, H3N2) or rhinovirus). Clusters of lipid species and associations between lipid profiles and the type of respiratory viral agent was determined using Bayesian profile regression and multinomial logistic regression. Results More than 600 lipid compounds were identified across the sputum samples with the most abundant lipid classes identified as triglycerides (TG), phosphatidylethanolamines (PE), phosphatidylcholines (PC), Sphingomyelins (SM), ether-PC, and ether-PE. A total of 12 lipid species were significantly different when stratified by infection type and included acylcarnitine (AcCar) (10:1, 16:1, 18:2), diacylglycerols (DG) (16:0_18:0, 18:0_18:0), Lysophosphatidylcholine (LPC) (12:0, 20:5), PE (18:0_18:0), and TG (14:1_16:0_18:2, 15:0_17:0_19:0, 16:0_17:0_18:0, 19:0_19:0_19:0). Cluster analysis yielded three clusters of lipid profiles that were driven by just 10 lipid species (TGs and DGs). Cluster 1 had the highest levels of each lipid species and the highest prevalence of influenza A H3 infection (56%, n = 5) whereas cluster 3 had lower levels of each lipid species and the highest prevalence of rhinovirus (60%; n = 6). Using cluster 3 as the reference group, the crude odds of influenza A H3 infection compared to rhinovirus in cluster 1 was significantly (p = 0.047) higher (OR = 15.00 [95% CI: 1.03, 218.29]). After adjustment for confounders (smoking status and pulmonary comorbidities), the odds ratio (OR) became only marginally significant (p = 0.099), but the magnitude of the effect estimate was similar (OR = 16.00 [0.59, 433.03]). Conclusions In this study, human sputum lipid profiles were shown to be associated with distinct types of viral infection. Better understanding the relationship between respiratory infections of global importance and lipids contributes to advancing knowledge of pathogenesis of infections including identifying populations with increased susceptibility and developing effective therapeutics and biomarkers of health status. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02091-w.
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Affiliation(s)
- Sara T Humes
- Department of Environmental and Global Health, Center for Environmental and Human Toxicology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Nicole Iovine
- Division of Infectious Diseases & Global Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Cindy Prins
- Department of Epidemiology, University of Florida, Gainesville, Florida, 32611, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine and Southeast Center for Integrated Metabolomics, University of Florida, Gainesville, Florida, 32611, USA
| | - John A Lednicky
- Department of Environmental and Global Health, Center for Environmental and Human Toxicology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Eric S Coker
- Department of Environmental and Global Health, Center for Environmental and Human Toxicology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, Center for Environmental and Human Toxicology, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, 32611, USA.
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Keen S, Lenton TM, Garrett TJ, Rae JWB, Hanley BP, Grasselli M. Estimates of economic and environmental damages from tipping points cannot be reconciled with the scientific literature. Proc Natl Acad Sci U S A 2022; 119:e2117308119. [PMID: 35588449 PMCID: PMC9173761 DOI: 10.1073/pnas.2117308119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Steve Keen
- Institute for Strategy, Resilience, and Security, University College London, London WC1E 6BT, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter EX4 4QE, United Kingdom
| | - Timothy J. Garrett
- Department of Atmospheric Sciences, University of Utah, Salt Lake City, UT 84112
| | - James W. B. Rae
- School of Earth and Environmental Sciences, University of St. Andrews, St. Andrews KY16 9AJ, United Kingdom
| | | | - Matheus Grasselli
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON, L8S 4K1 Canada
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Pillai S, Mahmud I, Mahar R, Griffith C, Langsen M, Nguyen J, Wojtkowiak JW, Swietach P, Gatenby RA, Bui MM, Merritt ME, McDonald P, Garrett TJ, Gillies RJ. Lipogenesis mediated by OGR1 regulates metabolic adaptation to acid stress in cancer cells via autophagy. Cell Rep 2022; 39:110796. [PMID: 35545051 PMCID: PMC9137419 DOI: 10.1016/j.celrep.2022.110796] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/03/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022] Open
Abstract
Malignant tumors exhibit altered metabolism resulting in a highly acidic extracellular microenvironment. Here, we show that cytoplasmic lipid droplet (LD) accumulation, indicative of a lipogenic phenotype, is a cellular adaption to extracellular acidity. LD marker PLIN2 is strongly associated with poor overall survival in breast cancer patients. Acid-induced LD accumulation is triggered by activation of the acid-sensing G-protein-coupled receptor (GPCR) OGR1, which is expressed highly in breast tumors. OGR1 depletion inhibits acid-induced lipid accumulation, while activation by a synthetic agonist triggers LD formation. Inhibition of OGR1 downstream signaling abrogates the lipogenic phenotype, which can be rescued with OGR1 ectopic expression. OGR1-depleted cells show growth inhibition under acidic growth conditions in vitro and tumor formation in vivo. Isotope tracing shows that the source of lipid precursors is primarily autophagy-derived ketogenic amino acids. OGR1-depleted cells are defective in endoplasmic reticulum stress response and autophagy and hence fail to accumulate LDs affecting survival under acidic stress.
