1
|
Teklemariam TA, Chou F, Kumaravel P, Van Buskrik J. ATR-FTIR spectroscopy and machine/deep learning models for detecting adulteration in coconut water with sugars, sugar alcohols, and artificial sweeteners. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124771. [PMID: 39032237 DOI: 10.1016/j.saa.2024.124771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/12/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024]
Abstract
Packaged coconut water offers various options, from pure to those with added sugars and other additives. While the purity of coconut water is esteemed for its health benefits, its popularity also exposes it to potential adulteration and misrepresentation. To address this concern, our study combines Fourier transform infrared spectroscopy (FTIR) and machine learning techniques to detect potential adulterants in coconut water through classification models. The dataset comprises infrared spectra from coconut water samples spiked with 15 different types of potential sugar substitutes, including: sugars, artificial sweeteners, and sugar alcohols. The interaction of infrared light with molecular bonds generates unique molecular fingerprints, forming the basis of our analysis. Departing from previous research predominantly reliant on linear-based chemometrics for adulterant detection, our study explored linear, non-linear, and combined feature extraction models. By developing an interactive application utilizing principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE), non-targeted sugar adulterant detection was streamlined through enhanced visualization and pattern recognition. Targeted analysis using ensemble learning random forest (RF) and deep learning 1-dimensional convolutional neural network (1D CNN) achieved higher classification accuracies (95% and 96%, respectively) compared to sparse partial least squares discriminant analysis (sPLS-DA) at 77% and support vector machine (SVM) at 88% on the same dataset. The CNN's demonstrated classification accuracy is complemented by exceptional efficiency through its ability to train and test on raw data.
Collapse
Affiliation(s)
- Thomas A Teklemariam
- Canadian Food Inspection Agency, Greater Toronto Area Laboratory, 2301 Midland Avenue, Toronto, ON M1P 4R7, Canada.
| | - Faith Chou
- Canadian Food Inspection Agency, 1400 Merivale Road, Ottawa, ON K1A 0Y9, Canada
| | - Pavisha Kumaravel
- University of Guelph, Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Jeremy Van Buskrik
- Canadian Food Inspection Agency, Greater Toronto Area Laboratory, 2301 Midland Avenue, Toronto, ON M1P 4R7, Canada
| |
Collapse
|
2
|
Dabdoub S, Greenlee A, Abboud G, Brengartner L, Zuiker E, Gorr MW, Wold LE, Kumar PS, Cray J. Acute exposure to electronic cigarette components alters mRNA expression of pre-osteoblasts. FASEB J 2024; 38:e70017. [PMID: 39213037 PMCID: PMC11371384 DOI: 10.1096/fj.202302014rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 08/01/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
The use of traditional nicotine delivery products such as tobacco has long been linked to detrimental health effects. However, little work to date has focused on the emerging market of aerosolized nicotine delivery known as electronic nicotine delivery systems (ENDS) or electronic cigarettes, and their potential for new effects on human health. Challenges studying these devices include heterogeneity in the formulation of the common components of most available ENDS, including nicotine and a carrier (commonly composed of propylene glycol and vegetable glycerin, or PG/VG). In the present study, we report on experiments interrogating the effects of major identified components in e-cigarettes. Specifically, the potential concomitant effects of nicotine and common carrier ingredients in commercial "vape" products are explored in vitro to inform the potential health effects on the craniofacial skeleton through novel vectors as compared to traditional tobacco products. MC3T3-E1 murine pre-osteoblast cells were cultured in vitro with clinically relevant liquid concentrations of nicotine, propylene glycol (PG), vegetable glycerin (VG), Nicotine+PG/VG, and the vape liquid of a commercial product (Juul). Cells were treated acutely for 24 h and RNA-Seq was utilized to determine segregating alteration in mRNA signaling. Influential gene targets identified with sparse partial least squares discriminant analysis (sPLS-DA) implemented in mixOmics were assessed using the PANTHER Classification system for molecular functions, biological processes, cellular components, and pathways of effect. Additional endpoint functional analyses were used to confirm cell cycle changes. The initial excitatory concentration (EC50) studied defined a target concentration of carrier PG/VG liquid that altered the cell cycle of the calvarial cells. Initial sPLS-DA analysis demonstrated the segregation of nicotine and non-nicotine exposures utilized in our in vitro modeling. Pathway analysis suggests a strong influence of nicotine exposures on cellular processes including metabolic processes and response to stimuli including autophagic flux. Further interrogation of the individual treatment conditions demonstrated segregation by treatment modality (Control, Nicotine, Carrier (PG+VG), Nicotine+PG/VG) along three dimensions best characterized by: latent variable 1 (PLSDA-1) showing strong segregation based on nicotine influence on cellular processes associated with cellular adhesion to collagen, osteoblast differentiation, and calcium binding and metabolism; latent variable 2 (PLSDA-2) showing strong segregation of influence based on PG+VG and Control influence on cell migration, survival, and cycle regulation; and latent variable 3 (PLSDA-3) showing strong segregation based on Nicotine and Control exposure influence on cell activity and growth and developmental processes. Further, gene co-expression network analysis implicates targets of the major pathway genes associated with bone growth and development, particularly craniofacial (FGF, Notch, TGFβ, WNT) and analysis of active subnetwork pathways found these additionally overrepresented in the Juul exposure relative to Nicotine+PG/VG. Finally, experimentation confirmed alterations in cell count, and increased evidence of cell stress (markers of autophagy), but no alteration in apoptosis. These data suggest concomitant treatment with Nicotine+PG/VG drives alterations in pre-osteoblast cell cycle signaling, specifically transcriptomic targets related to cell cycle and potentially cell stress. Although we suspected cell stress and well as cytotoxic effects of Nicotine+PG/VG, no great influence on apoptotic factors was observed. Further RNA-Seq analysis allowed for the direct interrogation of molecular targets of major pathways involved in bone and craniofacial development, each demonstrating segregation (altered signaling) due to e-cigarette-type exposure. These data have implications directed toward ENDS formulation as synergistic effects of Nicotine+PG/VG are evidenced here. Thus, future research will continue to interrogate how varied formulation of Nicotine+PG/VG affects overall cell functions in multiple vital systems.
