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Challa A, Maras JS, Nagpal S, Tripathi G, Taneja B, Kachhawa G, Sood S, Dhawan B, Acharya P, Upadhyay AD, Yadav M, Sharma R, Bajpai M, Gupta S. Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis. J Eur Acad Dermatol Venereol 2024; 38:1152-1165. [PMID: 38284174 DOI: 10.1111/jdv.19805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/06/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery. OBJECTIVES The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model. METHODS Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy. RESULTS Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model. CONCLUSION Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.
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Affiliation(s)
- A Challa
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - J S Maras
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Nagpal
- TCS Research, Tata Consultancy Services Ltd, Pune, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Tripathi
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - B Taneja
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Kachhawa
- Department of Obstetrics and Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - S Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - B Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - P Acharya
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - A D Upadhyay
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - M Yadav
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - R Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M Bajpai
- Department of Transfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Gupta
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
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Nuiyen A, Rattanasri A, Wipa P, Roytrakul S, Wangteeraprasert A, Pongcharoen S, Ngoenkam J. Lack of Nck1 protein and Nck-CD3 interaction caused the increment of lipid content in Jurkat T cells. BMC Mol Cell Biol 2022; 23:36. [PMID: 35902806 PMCID: PMC9330638 DOI: 10.1186/s12860-022-00436-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The non-catalytic region of tyrosine kinase (Nck) is an adaptor protein, which is ubiquitously expressed in many types of cells. In T cells, the Nck1 isoform promotes T cell receptor signalling as well as actin polymerisation. However, the role of Nck1 in the lipid metabolism in T cells is unknown. In the present study, we investigated the effect of the Nck1 protein and Nck–CD3 interaction on lipid metabolism and on the physical and biological properties of Jurkat T cells, using a newly developed holotomographic microscope.
Results
Holotomographic microscopy showed that Nck1-knocked-out cells had membrane blebs and were irregular in shape compared to the rounded control cells. The cell size and volume of Nck1-deficient cells were comparable to those of the control cells. Nck1-knocked-out Jurkat T cells had a greater lipid content, lipid mass/cell mass ratio, and lipid metabolite levels than the control cells. Interestingly, treatment with a small molecule, AX-024, which inhibited Nck–CD3 interaction, also caused an increase in the lipid content in wild-type Jurkat T cells, as found in Nck1-deficient cells.
Conclusions
Knockout of Nck1 protein and hindrance of the Nck–CD3 interaction cause the elevation of lipid content in Jurkat T cells.
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Bland JS. Therapeutic Use of Omega-3 Fatty Acids for Immune Disorders In Search of the Ideal Omega-3 Supplement. Integr Med (Encinitas) 2022; 21:14-18. [PMID: 36643210 PMCID: PMC9831136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
There has been continuing growth in the understanding of the role that omega-3 fatty acid supplements play in the support of immune function. The progress in both the basic science and clinical research surrounding the impact of various formulations of omega-3 fatty acid supplements on immune function has resulted in the recognition that the impact of these supplements is beyond that of the omega-3 fatty acids eicosapentaenoic acid (EPA) and docasahexaenoic acid (DHA) alone, and includes other fatty acids containing omega-3 derivatives termed pro-resolving mediators, along with vitamins A and D found naturally in some marine oils. The research on omega-3 oil supplements has also highlighted the importance that the supplement formulation be derived from a certified sustainable source, free of heavy metals and organic pollutants, minimally processed, and composed of the natural triglyceride form of the fatty acids for improved safety and effectiveness in providing immune support.
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Shi P, Xie S, Yang J, Zhang Y, Han S, Su S, Yao H. Pharmacological effects and mechanisms of bee venom and its main components: Recent progress and perspective. Front Pharmacol 2022; 13:1001553. [PMID: 36238572 PMCID: PMC9553197 DOI: 10.3389/fphar.2022.1001553] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
Bee venom (BV), a type of defensive venom, has been confirmed to have favorable activities, such as anti-tumor, neuroprotective, anti-inflammatory, analgesic, anti-infectivity effects, etc. This study reviewed the recent progress on the pharmacological effects and mechanisms of BV and its main components against cancer, neurological disorders, inflammatory diseases, pain, microbial diseases, liver, kidney, lung and muscle injury, and other diseases in literature during the years 2018–2021. The related target proteins of BV and its main components against the diseases include Akt, mTOR, JNK, Wnt-5α, HIF-1α, NF-κB, JAK2, Nrf2, BDNF, Smad2/3, AMPK, and so on, which are referring to PI3K/Akt/mTOR, MAPK, Wnt/β-catenin, HIF-1α, NF-κB, JAK/STAT, Nrf2/HO-1, TrkB/CREB/BDNF, TGF-β/Smad2/3, and AMPK signaling pathways, etc. Further, with the reported targets, the potential effects and mechanisms on diseases were bioinformatically predicted via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, disease ontology semantic and enrichment (DOSE) and protein-protein interaction (PPI) analyses. This review provides new insights into the therapeutic effects and mechanisms of BV and its main components on diseases.