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Affiliation(s)
- Smitha Pillai
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - Iqbal Mahmud
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Rohit Mahar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Crystal Griffith
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael Langsen
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jonathan Nguyen
- Analytical Microscopy Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jonathan W Wojtkowiak
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics Parks Road, Oxford OX1 3PT, UK
| | - Robert A Gatenby
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Marilyn M Bui
- Analytical Microscopy Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Department of Pathology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Patricia McDonald
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Robert J Gillies
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Elshikha AS, Brown J, Kanda N, Ge Y, Teng X, Abboud G, Choi SC, Terrell M, Garrett TJ, Mohamadzadeh M, Morel L. The gut microbiota transfers the therapeutic effect of inhibiting glucose metabolism in lupus-prone mice. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.174.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease in which autoantibodies induce tissue damage including the kidney. Gut microbial dysbiosis contributes to SLE pathogenesis. An abnormal metabolism is a characteristic feature of SLE in which the inflammatory functions of CD4+ T cells rely on glycolysis. We have shown that treatment with 2-deoxy-D-glucose (2DG), a glycolysis inhibitor, reduced the expansion of germinal centers and eliminated the production of autoantibodies, ameliorating disease in lupus-prone mice, including (NZB × NZW)F1 and (NZW x BXSB)F1. Here we show that the 2DG treatment also maintained gut bacterial diversity, reduced the changes in bacterial populations that occurred as disease developed in these mice, and that it altered the distribution of fecal metabolites. We investigated the effect of fecal microbiota transplantation (FMT) from 2DG-treated or control mice into pre-autoimmune lupus-prone mice of the same strain. In both strains, FMT from 2DG-treated mice was highly protective, with a reduction or elimination of anti-dsDNA IgG production, immune cell activation, and renal pathology compared to FMT from control mice. Overall, our results demonstrated for the first time that the therapeutic effect of glucose inhibition in lupus is transferable through the gut microbiota. This implicates either a direct effect of glucose on pathogenic gut bacteria, or an indirect effect through the immune system normalized by glucose inhibition.
Supported b R01 AI143313
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Affiliation(s)
| | - Josephine Brown
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | - Nathalie Kanda
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | - Yong Ge
- 2Department of Infectious Diseases and Immunology, Univ. of Florida
| | - Xiangyu Teng
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | - Georges Abboud
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | - Seung-Chul Choi
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | - Morgan Terrell
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | - Timothy J Garrett
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
| | | | - Laurence Morel
- 1Department of Pathology, Immunology, and Laboratory Medicine, Univ. of Florida
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Tikunov AP, Tipton JD, Garrett TJ, Shinde SV, Kim HJ, Gerber DA, Herring LE, Graves LM, Macdonald JM. Green Chemistry Preservation and Extraction of Biospecimens for Multi-omic Analyses. Methods Mol Biol 2022; 2394:267-298. [PMID: 35094334 DOI: 10.1007/978-1-0716-1811-0_17] [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: 05/16/2023]
Abstract
The Environmental Protection Agency's definition of "Green Chemistry" is "the design of chemical products and processes that reduces or eliminates the use or generation of hazardous substances. Green chemistry applies across the life cycle of a chemical product, including its design, manufacture, use, and ultimate disposal." Conventional omic tissue extraction procedures use solvents that are toxic and carcinogenic, such as chloroform and methyl-tert-butyl ether for lipidomics, or caustic chaotropic solutions for genomics and transcriptomics, such as guanidine or urea. A common preservation solution for pathology is formaldehyde, which is a carcinogen. Use of acetonitrile as a universal biospecimen preservation and extraction solvent will reduce these hazardous wastes, because it is less toxic and more environmentally friendly than the conventional solvents used in biorepository and biospecimen research. A new extraction method never applied to multi-omic, system biology research, called cold-induced phase separation (CIPS), uses freezing point temperatures to induce a phase separation of acetonitrile-water mixtures. Also, the CO2 exposure during CIPS will acidify the water precipitating DNA out of aqueous phase. The resulting phase separation brings hydrophobic lipids to the top acetonitrile fraction that is easily decanted from the bottom aqueous fraction, especially when the water is frozen. This CIPS acetonitrile extract contains the lipidome (lipids), the bottom aqueous fraction is sampled to obtain the transcriptome (RNA) fraction, and the remaining water and pellet is extracted with 60% acetonitrile to isolate the metabolome (<1 kD polar molecules). Finally, steps 4 and 5 use a TRIzol™ liquid-liquid extraction SOP of the pellet to isolate the genome (DNA) and proteome (proteins). This chapter details the multi-omic sequential extraction SOP and potential problems associated with each of the 5 steps, with steps 2, 4, and 5 still requiring validation. The metabolomic and lipidomic extraction efficiencies using the CIPS SOP is compared to conventional solvent extraction SOPs and is analyzed by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS), respectively. Acetonitrile biospecimen preservation combined with the CIPS multi-omic extraction SOP is green chemistry technology that will eliminate the generation of the hazardous substances associated with biospecimen processing and permits separation and safe disposal of acetonitrile avoiding environmental contamination.