Collapse
Affiliation(s)
- Shareef Dabdoub
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Periodontics, College of Dentistry, University of Iowa, Iowa City, Iowa 52242, USA
| | - Ashley Greenlee
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - George Abboud
- Undergraduate Biomedical Sciences Major, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Lexie Brengartner
- Undergraduate Biomedical Sciences Major, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Eryn Zuiker
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Matthew W. Gorr
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Loren E. Wold
- Division of Cardiac Surgery, Department of Surgery, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Purnima S. Kumar
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan
| | - James Cray
- Department of Biomedical Education and Anatomy, College of Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
- Divisions of Biosciences and Orthodontics, College of Dentistry, The Ohio State University, Columbus, Ohio, 43210, USA
| |
Collapse
|
3
|
Bayjanov JR, Doornbos C, Ozisik O, Shin W, Queralt-Rosinach N, Wijnbergen D, Saulnier-Blache JS, Schanstra JP, Buffin-Meyer B, Klein J, Fernández JM, Kaliyaperumal R, Baudot A, 't Hoen PAC, Ehrhart F. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Sci Rep 2024; 14:20731. [PMID: 39237660 DOI: 10.1038/s41598-024-71721-8] [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: 01/23/2024] [Accepted: 08/30/2024] [Indexed: 09/07/2024] Open
Abstract
Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is the leading cause of childhood chronic kidney failure and a significant cause of chronic kidney disease in adults. Genetic and environmental factors are known to influence CAKUT development, but the currently known disease mechanism remains incomplete. Our goal is to identify affected pathways and networks in CAKUT, and thereby aid in getting a better understanding of its pathophysiology. With this goal, the miRNome, peptidome, and proteome of over 30 amniotic fluid samples of patients with non-severe CAKUT was compared to patients with severe CAKUT. These omics data sets were made findable, accessible, interoperable, and reusable (FAIR) to facilitate their integration with external data resources. Furthermore, we analysed and integrated the omics data sets using three different bioinformatics strategies: integrative analysis with mixOmics, joint dimensionality reduction and pathway analysis. The three bioinformatics analyses provided complementary features, but all pointed towards an important role for collagen in CAKUT development and the PI3K-AKT signalling pathway. Additionally, several key genes (CSF1, IGF2, ITGB1, and RAC1) and microRNAs were identified. We published the three analysis strategies as containerized workflows. These workflows can be applied to other FAIR data sets and help gaining knowledge on other rare diseases.
Collapse
Affiliation(s)
- Jumamurat R Bayjanov
- Department of Medical BioSciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Cenna Doornbos
- Department of Medical BioSciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Ozan Ozisik
- Aix Marseille Univ, INSERM, MMG, Marseille, France
| | - Woosub Shin
- Department of Bioinformatics-BiGCaT, NUTRIM/MHeNs, Maastricht University, Maastricht, The Netherlands
| | | | - Daphne Wijnbergen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jean-Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Bénédicte Buffin-Meyer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Rajaram Kaliyaperumal
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anaïs Baudot
- Aix Marseille Univ, INSERM, MMG, Marseille, France
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- CNRS, Marseille, France
| | - Peter A C 't Hoen
- Department of Medical BioSciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics-BiGCaT, NUTRIM/MHeNs, Maastricht University, Maastricht, The Netherlands.
| |
Collapse
|
4
|
Tesfaw G, Siraj DS, Abdissa A, Jakobsen RR, Johansen ØH, Zangenberg M, Hanevik K, Mekonnen Z, Langeland N, Bjørang O, Safdar N, Mapes AC, Kates A, Krych L, Castro-Mejía JL, Nielsen DS. Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia. Nat Commun 2024; 15:7532. [PMID: 39223134 PMCID: PMC11369280 DOI: 10.1038/s41467-024-51464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Diarrhea claims >500,000 lives annually among children under five years of age in low- and middle-income countries. Mortality due to acute diarrhea (<7 days' duration) is decreasing, but prolonged (7-13 days) and persistent (≥14 days of duration) diarrhea remains a massive challenge. Here, we use a case-control study to decipher if fecal gut microbiota compositional differences between Ethiopian children with acute (n=554) or prolonged/persistent (n=95) diarrhea and frequency-matched non-diarrheal controls (n=663) are linked to diarrheal etiology. We show that diarrhea cases are associated with lower bacterial diversity and enriched in Escherichia spp., Campylobacter spp., and Streptococcus spp. Further, diarrhea cases are depleted in gut commensals such as Prevotella copri, Faecalibacterium prausnitzii, and Dialister succinatiphilus, with depletion being most pronounced in prolonged/persistent cases, suggesting that prolonged duration of diarrhea is accompanied by depletion of gut commensals and that re-establishing these via e.g., microbiota-directed food supplements offer a potential treatment strategy.
Collapse
Affiliation(s)
- Getnet Tesfaw
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia.
| | - Dawd S Siraj
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Alemseged Abdissa
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Øystein H Johansen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
- Microbiology Laboratory, Southern Health and Social Care Trust, Portadown, Northern Ireland
| | - Mike Zangenberg
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National Center for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Zeleke Mekonnen
- School of Medical Laboratory Sciences, Jimma University, Jimma, Ethiopia
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National Center for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ola Bjørang
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Nasia Safdar
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Abigail C Mapes
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Ashley Kates
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
5
|
White E, Papagno L, Samri A, Sugata K, Hejblum B, Henry AR, Rogan DC, Darko S, Recordon-Pinson P, Dudoit Y, Llewellyn-Lacey S, Chakrabarti LA, Buseyne F, Migueles SA, Price DA, Andreola MA, Satou Y, Thiebaut R, Katlama C, Autran B, Douek DC, Appay V. Clonal succession after prolonged antiretroviral therapy rejuvenates CD8 + T cell responses against HIV-1. Nat Immunol 2024; 25:1555-1564. [PMID: 39179934 DOI: 10.1038/s41590-024-01931-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/15/2024] [Indexed: 08/26/2024]
Abstract
Human immunodeficiency virus 1 (HIV-1) infection is characterized by a dynamic and persistent state of viral replication that overwhelms the host immune system in the absence of antiretroviral therapy (ART). The impact of prolonged treatment on the antiviral efficacy of HIV-1-specific CD8+ T cells has nonetheless remained unknown. Here, we used single-cell technologies to address this issue in a cohort of aging individuals infected early during the pandemic and subsequently treated with continuous ART. Our data showed that long-term ART was associated with a process of clonal succession, which effectively rejuvenated HIV-1-specific CD8+ T cell populations in the face of immune senescence. Tracking individual transcriptomes further revealed that initially dominant CD8+ T cell clonotypes displayed signatures of exhaustion and terminal differentiation, whereas newly dominant CD8+ T cell clonotypes displayed signatures of early differentiation and stemness associated with natural control of viral replication. These findings reveal a degree of immune resilience that could inform adjunctive treatments for HIV-1.