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Affiliation(s)
- Peiying Shi
- Department of Traditional Chinese Medicine Resource and Bee Products, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
- State and Local Joint Engineering Laboratory of Natural Biotoxins, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Peiying Shi, ; Hong Yao,
| | - Shihui Xie
- Department of Traditional Chinese Medicine Resource and Bee Products, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiali Yang
- Department of Traditional Chinese Medicine Resource and Bee Products, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi Zhang
- Department of Traditional Chinese Medicine Resource and Bee Products, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuo Han
- Department of Traditional Chinese Medicine Resource and Bee Products, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Songkun Su
- Department of Traditional Chinese Medicine Resource and Bee Products, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hong Yao
- Department of Pharmaceutical Analysis, School of Pharmacy, Fujian Medical University, Fuzhou, China
- *Correspondence: Peiying Shi, ; Hong Yao,
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de Macedo LH, Souza COS, Gardinassi LG, Faccioli LH. CD14 regulates the metabolomic profiles of distinct macrophage subsets under steady and activated states. Immunobiology 2022; 227:152191. [DOI: 10.1016/j.imbio.2022.152191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/05/2022]
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Pap N, Reshamwala D, Korpinen R, Kilpeläinen P, Fidelis M, Furtado MM, Sant'Ana AS, Wen M, Zhang L, Hellström J, Marnilla P, Mattila P, Sarjala T, Yang B, Lima ADS, Azevedo L, Marjomäki V, Granato D. Toxicological and bioactivity evaluation of blackcurrant press cake, sea buckthorn leaves and bark from Scots pine and Norway spruce extracts under a green integrated approach. Food Chem Toxicol 2021; 153:112284. [PMID: 34044082 DOI: 10.1016/j.fct.2021.112284] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
Aqueous extracts from blackcurrant press cake (BC), Norway spruce bark (NS), Scots pine bark (SP), and sea buckthorn leaves (SB) were obtained using maceration and pressurized hot water and tested for their bioactivities. Maceration provided the extraction of higher dry matter contents, including total phenolics (TPC), anthocyanins, and condensed tannins, which also impacted higher antioxidant activity. NS and SB extracts presented the highest mean values of TPC and antioxidant activity. Individually, NS extract presented high contents of proanthocyanidins, resveratrol, and some phenolic acids. In contrast, SB contained a high concentration of ellagitannins, ellagic acid, and quercetin, explaining the antioxidant activity and antibacterial effects. SP and BC extracts had the lowest TPC and antioxidant activity. However, BC had strong antiviral efficacy, whereas SP can be considered a potential ingredient to inhibit α-amylase. Except for BC, the other extracts decreased reactive oxygen species (ROS) generation in HCT8 and A549 cells. Extracts did not inhibit the production of TNF-alpha in lipopolysaccharide-stimulated THP-1 macrophages but inhibited the ROS generation during the THP-1 cell respiratory burst. The recovery of antioxidant compounds from these by-products is incentivized for high value-added applications.
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Affiliation(s)
- Nora Pap
- Biorefinery and Bioproducts, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland.
| | - Dhanik Reshamwala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Risto Korpinen
- Biorefinery and Bioproducts, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland
| | - Petri Kilpeläinen
- Biorefinery and Bioproducts, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland
| | - Marina Fidelis
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland
| | - Marianna M Furtado
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Mingchun Wen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jarkko Hellström
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - Pertti Marnilla
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-31600, Jokioinen, Finland
| | - Pirjo Mattila
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI- 20520, Turku, Finland
| | - Tytti Sarjala
- Biomass Characterization and Properties, Natural Resources Institute Finland (Luke), FI-39700, Parkano, Finland
| | - Baoru Yang
- Food Chemistry and Food Development, Department of Biochemistry, University of Turku, 20014, Turku, Finland
| | - Amanda Dos Santos Lima
- Department of Food, Faculty of Nutrition, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 714, 37130-000, Alfenas, Brazil
| | - Luciana Azevedo
- Department of Food, Faculty of Nutrition, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 714, 37130-000, Alfenas, Brazil
| | - Varpu Marjomäki
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Daniel Granato
- Food Processing and Quality, Natural Resources Institute Finland (Luke), FI-02150, Espoo, Finland.