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Affiliation(s)
- Andrey P Tikunov
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah D Tipton
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Sachi V Shinde
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Hong Jin Kim
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - David A Gerber
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Laura E Herring
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Lee M Graves
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey M Macdonald
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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Koelmel JP, Tan WY, Li Y, Bowden JA, Ahmadireskety A, Patt AC, Orlicky DJ, Mathé E, Kroeger NM, Thompson DC, Cochran JA, Golla JP, Kandyliari A, Chen Y, Charkoftaki G, Guingab‐Cagmat JD, Tsugawa H, Arora A, Veselkov K, Kato S, Otoki Y, Nakagawa K, Yost RA, Garrett TJ, Vasiliou V. Lipidomics and Redox Lipidomics Indicate Early Stage Alcohol-Induced Liver Damage. Hepatol Commun 2022; 6:513-525. [PMID: 34811964 PMCID: PMC8870008 DOI: 10.1002/hep4.1825] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022] Open
Abstract
Alcoholic fatty liver disease (AFLD) is characterized by lipid accumulation and inflammation and can progress to cirrhosis and cancer in the liver. AFLD diagnosis currently relies on histological analysis of liver biopsies. Early detection permits interventions that would prevent progression to cirrhosis or later stages of the disease. Herein, we have conducted the first comprehensive time-course study of lipids using novel state-of-the art lipidomics methods in plasma and liver in the early stages of a mouse model of AFLD, i.e., Lieber-DeCarli diet model. In ethanol-treated mice, changes in liver tissue included up-regulation of triglycerides (TGs) and oxidized TGs and down-regulation of phosphatidylcholine, lysophosphatidylcholine, and 20-22-carbon-containing lipid-mediator precursors. An increase in oxidized TGs preceded histological signs of early AFLD, i.e., steatosis, with these changes observed in both the liver and plasma. The major lipid classes dysregulated by ethanol play important roles in hepatic inflammation, steatosis, and oxidative damage. Conclusion: Alcohol consumption alters the liver lipidome before overt histological markers of early AFLD. This introduces the exciting possibility that specific lipids may serve as earlier biomarkers of AFLD than those currently being used.
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Affiliation(s)
- Jeremy P. Koelmel
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
- Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA
| | - Wan Y. Tan
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
- Internal Medicine Residency ProgramDepartment of Internal MedicineNorwalk HospitalNorwalkCTUSA
| | - Yang Li
- Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA
| | - John A. Bowden
- Department of ChemistryUniversity of FloridaGainesvilleFLUSA
- Center for Environmental and Human Toxicology and Department of Physiological SciencesUniversity of FloridaGainesvilleFLUSA
| | | | - Andrew C. Patt
- Division of Preclinical InnovationNational Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMDUSA
| | - David J. Orlicky
- Department of PathologyUniversity of Colorado School of MedicineDenverCOUSA
| | - Ewy Mathé
- Division of Preclinical InnovationNational Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMDUSA
| | - Nicholas M. Kroeger
- Computer and Information Science and EngineeringUniversity of FloridaGainesvilleFLUSA
| | - David C. Thompson
- Department of Clinical PharmacyUniversity of Colorado Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of ColoradoAuroraCOUSA
| | - Jason A. Cochran
- Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA
- Computer and Information Science and EngineeringUniversity of FloridaGainesvilleFLUSA
| | - Jaya Prakash Golla
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
| | - Aikaterini Kandyliari
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
- Unit of Human NutritionDepartment of Food Science and Human NutritionAgricultural University of AthensAthensGreece
| | - Ying Chen
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
| | - Georgia Charkoftaki
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
| | - Joy D. Guingab‐Cagmat
- Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource ScienceKanagawaJapan
- RIKEN Center for Integrative Medical SciencesKanagawaJapan
- Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyTokyoJapan
| | - Anmol Arora
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
- School of Clinical MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Kirill Veselkov
- Department of Metabolism, Digestion and ReproductionImperial CollegeLondonUnited Kingdom
| | - Shunji Kato
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Yurika Otoki
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Kiyotaka Nakagawa
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Richard A. Yost
- Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA
- Department of ChemistryUniversity of FloridaGainesvilleFLUSA
| | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleFLUSA
- Department of ChemistryUniversity of FloridaGainesvilleFLUSA
| | - Vasilis Vasiliou
- Department of Environmental Health SciencesYale School of Public HealthNew HavenCTUSA
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Pinto FG, Mahmud I, Rubio VY, Máquina ADV, Furtado Durans AF, Neto WB, Garrett TJ. Data-Driven Soft Independent Modeling of Class Analogy in Paper Spray Ionization Mass Spectrometry-Based Metabolomics for Rapid Detection of Prostate Cancer. Anal Chem 2022; 94:1925-1931. [DOI: 10.1021/acs.analchem.1c04004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Frederico G. Pinto
- Institute of Chemistry, Federal University of Viçosa, Campus de Rio Paranaíba, Rio Paranaíba, Minas Gerais 36570-900, Brazil
| | - Iqbal Mahmud
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Vanessa Y. Rubio
- Department of Chemistry, University of Florida, Gainesville, Florida 32603, United States
| | - Ademar Domingos Viagem Máquina
- Institute of Chemistry, Federal University of Uberlândia, Campus Santa Mônica, Uberlândia, Minas Gerais 38400-902, Brazil