Collapse
Affiliation(s)
- Eoghann White
- ImmunoConcEpT, UMR 5164, Université de Bordeaux, CNRS, INSERM, Bordeaux, France
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM, Paris, France
| | - Laura Papagno
- ImmunoConcEpT, UMR 5164, Université de Bordeaux, CNRS, INSERM, Bordeaux, France
| | - Assia Samri
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM, Paris, France
| | - Kenji Sugata
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Boris Hejblum
- Bordeaux Population Health Research Centre, U1219, Université de Bordeaux, INSERM, Inria SISTM, Bordeaux, France
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Rogan
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patricia Recordon-Pinson
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Université de Bordeaux, CNRS, Bordeaux, France
| | - Yasmine Dudoit
- Institut Pierre Louis d'Epidémiologie et de Sante Publique, AP-HP, Pitié-Salpêtrière Hospital, Department of Infectious Diseases, Sorbonne Université, INSERM, Paris, France
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Lisa A Chakrabarti
- CIVIC Group, Virus and Immunity Unit, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
| | - Florence Buseyne
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, CNRS UMR 3569, Université Paris Cité, Paris, France
| | - Stephen A Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Marie-Aline Andreola
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Université de Bordeaux, CNRS, Bordeaux, France
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Rodolphe Thiebaut
- Bordeaux Population Health Research Centre, U1219, Université de Bordeaux, INSERM, Inria SISTM, Bordeaux, France
- CHU de Bordeaux, Service d'Information Médicale, Bordeaux, France
| | - Christine Katlama
- Institut Pierre Louis d'Epidémiologie et de Sante Publique, AP-HP, Pitié-Salpêtrière Hospital, Department of Infectious Diseases, Sorbonne Université, INSERM, Paris, France
| | - Brigitte Autran
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM, Paris, France
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Victor Appay
- ImmunoConcEpT, UMR 5164, Université de Bordeaux, CNRS, INSERM, Bordeaux, France.
| |
Collapse
|
6
|
De Flaviis R, Santarelli V, Giuliani M, Neri L, Sacchetti G. Influence of wheat content and origin on the volatilome of craft wheat beer: An investigation by combined multivariate statistical approaches. Food Res Int 2024; 191:114709. [PMID: 39059911 DOI: 10.1016/j.foodres.2024.114709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/29/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
A deeper knowledge of the effect of wheat origin on the volatile organic compounds (VOCs) profile of craft wheat beer is crucial for its quality improvement and local product valorisation. The VOCs profile of 17 craft wheat beers obtained by common and durum, heritage and modern, wheat varieties grown in different fields sited at different altitudes was analysed. Data were processed by multivariate analysis using different approaches. Partial least square (PLS) analysis evidenced that wheat concentration was the highest source of VOCs variance, followed by, wheat species, wheat ancientness, and altitude of cultivation. An insight into the effect of wheat concentration was given by sparse PLS analysis (sPLS). The effect of wheat variety was explored by linear discriminant analysis (LDA), which permitted to correctly classify craft beers made with wheat of different origin (species and variety) on the basis of their VOCs profile. sPLS regression analysis permitted to find a combination of VOCs able to predict the altitude of wheat cultivation as well as to correctly classify wheat beers made with wheat cultivated at different altitudes. A further 'one versus all' approach by Soft Independent Modelling of Class Analogies (SIMCA) permitted to correctly authenticate beers made with different cereal species. Finally, shape analysis by generalized Procrustes analysis (GPA) revealed that the differences among samples were conserved and reflected from wheat kernels to wheat beers. This study suggests a promising use of volatiles fingerprinting with a combination of different statistical approaches to authenticate beer made with wheat of different origin and cultivated at different altitudes, thus stressing out the importance of territory in craft beer production, which, until now, was a neglected topic.
Collapse
Affiliation(s)
- Riccardo De Flaviis
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy
| | - Veronica Santarelli
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy
| | - Marialisa Giuliani
- Food consultant as BeerStudioLab, Via Nazionale per Teramo 75, 64021, Giulianova, Italy
| | - Lilia Neri
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy
| | - Giampiero Sacchetti
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy.
| |
Collapse
|
7
|
Kobel CM, Merkesvik J, Burgos IMT, Lai W, Øyås O, Pope PB, Hvidsten TR, Aho VTE. Integrating host and microbiome biology using holo-omics. Mol Omics 2024; 20:438-452. [PMID: 38963125 DOI: 10.1039/d4mo00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.
Collapse
Affiliation(s)
- Carl M Kobel
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Jenny Merkesvik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Wanxin Lai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ove Øyås
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Velma T E Aho
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| |
Collapse
|
8
|
Lin D, Fu Z, Liu J, Perrone-Bizzozero N, Hutchison KE, Bustillo J, Du Y, Pearlson G, Calhoun VD. Association between the oral microbiome and brain resting state connectivity in schizophrenia. Schizophr Res 2024; 270:392-402. [PMID: 38986386 DOI: 10.1016/j.schres.2024.06.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/03/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Recent microbiome-brain axis findings have shown evidence of the modulation of microbiome community as an environmental mediator in brain function and psychiatric illness. This work is focused on the role of the microbiome in understanding a rarely investigated environmental involvement in schizophrenia (SZ), especially in relation to brain circuit dysfunction. We leveraged high throughput microbial 16s rRNA sequencing and functional neuroimaging techniques to enable the delineation of microbiome-brain network links in SZ. N = 213 SZ and healthy control subjects were assessed for the oral microbiome. Among them, 139 subjects were scanned by resting-state functional magnetic resonance imaging (rsfMRI) to derive brain functional connectivity. We found a significant microbiome compositional shift in SZ beta diversity (weighted UniFrac distance, p = 6 × 10-3; Bray-Curtis distance p = 0.021). Fourteen microbial species involving pro-inflammatory and neurotransmitter signaling and H2S production, showed significant abundance alterations in SZ. Multivariate analysis revealed one pair of microbial and functional connectivity components showing a significant correlation of 0.46. Thirty five percent of microbial species and 87.8 % of brain functional network connectivity from each component also showed significant differences between SZ and healthy controls with strong performance in classifying SZ from healthy controls, with an area under curve (AUC) = 0.84 and 0.87, respectively. The results suggest a potential link between oral microbiome dysbiosis and brain functional connectivity alteration in relation to SZ, possibly through immunological and neurotransmitter signaling pathways and the hypothalamic-pituitary-adrenal axis, supporting for future work in characterizing the role of oral microbiome in mediating effects on SZ brain functional activity.