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Ashokcoomar S, Loots DT, Beukes D, van Reenen M, Pillay B, Pillay M. M. tuberculosis curli pili (MTP) is associated with alterations in carbon, fatty acid and amino acid metabolism in a THP-1 macrophage infection model. Microb Pathog 2021; 154:104806. [PMID: 33610716 DOI: 10.1016/j.micpath.2021.104806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/28/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022]
Abstract
The initial host-pathogen interaction is crucial for the establishment of infection. An improved understanding of the pathophysiology of Mycobacterium tuberculosis (M. tuberculosis) during macrophage infection can aid the development of intervention therapeutics against tuberculosis. M. tuberculosis curli pili (MTP) is a surface located adhesin, involved in the first point-of-contact between pathogen and host. This study aimed to better understand the role of MTP in modulating the intertwined metabolic pathways of M. tuberculosis and its THP-1 macrophage host. Metabolites were extracted from pelleted wet cell mass of THP-1 macrophages infected with M. tuberculosis wild-type V9124 (WT), Δmtp-deletion mutant and the mtp-complemented strains, respectively, via a whole metabolome extraction method using a 1:3:1 ratio of chloroform:methanol:water. Metabolites were detected by two-dimensional gas chromatography time-of-flight mass spectrometry. Significant metabolites were determined through univariate and multivariate statistical tests and online pathway databases. Relative to the WT, a total of nine and ten metabolites were significantly different in the Δmtp and complement strains, respectively. All nine significant metabolites were found in elevated levels in the Δmtp relative to the WT. Additionally, of the ten significant metabolites, eight were detected in lower levels and two were detected in higher levels in the complement relative to the WT. The absence of the MTP adhesin resulted in reduced virulence of M. tuberculosis leading to alterations in metabolites involved in carbon, fatty acid and amino acid metabolism during macrophage infection, suggesting that MTP plays an important role in the modulation of host metabolic activity. These findings support the prominent role of the MTP adhesin as a virulence factor as well as a promising biomarker for possible diagnostic and therapeutic intervention.
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Affiliation(s)
- Shinese Ashokcoomar
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa.
| | - Du Toit Loots
- Human Metabolomics, North-West University, Potchefstroom, Private Bag X6001, Box 269, 2531, South Africa.
| | - Derylize Beukes
- Human Metabolomics, North-West University, Potchefstroom, Private Bag X6001, Box 269, 2531, South Africa.
| | - Mari van Reenen
- Human Metabolomics, North-West University, Potchefstroom, Private Bag X6001, Box 269, 2531, South Africa.
| | - Balakrishna Pillay
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban. 4000, South Africa.
| | - Manormoney Pillay
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa.
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Karkossa I, Raps S, von Bergen M, Schubert K. Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages. Int J Mol Sci 2020; 21:E9371. [PMID: 33317022 PMCID: PMC7764599 DOI: 10.3390/ijms21249371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022] Open
Abstract
Insights into the modes of action (MoAs) of xenobiotics are of utmost importance for the definition of adverse outcome pathways (AOPs), which are essential for a mechanism-based risk assessment. A well-established strategy to reveal MoAs of xenobiotics is the use of omics. However, often an even more comprehensive approach is needed, which can be achieved using multi-omics. Since the immune system plays a central role in the defense against foreign substances and pathogens, with the innate immune system building a first barrier, we systematically reviewed multi-omics studies investigating the effects of xenobiotics on macrophages. Surprisingly, only nine publications were identified, combining proteomics with transcriptomics or metabolomics. We summarized pathways and single proteins, transcripts, or metabolites, which were described to be affected upon treatment with xenobiotics in the reviewed studies, thus revealing a broad range of effects. In summary, we show that macrophages are a relevant model system to investigate the toxicological effects induced by xenobiotics. Furthermore, the multi-omics approaches led to a more comprehensive overview compared to only one omics layer with slight advantages for combinations that complement each other directly, e.g., proteome and metabolome.
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Affiliation(s)
- Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
| | - Stefanie Raps
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
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