| | - Anízia Fausta Furtado Durans
- Institute of Chemistry, Federal University of Uberlândia, Campus Santa Mônica, Uberlândia, Minas Gerais 38400-902, Brazil
| | - Waldomiro Borges Neto
- Institute of Chemistry, Federal University of Uberlândia, Campus Santa Mônica, Uberlândia, Minas Gerais 38400-902, Brazil
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, Florida 32610, United States
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Du X, Aristizabal-Henao JJ, Garrett TJ, Brochhausen M, Hogan WR, Lemas DJ. A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research. Metabolites 2022; 12:87. [PMID: 35050209 PMCID: PMC8779534 DOI: 10.3390/metabo12010087] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/25/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Clinical metabolomics emerged as a novel approach for biomarker discovery with the translational potential to guide next-generation therapeutics and precision health interventions. However, reproducibility in clinical research employing metabolomics data is challenging. Checklists are a helpful tool for promoting reproducible research. Existing checklists that promote reproducible metabolomics research primarily focused on metadata and may not be sufficient to ensure reproducible metabolomics data processing. This paper provides a checklist including actions that need to be taken by researchers to make computational steps reproducible for clinical metabolomics studies. We developed an eight-item checklist that includes criteria related to reusable data sharing and reproducible computational workflow development. We also provided recommended tools and resources to complete each item, as well as a GitHub project template to guide the process. The checklist is concise and easy to follow. Studies that follow this checklist and use recommended resources may facilitate other researchers to reproduce metabolomics results easily and efficiently.
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Affiliation(s)
- Xinsong Du
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (X.D.); (W.R.H.)
| | | | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Mathias Brochhausen
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - William R. Hogan
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (X.D.); (W.R.H.)
| | - Dominick J. Lemas
- Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; (X.D.); (W.R.H.)
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O'Kell AL, Wasserfall C, Guingab-Cagmat J, Webb-Robertson BJM, Atkinson MA, Garrett TJ. Correction to: Targeted metabolomic analysis identifies increased serum levels of GABA and branched chain amino acids in canine diabetes. Metabolomics 2021; 18:3. [PMID: 34923611 DOI: 10.1007/s11306-021-01865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Allison L O'Kell
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, The University of Florida, 2015 SW 16th Ave, Box 100116, Gainesville, FL, 32608, USA.
| | - Clive Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
| | - Joy Guingab-Cagmat
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, The University of Florida, Gainesville, FL, USA
| | - Bobbie-Jo M Webb-Robertson
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
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Jibrin MO, Liu Q, Guingab-Cagmat J, Jones JB, Garrett TJ, Zhang S. Metabolomics Insights into Chemical Convergence in Xanthomonas perforans and Metabolic Changes Following Treatment with the Small Molecule Carvacrol. Metabolites 2021; 11:879. [PMID: 34940636 PMCID: PMC8706651 DOI: 10.3390/metabo11120879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 01/20/2023] Open
Abstract
Microbes are natural chemical factories and their metabolome comprise diverse arrays of chemicals. The genus Xanthomonas comprises some of the most important plant pathogens causing devastating yield losses globally and previous studies suggested that species in the genus are untapped chemical minefields. In this study, we applied an untargeted metabolomics approach to study the metabolome of a globally spread important xanthomonad, X. perforans. The pathogen is difficult to manage, but recent studies suggest that the small molecule carvacrol was efficient in disease control. Bacterial strains were treated with carvacrol, and samples were taken at time intervals (1 and 6 h). An untreated control was also included. There were five replicates for each sample and samples were prepared for metabolomics profiling using the standard procedure. Metabolomics profiling was carried out using a thermo Q-Exactive orbitrap mass spectrometer with Dionex ultra high-performance liquid chromatography (UHPLC) and an autosampler. Annotation of significant metabolites using the Metabolomics Standards Initiative level 2 identified an array of novel metabolites that were previously not reported in Xanthomonas perforans. These metabolites include methoxybrassinin and cyclobrassinone, which are known metabolites of brassicas; sarmentosin, a metabolite of the Passiflora-heliconiine butterfly system; and monatin, a naturally occurring sweetener found in Sclerochiton ilicifolius. To our knowledge, this is the first report of these metabolites in a microbial system. Other significant metabolites previously identified in non-Xanthomonas systems but reported in this study include maculosin; piperidine; β-carboline alkaloids, such as harman and derivatives; and several important medically relevant metabolites, such as valsartan, metharbital, pirbuterol, and ozagrel. This finding is consistent with convergent evolution found in reported biological systems. Analyses of the effect of carvacrol in time-series and associated pathways suggest that carvacrol has a global effect on the metabolome of X. perforans, showing marked changes in metabolites that are critical in energy biosynthesis and degradation pathways, amino acid pathways, nucleic acid pathways, as well as the newly identified metabolites whose pathways are unknown. This study provides the first insight into the X. perforans metabolome and additionally lays a metabolomics-guided foundation for characterization of novel metabolites and pathways in xanthomonad systems.