Collapse
Affiliation(s)
- Dongdong Lin
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia, Tech, Emory, Atlanta, GA 30303, United States of America.
| | - Zening Fu
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia, Tech, Emory, Atlanta, GA 30303, United States of America
| | - Jingyu Liu
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia, Tech, Emory, Atlanta, GA 30303, United States of America
| | - Nora Perrone-Bizzozero
- Department of neuroscience, University of New Mexico, Albuquerque, NM, 87109, United States of America
| | - Kent E Hutchison
- Department of psychology and neuroscience, University of Colorado Boulder, Boulder, CO 80309, United States of America
| | - Juan Bustillo
- Department of psychiatry, University of New Mexico, Albuquerque, NM 87109, United States of America
| | - Yuhui Du
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia, Tech, Emory, Atlanta, GA 30303, United States of America
| | - Godfrey Pearlson
- Olin Research Center, Institute of Living Hartford, CT 06102, United States of America; Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06511, United States of America; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06511, United States of America
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State, Georgia, Tech, Emory, Atlanta, GA 30303, United States of America
| |
Collapse
|
9
|
Rohaut B, Calligaris C, Hermann B, Perez P, Faugeras F, Raimondo F, King JR, Engemann D, Marois C, Le Guennec L, Di Meglio L, Sangaré A, Munoz Musat E, Valente M, Ben Salah A, Demertzi A, Belloli L, Manasova D, Jodaitis L, Habert MO, Lambrecq V, Pyatigorskaya N, Galanaud D, Puybasset L, Weiss N, Demeret S, Lejeune FX, Sitt JD, Naccache L. Multimodal assessment improves neuroprognosis performance in clinically unresponsive critical-care patients with brain injury. Nat Med 2024; 30:2349-2355. [PMID: 38816609 PMCID: PMC11333287 DOI: 10.1038/s41591-024-03019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/24/2024] [Indexed: 06/01/2024]
Abstract
Accurately predicting functional outcomes for unresponsive patients with acute brain injury is a medical, scientific and ethical challenge. This prospective study assesses how a multimodal approach combining various numbers of behavioral, neuroimaging and electrophysiological markers affects the performance of outcome predictions. We analyzed data from 349 patients admitted to a tertiary neurointensive care unit between 2009 and 2021, categorizing prognoses as good, uncertain or poor, and compared these predictions with observed outcomes using the Glasgow Outcome Scale-Extended (GOS-E, levels ranging from 1 to 8, with higher levels indicating better outcomes). After excluding cases with life-sustaining therapy withdrawal to mitigate the self-fulfilling prophecy bias, our findings reveal that a good prognosis, compared with a poor or uncertain one, is associated with better one-year functional outcomes (common odds ratio (95% CI) for higher GOS-E: OR = 14.57 (5.70-40.32), P < 0.001; and 2.9 (1.56-5.45), P < 0.001, respectively). Moreover, increasing the number of assessment modalities decreased uncertainty (OR = 0.35 (0.21-0.59), P < 0.001) and improved prognostic accuracy (OR = 2.72 (1.18-6.47), P = 0.011). Our results underscore the value of multimodal assessment in refining neuroprognostic precision, thereby offering a robust foundation for clinical decision-making processes for acutely brain-injured patients. ClinicalTrials.gov registration: NCT04534777 .
Collapse
Affiliation(s)
- B Rohaut
- Sorbonne Université, Paris, France.
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France.
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France.
| | - C Calligaris
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
- GHU Paris Psychiatrie et Neurosciences, Pole Neuro, Sainte‑Anne Hospital, Anesthesia and Intensive Care Department, Paris, France
| | - B Hermann
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
- GHU Paris Psychiatrie et Neurosciences, Pole Neuro, Sainte‑Anne Hospital, Anesthesia and Intensive Care Department, Paris, France
| | - P Perez
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
| | - F Faugeras
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - F Raimondo
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - J-R King
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- Laboratoire des systèmes perceptifs, Département d'études cognitives, École normale supérieure, PSL University, CNRS, Paris, France
| | - D Engemann
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - C Marois
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
| | - L Le Guennec
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
| | - L Di Meglio
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
- GHU Paris Psychiatrie et Neurosciences, Pole Neuro, Sainte‑Anne Hospital, Anesthesia and Intensive Care Department, Paris, France
| | - A Sangaré
- Sorbonne Université, Paris, France
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neurophysiology, Paris, France
| | - E Munoz Musat
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neurophysiology, Paris, France
| | - M Valente
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - A Ben Salah
- Sorbonne Université, Paris, France
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - A Demertzi
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- Physiology of Cognition GIGA-CRC In Vivo Imaging Center, University of Liège, Liège, Belgium
| | - L Belloli
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - D Manasova
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - L Jodaitis
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
| | - M O Habert
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, Departement of Nuclear Medicine, Laboratoire d'Imagerie Biomédicale, Inserm, CNRS, Paris, France
| | - V Lambrecq
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neurophysiology, Paris, France
| | - N Pyatigorskaya
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, Departement of Neuro-radiology, Paris, France
| | - D Galanaud
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, Departement of Neuro-radiology, Paris, France
| | - L Puybasset
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, Departement of Neuro-anaesthesiology and Neurocritical care, Paris, France
| | - N Weiss
- Sorbonne Université, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
| | - S Demeret
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neuro ICU, Paris, France
| | - F X Lejeune
- Paris Brain Institute - ICM, Inserm, CNRS, Data Analysis Core, Paris, France
| | - J D Sitt
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
| | - L Naccache
- Sorbonne Université, Paris, France
- Paris Brain Institute - ICM, Inserm, CNRS, PICNIC-Lab, Paris, France
- APHP, Hôpital de la Pitié Salpêtrière, DMU Neurosciences - Neurophysiology, Paris, France
| |
Collapse
|
10
|
Merkhassine M, Coch RW, Frederick CE, Bennett LL, Peng SA, Morse B, Cummings BP, Loftus JP. Glucagon infusion alters the circulating metabolome and urine amino acid excretion in dogs. J Endocrinol 2024; 262:e240051. [PMID: 38814331 PMCID: PMC11301426 DOI: 10.1530/joe-24-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/30/2024] [Indexed: 05/31/2024]
Abstract
Glucagon plays a central role in amino acid (AA) homeostasis. The dog is an established model of glucagon biology, and recently, metabolomic changes in people associated with glucagon infusions have been reported. Glucagon also has effects on the kidney; however, changes in urinary AA concentrations associated with glucagon remain under investigation. Therefore, we aimed to fill these gaps in the canine model by determining the effects of glucagon on the canine plasma metabolome and measuring urine AA concentrations. Employing two constant rate glucagon infusions (CRI) - low-dose (CRI-LO: 3 ng/kg/min) and high-dose (CRI-HI: 50 ng/kg/min) on five research beagles, we monitored interstitial glucose and conducted untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) on plasma samples and urine AA concentrations collected pre- and post-infusion. The CRI-HI induced a transient glucose peak (90-120 min), returning near baseline by infusion end, while only the CRI-LO resulted in 372 significantly altered plasma metabolites, primarily reductions (333). Similarly, CRI-HI affected 414 metabolites, with 369 reductions, evidenced by distinct clustering post-infusion via data reduction (PCA and sPLS-DA). CRI-HI notably decreased circulating AA levels, impacting various AA-related and energy-generating metabolic pathways. Urine analysis revealed increased 3-methyl-l-histidine and glutamine, and decreased alanine concentrations post-infusion. These findings demonstrate glucagon's glucose-independent modulation of the canine plasma metabolome and highlight the dog's relevance as a translational model for glucagon biology. Understanding these effects contributes to managing dysregulated glucagon conditions and informs treatments impacting glucagon homeostasis.
Collapse
Affiliation(s)
- Michael Merkhassine
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
- VCA Colonial Animal Hospital, Ithaca, New York, USA
| | - Reilly W Coch
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
- Weill Cornell College of Medicine, New York, New York, USA
| | - Carol E Frederick
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
| | - Lucinda L Bennett
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
| | - Seth A Peng
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
- Fate Therapeutics, San Diego, California, USA
| | - Benjamin Morse
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
| | - Bethany P Cummings
- Center for Alimentary and Metabolic Science, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, California, USA
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - John P Loftus
- Loftus Laboratory, Department of Clinical Sciences, Cornell University, College of Veterinary Medicine, Ithaca, New York, USA
| |
Collapse
|
11
|
Xu J, Xu H, Yang F, Xie Y, Cai F, Mao S, Lu M, Zhuang H, Hua Z. Different depths of food restriction and high-fat diet refeeding in mice impact host obesity and metabolic phenotypes with correlative changes in the gut microbiota. MedComm (Beijing) 2024; 5:e641. [PMID: 39021516 PMCID: PMC11253304 DOI: 10.1002/mco2.641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/20/2024] Open
Abstract
Overweight and obesity affect almost 2 billion adults worldwide, and food restriction (FR) is commonly used to reduce body fat. Whether refeeding (Re) after FR at different ages and to different degrees leads to overweight and its possible mechanisms are uncertain. In this study, adult and young mice were both restricted to 15% and 40% of their casual food intake, and then were fed 60% high-fat chow (FR15%-Re, FR40%-Re), whereas the control groups(CON) consumed high-fat or normal food throughout, respectively. The results of the study suggest that mild FR-heavy feeding may lead to more significant abnormal fat accumulation, liver damage, and increased recruitment of intestinal inflammatory factors and immune cells in mice of different ages and involves multiple types of alterations in the gut microbiota. Further fecal transplantation experiments as well as serum and liver enzyme-linked immunosorbent assay experiments preliminarily suggest that the link between lipid metabolism and inflammatory responses and the gut microbiota may be related to the regulation of the gut and live by Lipopolysaccharides(LPS) and Peroxisome Proliferator-Activated Receptor-Alpha(PPAR-α). In addition, our study may also serve as a reference for studying obesity prevention and treatment programs at different ages.
Collapse
Affiliation(s)
- Jiaqi Xu
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Huangru Xu
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Feiyan Yang
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Yawen Xie
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Fangfang Cai
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Siyu Mao
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Min Lu
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Hongqin Zhuang
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
| | - Zi‐Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology and Department of Neurology of Nanjing Drum Tower HospitalSchool of Life Sciences and The Affiliated Hospital of Nanjing University Medical School, Nanjing UniversityNanjingChina
- Faculty of Pharmaceutical SciencesXinxiang Medical UniversityXinxiangChina
- Changzhou High‐Tech Research Institute of Nanjing University and Jiangsu TargetPharma Laboratories Inc.ChangzhouChina
| |
Collapse
|
12
|
Ávila G, Ceciliani F, Viala D, Dejean S, Sala G, Lecchi C, Bonnet M. Conjugated linoleic acid (CLA) modulates bovine peripheral blood mononuclear cells (PBMC) proteome in vitro. J Proteomics 2024; 304:105232. [PMID: 38909954 DOI: 10.1016/j.jprot.2024.105232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/16/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Conjugated linoleic acid (CLA) is a group of natural isomers of the n-6 polyunsaturated fatty acid (PUFA) linoleic acid, exerting biological effects on cow physiology. This study assessed the impact of the mixture 50:50 (vol:vol) of CLA isomers (cis-9, trans-11 and trans-10, cis-12) on bovine peripheral blood mononuclear cells (PBMC) proteome, identifying 1608 quantifiable proteins. A supervised multivariate statistical analysis, sparse variant partial least squares - discriminant analysis (sPLS-DA) for paired data identified 407 discriminant proteins (DP), allowing the clustering between the CLA and controls. The ProteINSIDE workflow found that DP with higher abundance in the CLA group included proteins related to innate immune defenses (PLIN2, CD36, C3, C4, and AGP), with antiapoptotic (SERPINF2 and ITIH4) and antioxidant effects (HMOX1). These results demonstrated that CLA modulates the bovine PBMC proteome, supports the antiapoptotic and immunomodulatory effects observed in previous in vitro studies on bovine PBMC, and suggests a cytoprotective role against oxidative stress. SIGNIFICANCE: In this study, we report for the first time that the mixture 50:50 (vol:vol) of cis-9, trans-11, and trans-10, cis-12-CLA isomers modulates the bovine PBMC proteome. Our results support the immunomodulatory and antiapoptotic effects observed in bovine PBMC in vitro. In addition, the present study proposes a cytoprotective role of CLA mixture against oxidative stress. We suggest a molecular signature of CLA treatment based on combining a multivariate sparse discriminant analysis and a clustering method. This demonstrates the great value of sPLS-DA as an alternative option to identify discriminant proteins with relevant biological significance.