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Affiliation(s)
- Mustafa Ojonuba Jibrin
- Tropical Research and Education Center, IFAS, University of Florida, Homestead, FL 33031, USA; (M.O.J.); (Q.L.)
- Department of Crop Protection, Ahmadu Bello University, Zaria 810103, Nigeria
| | - Qingchun Liu
- Tropical Research and Education Center, IFAS, University of Florida, Homestead, FL 33031, USA; (M.O.J.); (Q.L.)
| | - Joy Guingab-Cagmat
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (J.G.-C.); (T.J.G.)
| | - Jeffrey B. Jones
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA;
| | - Timothy J. Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (J.G.-C.); (T.J.G.)
| | - Shouan Zhang
- Tropical Research and Education Center, IFAS, University of Florida, Homestead, FL 33031, USA; (M.O.J.); (Q.L.)
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA;
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O'Kell AL, Wasserfall C, Guingab-Cagmat J, Webb-Roberston BJM, Atkinson MA, Garrett TJ. Targeted metabolomic analysis identifies increased serum levels of GABA and branched chain amino acids in canine diabetes. Metabolomics 2021; 17:100. [PMID: 34775536 PMCID: PMC8693811 DOI: 10.1007/s11306-021-01850-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dogs with naturally occurring diabetes mellitus represent a potential model for human type 1 diabetes, yet significant knowledge voids exist in terms of the pathogenic mechanisms underlying the canine disorder. Untargeted metabolomic studies from a limited number of diabetic dogs identified similarities to humans with the disease. OBJECTIVE To expand and validate earlier metabolomic studies, identify metabolites that differ consistently between diabetic and healthy dogs, and address whether certain metabolites might serve as disease biomarkers. METHODS Untargeted metabolomic analysis via liquid chromatography-mass spectrometry was performed on serum from diabetic (n = 15) and control (n = 15) dogs. Results were combined with those of our previously published studies using identical methods (12 diabetic and 12 control dogs) to identify metabolites consistently different between the groups in all 54 dogs. Thirty-two candidate biomarkers were quantified using targeted metabolomics. Biomarker concentrations were compared between the groups using multiple linear regression (corrected P < 0.0051 considered significant). RESULTS Untargeted metabolomics identified multiple persistent differences in serum metabolites in diabetic dogs compared with previous studies. Targeted metabolomics showed increases in gamma amino butyric acid, valine, leucine, isoleucine, citramalate, and 2-hydroxyisobutyric acid in diabetic versus control dogs while indoxyl sulfate, N-acetyl-L-aspartic acid, kynurenine, anthranilic acid, tyrosine, glutamine, and tauroursodeoxycholic acid were decreased. CONCLUSION Several of these findings parallel metabolomic studies in both human diabetes and other animal models of this disease. Given recent studies on the role of GABA and branched chain amino acids in human diabetes, the increase in serum concentrations in canine diabetes warrants further study of these metabolites as potential biomarkers, and to identify similarity in mechanisms underlying this disease in humans and dogs.
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Affiliation(s)
- Allison L O'Kell
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, The University of Florida, 2015 SW 16th Ave, Box 100116, Gainesville, FL, 32608, USA.