Collapse
Affiliation(s)
- G Ávila
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - F Ceciliani
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy.
| | - D Viala
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122 Saint-Genès-Champanelle, France; INRAE, Metabolomic and Proteomic Exploration Facility (PFEM), F-63122 Saint-Genès-Champanelle, France
| | - S Dejean
- Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, UPS, UMR 5219, 31062 Toulouse, France
| | - G Sala
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - C Lecchi
- Department of Veterinary Medicine and Animal Science, Università Degli Studi di Milano, Via dell'Università 6, 26900 Lodi, Italy
| | - M Bonnet
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMRH, 63122 Saint-Genès-Champanelle, France
| |
Collapse
|
13
|
Filaire F, Sécula A, Bessière P, Pagès-Homs M, Guérin JL, Violleau F, Till U. High and low pathogenicity avian influenza virus discrimination and prediction based on volatile organic compounds signature by SIFT-MS: a proof-of-concept study. Sci Rep 2024; 14:17051. [PMID: 39048690 PMCID: PMC11269574 DOI: 10.1038/s41598-024-67219-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
High and low pathogenicity avian influenza viruses (HPAIV, LPAIV) are the primary causes of poultry diseases worldwide. HPAIV and LPAIV constitute a major threat to the global poultry industry. Therefore, early detection and well-adapted surveillance strategies are of the utmost importance to control the spread of these viruses. Volatile Organic Compounds (VOCs) released from living organisms have been investigated over the last decades as a diagnostic strategy. Mass spectrometry instruments can analyze VOCs emitted upon viral infection. Selected ion flow tube mass spectrometry (SIFT-MS) enables direct analysis of cell headspace in less than 20 min. As a proof-of-concept study, we investigated the ability of a SIFT-MS coupled sparse Partial Least Square-Discriminant Analysis analytical workflow to discriminate IAV-infected cells. Supernatants of HPAIV, LPAIV, and control cells were collected from 1 to 72 h post-infection and analyzed using our analytical workflow. At each collection point, VOCs' signatures were first identified based on four independent experiments and then used to discriminate the infectious status of external samples. Our results indicate that the identified VOCs signatures successfully discriminate, as early as 1-h post-infection, infected cells from the control cells and differentiated the HPAIV from the LPAIV infection. These results suggest a virus-dependent VOCs signature. Overall, the external samples' status was identified with 96.67% sensitivity, 100% specificity, and 97.78% general accuracy.
Collapse
Affiliation(s)
- Fabien Filaire
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France.
- Physiologie, Pathologie et Génétique Végétales PPGV, INP-PURPAN, Toulouse, France.
- THESEO France, Lanxess Biosecurity, LanXess Group, Laval, France.
| | - Aurélie Sécula
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Marielle Pagès-Homs
- Physiologie, Pathologie et Génétique Végétales PPGV, INP-PURPAN, Toulouse, France.
| | | | - Frederic Violleau
- Laboratoire de Chimie Agro-industrielle, LCA, Université de Toulouse, INP-PURPAN, Toulouse, France
| | - Ugo Till
- THESEO France, Lanxess Biosecurity, LanXess Group, Laval, France
| |
Collapse
|
14
|
Hoorn QA, Rabaglino MB, Amaral TF, Maia TS, Yu F, Cole JB, Hansen PJ. Machine learning to identify endometrial biomarkers predictive of pregnancy success following artificial insemination in dairy cows†. Biol Reprod 2024; 111:54-62. [PMID: 38590174 DOI: 10.1093/biolre/ioae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/06/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
The objective was to identify a set of genes whose transcript abundance is predictive of a cow's ability to become pregnant following artificial insemination. Endometrial epithelial cells from the uterine body were collected for RNA sequencing using the cytobrush method from 193 first-service Holstein cows at estrus prior to artificial insemination (day 0). A group of 253 first-service cows not used for cytobrush collection were controls. There was no effect of cytobrush collection on pregnancy outcomes at day 30 or 70 or on pregnancy loss between days 30 and 70. There were 2 upregulated and 214 downregulated genes (false discovery rate < 0.05, absolute fold change >2-fold) for cows pregnant at day 30 versus those that were not pregnant. Functional terms overrepresented in the downregulated genes included those related to immune and inflammatory responses. Machine learning for fertility biomarkers with the R package BORUTA resulted in identification of 57 biomarkers that predicted pregnancy outcome at day 30 with an average accuracy of 77%. Thus, machine learning can identify predictive biomarkers of pregnancy in endometrium with high accuracy. Moreover, sampling of endometrial epithelium using the cytobrush can help understand functional characteristics of the endometrium at artificial insemination without compromising cow fertility. Functional characteristics of the genes comprising the set of biomarkers is indicative that a major determinant of cow fertility, at least for first insemination after calving, is immune status of the uterus, which, in turn, is likely to reflect the previous history of uterine disease.
Collapse
Affiliation(s)
- Quinn A Hoorn
- Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program, and the Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Maria B Rabaglino
- Department of Population Health Science, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Thiago F Amaral
- Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program, and the Genetics Institute, University of Florida, Gainesville, FL, USA
- Genus plc PLC/ABS, Mogi Mirim, São Paulo, Brazil
| | - Tatiane S Maia
- Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program, and the Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Fahong Yu
- University of Florida Interdisciplinary Center for Biotechnology Research, Gainesville, FL, USA
| | - John B Cole
- Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program, and the Genetics Institute, University of Florida, Gainesville, FL, USA
- URUS Group LP, Madison, WI, USA
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Peter J Hansen
- Department of Animal Sciences, Donald Henry Barron Reproductive and Perinatal Biology Research Program, and the Genetics Institute, University of Florida, Gainesville, FL, USA
| |
Collapse
|
15
|
Regueira-Iglesias A, Suárez-Rodríguez B, Blanco-Pintos T, Relvas M, Alonso-Sampedro M, Balsa-Castro C, Tomás I. The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects. Front Cell Infect Microbiol 2024; 14:1405699. [PMID: 39071165 PMCID: PMC11272481 DOI: 10.3389/fcimb.2024.1405699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/30/2024] Open
Abstract
Introduction Microbiome-based clinical applications that improve diagnosis related to oral health are of great interest to precision dentistry. Predictive studies on the salivary microbiome are scarce and of low methodological quality (low sample sizes, lack of biological heterogeneity, and absence of a validation process). None of them evaluates the impact of confounding factors as batch effects (BEs). This is the first 16S multi-batch study to analyze the salivary microbiome at the amplicon sequence variant (ASV) level in terms of differential abundance and machine learning models. This is done in periodontally healthy and periodontitis patients before and after removing BEs. Methods Saliva was collected from 124 patients (50 healthy, 74 periodontitis) in our setting. Sequencing of the V3-V4 16S rRNA gene region was performed in Illumina MiSeq. In parallel, searches were conducted on four databases to identify previous Illumina V3-V4 sequencing studies on the salivary microbiome. Investigations that met predefined criteria were included in the analysis, and the own and external sequences were processed using the same bioinformatics protocol. The statistical analysis was performed in the R-Bioconductor environment. Results The elimination of BEs reduced the number of ASVs with differential abundance between the groups by approximately one-third (Before=265; After=190). Before removing BEs, the model constructed using all study samples (796) comprised 16 ASVs (0.16%) and had an area under the curve (AUC) of 0.944, sensitivity of 90.73%, and specificity of 87.16%. The model built using two-thirds of the specimens (training=531) comprised 35 ASVs (0.36%) and had an AUC of 0.955, sensitivity of 86.54%, and specificity of 90.06% after being validated in the remaining one-third (test=265). After removing BEs, the models required more ASVs (all samples=200-2.03%; training=100-1.01%) to obtain slightly lower AUC (all=0.935; test=0.947), lower sensitivity (all=81.79%; test=78.85%), and similar specificity (all=91.51%; test=90.68%). Conclusions The removal of BEs controls false positive ASVs in the differential abundance analysis. However, their elimination implies a significantly larger number of predictor taxa to achieve optimal performance, creating less robust classifiers. As all the provided models can accurately discriminate health from periodontitis, implying good/excellent sensitivities/specificities, the salivary microbiome demonstrates potential clinical applicability as a precision diagnostic tool for periodontitis.