| | - Clive Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
| | - Joy Guingab-Cagmat
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, The University of Florida, Gainesville, FL, USA
| | - Bobbie-Jo M Webb-Roberston
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida, Gainesville, FL, USA
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Teixeira LD, Torrez Lamberti MF, DeBose-Scarlett E, Bahadiroglu E, Garrett TJ, Gardner CL, Meyer JL, Lorca GL, Gonzalez CF. Lactobacillus johnsonii N6.2 and Blueberry Phytophenols Affect Lipidome and Gut Microbiota Composition of Rats Under High-Fat Diet. Front Nutr 2021; 8:757256. [PMID: 34722616 PMCID: PMC8551501 DOI: 10.3389/fnut.2021.757256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 12/19/2022] Open
Abstract
Obesity is considered a primary contributing factor in the development of many diseases, including cancer, diabetes, and cardiovascular illnesses. Phytochemical-rich foods, associated to healthy gastrointestinal microbiota, have been shown to reduce obesity and associated comorbidities. In the present article, we describe the effects of the probiotic Lactobacillus johnsonii N6.2 and blueberry extracts (BB) on the gut microbiota and lipid profile of rats under a high-fat (HF) or low-calorie (LC) diet. L. johnsonii was found to increase the levels of long chain fatty acids (LCFA) in the serum of all animals under HF diet, while reduced LCFA concentrations were observed in the adipose tissue of animals under HF diet supplemented with BB extracts. All animals under HF diet also showed lower protein levels of SREBP1 and SCAP when treated with L. johnsonii. The gut microbiota diversity, β-diversity was significantly changed by L. johnsonii in the presence of BB. A significant reduction in α-diversity was observed in the ileum of animals under HF diet supplemented with L. johnsonii and BB, while increased α-diversity was observed in the ilium of animals under LC diet supplemented with L. johnsonii or BB. In summary, L. johnsonii and BB supplementation induced significant changes in gut microbiota diversity and lipid metabolism. The phospholipids pool was the lipidome component directly affected by the interventions. The ileum and colon microbiota showed clear differences depending on the diet and the treatments examined.
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Affiliation(s)
- Leandro Dias Teixeira
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Monica F Torrez Lamberti
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Evon DeBose-Scarlett
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Erol Bahadiroglu
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Christopher L Gardner
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Julie L Meyer
- Department of Soil and Water Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Graciela L Lorca
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Claudio F Gonzalez
- Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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Yazd HS, Bazargani SF, Vanbeek CA, King-Morris K, Heldermon C, Segal MS, Clapp WL, Garrett TJ. LC-MS lipidomics of renal biopsies for the diagnosis of Fabry disease. J Mass Spectrom Adv Clin Lab 2021; 22:71-78. [PMID: 34918004 PMCID: PMC8646168 DOI: 10.1016/j.jmsacl.2021.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
Fabry is an X-linked lysosomal storage disease with deficiency in α-galactosidase. This deficiency results in the accumulation of glycosphinogolipids. Diagnosis is often made by analysis of globotriaosylceramide in fluids and tissues. Fabry is often misdiagnosed in female patients due to residual enzyme activity. Lipidomics by LC-HRMS enables identification of new biomarkers in Fabry.
Introduction Lipidomics analysis or lipid profiling is a system-based analysis of all lipids in a sample to provide a comprehensive understanding of lipids within a biological system. In the last few years, lipidomics has made it possible to better understand the metabolic processes associated with several rare disorders and proved to be a powerful tool for their clinical investigation. Fabry disease is a rare X-linked lysosomal storage disorder (LSD) caused by a deficiency in α-galactosidase A (α-GAL A). This deficiency results in the progressive accumulation of glycosphingolipids, mostly globotriaosylceramide (Gb3), globotriaosylsphingosine (lyso-Gb3), as well as galabiosylceramide (Ga2) and their isoforms/analogs in the vascular endothelium, nerves, cardiomyocytes, renal glomerular podocytes, and biological fluids. Objectives The primary objective of this study was to evaluate lipidomic signatures in renal biopsies to help understand variations in Fabry disease markers that could be used in future diagnostic tests. Methods Lipidomic analysis was performed by ultra-high pressure liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) on kidney biopsies that were left over after clinical pathology analysis to diagnose Fabry disease. Results We employed UHPLC-HRMS lipidomics analysis on the renal biopsy of a patient suspicious for Fabry disease. Our result confirmed α-GAL A enzyme activity declined in this patient since a Ga2-related lipid biomarker was substantially higher in the patient's renal tissue biopsy compared with two controls. This suggests this patient has a type of LSD that could be non-classical Fabry disease. Conclusion This study shows that lipidomics analysis is a valuable tool for rare disorder diagnosis, which can be conducted on leftover tissue samples without disrupting normal patient care.