Collapse
Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Berta Suárez-Rodríguez
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Relvas
- Instituto Universitário de Ciências da Saúde, Cooperativa de Ensino Superior Politécnico e Universitário (IUCS-CESPU), Unidade de Investigação em Patologia e Reabilitação Oral (UNIPRO), Gandra, Portugal
| | - Manuela Alonso-Sampedro
- Department of Internal Medicine and Clinical Epidemiology, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
16
|
Danzer B, Jukic M, Dunkel A, Andersen G, Lieder B, Schaudy E, Stadlmayr S, Lietard J, Michel T, Krautwurst D, Haller B, Knolle P, Somoza M, Lingor P, Somoza V. Impaired metal perception and regulation of associated human foliate papillae tongue transcriptome in long-COVID-19. Sci Rep 2024; 14:15408. [PMID: 38965271 PMCID: PMC11224223 DOI: 10.1038/s41598-024-66079-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Chemosensory impairment is an outstanding symptom of SARS-CoV-2 infections. We hypothesized that measured sensory impairments are accompanied by transcriptomic changes in the foliate papillae area of the tongue. Hospital personnel with known SARS-CoV-2 immunoglobulin G (IgG) status completed questionnaires on sensory perception (n = 158). A subcohort of n = 141 participated in forced choice taste tests, and n = 43 participants consented to donate tongue swabs of the foliate papillae area for whole transcriptome analysis. The study included four groups of participants differing in IgG levels (≥ 10 AU/mL = IgG+; < 10 AU/mL = IgG-) and self-reported sensory impairment (SSI±). IgG+ subjects not detecting metallic taste had higher IgG+ levels than IgG+ participants detecting iron gluconate (p = 0.03). Smell perception was the most impaired biological process in the transcriptome data from IgG+/SSI+ participants subjected to gene ontology enrichment. IgG+/SSI+ subjects demonstrated lower expression levels of 166 olfactory receptors (OR) and 9 taste associated receptors (TAS) of which OR1A2, OR2J2, OR1A1, OR5K1 and OR1G1, as well as TAS2R7 are linked to metallic perception. The question raised by this study is whether odorant receptors on the tongue (i) might play a role in metal sensation, and (ii) are potential targets for virus-initiated sensory impairments, which needs to be investigated in future functional studies.
Collapse
Affiliation(s)
- Barbara Danzer
- School of Life Science, Technical University of Munich, Freising, Germany
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Mateo Jukic
- Department of Neurology, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Andreas Dunkel
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Gaby Andersen
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Barbara Lieder
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Institute of Clinical Nutrition, University of Hohenheim, Stuttgart, Germany
| | - Erika Schaudy
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Sarah Stadlmayr
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Jory Lietard
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Timm Michel
- School of Life Science, Technical University of Munich, Freising, Germany
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Dietmar Krautwurst
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Bernhard Haller
- Institute of AI and Informatics in Medicine, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Percy Knolle
- Institute of Molecular Immunology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Mark Somoza
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Paul Lingor
- Department of Neurology, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Veronika Somoza
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.
- Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
- Chair of Nutritional Systems Biology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
17
|
Gusdon AM, Savarraj JPJ, Feng D, Starkman A, Li G, Bodanapally U, Zimmerman W, Ryan AS, Choi HA, Badjatia N. Identification of metabolites associated with preserved muscle volume after aneurysmal subarachnoid hemorrhage due to high protein supplementation and neuromuscular electrical stimulation. Sci Rep 2024; 14:15071. [PMID: 38956192 PMCID: PMC11219968 DOI: 10.1038/s41598-024-64666-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/11/2024] [Indexed: 07/04/2024] Open
Abstract
The INSPIRE randomized clinical trial demonstrated that a high protein diet (HPRO) combined with neuromuscular electrical stimulation (NMES) attenuates muscle atrophy and may improve outcomes after aneurysmal subarachnoid hemorrhage We sought to identify specific metabolites mediating these effects. Blood samples were collected from subjects on admission prior to randomization to either standard of care (SOC; N = 12) or HPRO + NMES (N = 12) and at 7 days. Untargeted metabolomics were performed for each plasma sample. Sparse partial least squared discriminant analysis identified metabolites differentiating each group. Correlation coefficients were calculated between each metabolite and total protein per day and muscle volume. Multivariable models determined associations between metabolites and muscle volume. Unique metabolites (18) were identified differentiating SOC from HPRO + NMES. Of these, 9 had significant positive correlations with protein intake. In multivariable models, N-acetylleucine was significantly associated with preserved temporalis [OR 1.08 (95% CI 1.01, 1.16)] and quadricep [OR 1.08 (95% CI 1.02, 1.15)] muscle volume. Quinolinate was also significantly associated with preserved temporalis [OR 1.05 (95% CI 1.01, 1.09)] and quadricep [OR 1.04 (95% CI 1.00, 1.07)] muscle volume. N-acetylserine and β-hydroxyisovaleroylcarnitine were associated with preserved temporalis or quadricep volume. Metabolites defining HPRO + NMES had strong correlations with protein intake and were associated with preserved muscle volume.