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Suganuma T, Swanson SK, Gogol M, Garrett TJ, Florens L, Workman JL. MOCS2 links nucleotide metabolism to nucleoli function. J Mol Cell Biol 2021; 13:838-840. [PMID: 34698840 DOI: 10.1093/jmcb/mjab069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Selene K Swanson
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, 32610 USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110 USA
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Wakefield ZR, Tanaka M, Pampo C, Lepler S, Rice L, Guingab-Cagmat J, Garrett TJ, Siemann DW. Normal tissue and tumor microenvironment adaptations to aerobic exercise enhance doxorubicin anti-tumor efficacy and ameliorate its cardiotoxicity in retired breeder mice. Oncotarget 2021; 12:1737-1748. [PMID: 34504647 PMCID: PMC8416558 DOI: 10.18632/oncotarget.28057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/26/2021] [Accepted: 08/13/2021] [Indexed: 11/25/2022] Open
Abstract
Aerobic exercise is receiving increased recognition in oncology for its multiple purported benefits. Exercise is known to induce physiologic adaptations that improve patient quality-of-life parameters as well as all-cause mortality. There also is a growing body of evidence that exercise may directly alter the tumor microenvironment to influence tumor growth, metastasis, and response to anticancer therapies. Furthermore, the physiologic adaptations to exercise in normal tissues may protect against treatment-associated toxicity and allow for greater treatment tolerance. However, the exercise prescription required to induce these beneficial tumor-related outcomes remains unclear. This study characterized the aerobic adaptations to voluntary wheel running in normal tissues and the tumor microenvironment. Female, retired breeder BALB/c mice and syngeneic breast adenocarcinoma cells were utilized in primary tumor and metastasis models. Aerobic exercise was found to induce numerous adaptations across various tissues in these mice, although primary tumor growth and metastasis were largely unaffected. However, intratumoral hypoxia and global metabolism were altered in the tumors of exercising hosts relative to non-wheel running controls. Doxorubicin chemotherapy also was found to be more efficacious at delaying tumor growth with adjuvant aerobic exercise. Additionally, doxorubicin-induced cardiac toxicity was ameliorated in exercising hosts relative to non-wheel running controls. Taken together, these data suggest that the normal tissue and tumor microenvironment adaptations to aerobic exercise can improve doxorubicin efficacy while simultaneously limiting its toxicity.
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Affiliation(s)
- Zachary R Wakefield
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mai Tanaka
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Christine Pampo
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Sharon Lepler
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Lori Rice
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Joy Guingab-Cagmat
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Dietmar W Siemann
- Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Hadrava Vanova K, Pang Y, Krobova L, Kraus M, Nahacka Z, Boukalova S, Pack SD, Zobalova R, Zhu J, Huynh TT, Jochmanova I, Uher O, Hubackova S, Dvorakova S, Garrett TJ, Ghayee HK, Wu X, Schuster B, Knapp PE, Frysak Z, Hartmann I, Nilubol N, Cerny J, Taieb D, Rohlena J, Neuzil J, Yang C, Pacak K. Germline SUCLG2 Variants in Patients with Pheochromocytoma and Paraganglioma. J Natl Cancer Inst 2021; 114:130-138. [PMID: 34415331 DOI: 10.1093/jnci/djab158] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/14/2020] [Accepted: 08/18/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Pheochromocytoma and paraganglioma (PPGL) are neuroendocrine tumors with frequent mutations in genes linked to the tricarboxylic acid cycle. However, no pathogenic variant has been found to date in succinyl-CoA ligase (SUCL), an enzyme that provides substrate for succinate dehydrogenase (SDH; mitochondrial complex II; CII), a known tumor suppressor in PPGL. METHODS A cohort of 352 subjects with apparently sporadic PPGL underwent genetic testing using a panel of 54 genes developed at the National Institutes of Health, including the SUCLG2 subunit of SUCL. Gene deletion, succinate levels, and protein levels were assessed in tumors where possible. To confirm the possible mechanism, we used a progenitor cell line, hPheo1, derived from a human pheochromocytoma, and ablated and re-expressed SUCLG2. RESULTS We describe eight germline variants in the GTP-binding domain of SUCLG2 in 15 patients (15 of 352, 4.3%) with apparently sporadic PPGL. Analysis of SUCLG2-mutated tumors and SUCLG2-deficient hPheo1 cells revealed absence of SUCLG2 protein, decrease in the level of the SDHB subunit of CII and faulty assembly of the complex, resulting in aberrant respiration and elevated succinate accumulation. CONCLUSIONS Our study suggests SUCLG2 as a novel candidate gene in the genetic landscape of PPGL. Large-scale sequencing may uncover additional cases harboring SUCLG2 variants and provide more detailed information about their prevalence and penetrance.
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Affiliation(s)
- Katerina Hadrava Vanova
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Ying Pang
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Linda Krobova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Michal Kraus
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Zuzana Nahacka
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Stepana Boukalova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Svetlana D Pack
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Renata Zobalova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Jun Zhu
- Systems Biology Center, National Heart Lung Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thanh-Truc Huynh
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Ivana Jochmanova
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,1st Department of Internal Medicine, Pavol Jozef Safarik University in Kosice, Faculty of Medicine and Teaching Hospital of Louis Pasteur, Kosice, Slovakia
| | - Ondrej Uher
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Department of Medical Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Sona Hubackova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Sarka Dvorakova
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Timothy J Garrett
- Southeast Center for Integrated Metabolomics, Clinical and Translational Science Institute, University of Florida, Gainesville, FL, USA
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology, Malcom Randall VA Medical Center, University of Florida, Gainesville, FL, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bjoern Schuster
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Philip E Knapp
- Section of Endocrinology, Boston Medical Center, Boston University, Boston, MA, USA
| | - Zdenek Frysak
- 3rd Department of Internal Medicine, University Hospital and Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Igor Hartmann
- Department of Urology, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Naris Nilubol
- Endocrine Surgery Section, Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiri Cerny
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - David Taieb
- Department of Nuclear Medicine, La Timone University Hospital, CERIMED, Aix-Marseille University, Marseille, France
| | - Jakub Rohlena
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic
| | - Jiri Neuzil
- Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec, Prague West, Czech Republic.,School of Pharmacy and Medical Science, Griffith University, Southport, Qld, Australia
| | - Chunzhang Yang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Karel Pacak
- Section of Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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Fu Z, Dean JW, Xiong L, Dougherty MW, Oliff KN, Chen ZME, Jobin C, Garrett TJ, Zhou L. Mitochondrial transcription factor A in RORγt + lymphocytes regulate small intestine homeostasis and metabolism. Nat Commun 2021; 12:4462. [PMID: 34294718 PMCID: PMC8298438 DOI: 10.1038/s41467-021-24755-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/30/2020] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
RORγt+ lymphocytes, including interleukin 17 (IL-17)-producing gamma delta T (γδT17) cells, T helper 17 (Th17) cells, and group 3 innate lymphoid cells (ILC3s), are important immune regulators. Compared to Th17 cells and ILC3s, γδT17 cell metabolism and its role in tissue homeostasis remains poorly understood. Here, we report that the tissue milieu shapes splenic and intestinal γδT17 cell gene signatures. Conditional deletion of mitochondrial transcription factor A (Tfam) in RORγt+ lymphocytes significantly affects systemic γδT17 cell maintenance and reduces ILC3s without affecting Th17 cells in the gut. In vivo deletion of Tfam in RORγt+ lymphocytes, especially in γδT17 cells, results in small intestine tissue remodeling and increases small intestine length by enhancing the type 2 immune responses in mice. Moreover, these mice show dysregulation of the small intestine transcriptome and metabolism with less body weight but enhanced anti-helminth immunity. IL-22, a cytokine produced by RORγt+ lymphocytes inhibits IL-13-induced tuft cell differentiation in vitro, and suppresses the tuft cell-type 2 immune circuit and small intestine lengthening in vivo, highlighting its key role in gut tissue remodeling.
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Affiliation(s)
- Zheng Fu
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Joseph W Dean
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Lifeng Xiong
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | | | - Kristen N Oliff
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Zong-Ming E Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Christian Jobin
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32608, USA
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA.
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50
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Koelmel JP, Aristizabal-Henao JJ, Ni Z, Fedorova M, Kato S, Otoki Y, Nakagawa K, Lin EZ, Godri Pollitt KJ, Vasiliou V, Guingab JD, Garrett TJ, Williams TL, Bowden JA, Penumetcha M. A Novel Technique for Redox Lipidomics Using Mass Spectrometry: Application on Vegetable Oils Used to Fry Potatoes. J Am Soc Mass Spectrom 2021; 32:1798-1809. [PMID: 34096708 DOI: 10.1021/jasms.1c00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Vegetables oils, rich in polyunsaturated fatty acids, are vulnerable to oxidation during manufacturing, processing, and food preparation. Currently, individual oxidation products are not well characterized, and hence, the health impacts of these unique lipid species remain unknown. Here, we introduce an extensive oxidized lipidomics in silico tandem mass spectrometry library and integrate these libraries within a user-friendly software covering a comprehensive redox lipidomics workflow. We apply this workflow to olive, soy, and walnut cooking oil; comparing unheated oil, oil after deep frying potatoes, and oil after oven frying potatoes. We annotated over a thousand oxidized triglycerides across 273 features (many coeluted). This software was validated against traditional chemical assays of oxidation, known oxidized lipids in castor oil, synthesized standards, and an alternate software LPPtiger. Development of these new software programs for redox lipidomics opens the door to characterize health implications of individual oxidation products.
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Affiliation(s)
- Jeremy P Koelmel
- School of Public Health, Yale University, New Haven, Connecticut, 06520, United States
| | - Juan J Aristizabal-Henao
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida 32608, United States
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig 01403Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, 04103, Germany
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig 01403Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, 04103, Germany
| | - Shunji Kato
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8577, Japan
| | - Yurika Otoki
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8577, Japan
| | - Kiyotaka Nakagawa
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8577, Japan
| | - Elizabeth Z Lin
- School of Public Health, Yale University, New Haven, Connecticut, 06520, United States
| | | | - Vasilis Vasiliou
- School of Public Health, Yale University, New Haven, Connecticut, 06520, United States
| | - Joy D Guingab
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | - Traycie L Williams
- School of Nutrition, Kinesiology and Psychological Science, University of Central Missouri, Warrensburg, Missouri 64093, United States
| | - John A Bowden
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida 32608, United States
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | - Meera Penumetcha
- School of Nutrition, Kinesiology and Psychological Science, University of Central Missouri, Warrensburg, Missouri 64093, United States
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