Collapse
Affiliation(s)
- Aaron M Gusdon
- Division of Neurocritical Care, Department of Neurosurgery, McGovern School of Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - Jude P J Savarraj
- Division of Neurocritical Care, Department of Neurosurgery, McGovern School of Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - Diana Feng
- Division of Neurocritical Care, Department of Neurosurgery, McGovern School of Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - Adam Starkman
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Guoyan Li
- Division of Gerontology, Geriatric, and Palliative Medicine, Department of Medicine, Geriatric Research, Education, and Clinical Center (GRECC), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Uttam Bodanapally
- Department of Radiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William Zimmerman
- Program in Trauma, Shock Trauma Neurocritical Care and Department of Neurology, University of Maryland School of Medicine, 22 S. Greene Street, G7K19, Baltimore, MD, 21201, USA
| | - Alice S Ryan
- Division of Gerontology, Geriatric, and Palliative Medicine, Department of Medicine, Geriatric Research, Education, and Clinical Center (GRECC), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Huimahn A Choi
- Division of Neurocritical Care, Department of Neurosurgery, McGovern School of Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - Neeraj Badjatia
- Program in Trauma, Shock Trauma Neurocritical Care and Department of Neurology, University of Maryland School of Medicine, 22 S. Greene Street, G7K19, Baltimore, MD, 21201, USA.
| |
Collapse
|
18
|
Mantri A, Klümpen L, Seel W, Krawitz P, Stehle P, Weber B, Koban L, Plassmann H, Simon MC. Beneficial Effects of Synbiotics on the Gut Microbiome in Individuals with Low Fiber Intake: Secondary Analysis of a Double-Blind, Randomized Controlled Trial. Nutrients 2024; 16:2082. [PMID: 38999830 PMCID: PMC11243043 DOI: 10.3390/nu16132082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Insufficient dietary fiber intake can negatively affect the intestinal microbiome and, over time, may result in gut dysbiosis, thus potentially harming overall health. This randomized controlled trial aimed to improve the gut microbiome of individuals with low dietary fiber intake (<25 g/day) during a 7-week synbiotic intervention. The metabolically healthy male participants (n = 117, 32 ± 10 y, BMI 25.66 ± 3.1 kg/m2) were divided into two groups: one receiving a synbiotic supplement (Biotic Junior, MensSana AG, Forchtenberg, Germany) and the other a placebo, without altering their dietary habits or physical activity. These groups were further stratified by their dietary fiber intake into a low fiber group (LFG) and a high fiber group (HFG). Stool samples for microbiome analysis were collected before and after intervention. Statistical analysis was performed using linear mixed effects and partial least squares models. At baseline, the microbiomes of the LFG and HFG were partially separated. After seven weeks of intervention, the abundance of SCFA-producing microbes significantly increased in the LFG, which is known to improve gut health; however, this effect was less pronounced in the HFG. Beneficial effects on the gut microbiome in participants with low fiber intake may be achieved using synbiotics, demonstrating the importance of personalized synbiotics.
Collapse
Affiliation(s)
- Aakash Mantri
- Institute of Nutrition and Food Science, Nutrition and Microbiota, University of Bonn, 53115 Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, 53127 Bonn, Germany
| | - Linda Klümpen
- Institute of Nutrition and Food Science, Nutrition and Microbiota, University of Bonn, 53115 Bonn, Germany
| | - Waldemar Seel
- Institute of Nutrition and Food Science, Nutrition and Microbiota, University of Bonn, 53115 Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, 53127 Bonn, Germany
| | - Peter Stehle
- Institute of Nutrition and Food Science, Nutritional Physiology, University of Bonn, 53115 Bonn, Germany
| | - Bernd Weber
- Institute of Experimental Epileptology and Cognition Research, University of Bonn, 53115 Bonn, Germany
- Center for Economics and Neuroscience, University of Bonn, 53113 Bonn, Germany
| | - Leonie Koban
- Lyon Neuroscience Research Center (CRNL), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Claude Bernard Lyon 1, 69500 Lyon, France
- Institut Européen d‘Administration des Affaires (INSEAD), 77300 Paris, France
- Control-Interoception-Attention Team, Paris Brain Institute (ICM), 75013 Paris, France
| | - Hilke Plassmann
- Lyon Neuroscience Research Center (CRNL), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Claude Bernard Lyon 1, 69500 Lyon, France
- Institut Européen d‘Administration des Affaires (INSEAD), 77300 Paris, France
| | - Marie-Christine Simon
- Institute of Nutrition and Food Science, Nutrition and Microbiota, University of Bonn, 53115 Bonn, Germany
| |
Collapse
|
19
|
Mahmoud FM, Pritsch K, Siani R, Benning S, Radl V, Kublik S, Bunk B, Spröer C, Schloter M. Comparative genomic analysis of strain Priestia megaterium B1 reveals conserved potential for adaptation to endophytism and plant growth promotion. Microbiol Spectr 2024; 12:e0042224. [PMID: 38916310 PMCID: PMC11302069 DOI: 10.1128/spectrum.00422-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
In our study, we aimed to explore the genomic and phenotypic traits of Priestia megaterium strain B1, which was isolated from root material of healthy apple plants, to adapt to the endophytic lifestyle and promote plant growth. We identified putative genes encoding proteins involved in chemotaxis, flagella biosynthesis, biofilm formation, secretory systems, detoxification, transporters, and transcription regulation. Furthermore, B1 exhibited both swarming and swimming motilities, along with biofilm formation. Both genomic and physiological analyses revealed the potential of B1 to promote plant growth through the production of indole-3-acetic acid and siderophores, as well as the solubilization of phosphate and zinc. To deduce potential genomic features associated with endophytism across members of P. megaterium strains, we conducted a comparative genomic analysis involving 27 and 31 genomes of strains recovered from plant and soil habitats, respectively, in addition to our strain B1. Our results indicated a closed pan genome and comparable genome size of strains from both habitats, suggesting a facultative host association and adaptive lifestyle to both habitats. Additionally, we performed a sparse Partial Least Squares Discriminant Analysis to infer the most discriminative functional features of the two habitats based on Pfam annotation. Despite the distinctive clustering of both groups, functional enrichment analysis revealed no significant enrichment of any Pfam domain in both habitats. Furthermore, when assessing genetic elements related to adaptation to endophytism in each individual strain, we observed their widespread presence among strains from both habitats. Moreover, all members displayed potential genetic elements for promoting plant growth.IMPORTANCEBoth genomic and phenotypic analyses yielded valuable insights into the capacity of P. megaterium B1 to adapt to the plant niche and enhance its growth. The comparative genomic analysis revealed that P. megaterium members, whether derived from soil or plant sources, possess the essential genetic machinery for interacting with plants and enhancing their growth. The conservation of these traits across various strains of this species extends its potential application as a bio-stimulant in diverse environments. This significance also applies to strain B1, particularly regarding its application to enhance the growth of plants facing apple replant disease conditions.
Collapse
Affiliation(s)
- Fatma M. Mahmoud
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Karin Pritsch
- Research Unit for Environmental Simulations, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Environmental Microbiology, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| |
Collapse
|
20
|
Hulahan TS, Spruill L, Wallace EN, Park Y, West RB, Marks JR, Hwang ES, Drake RR, Angel PM. Extracellular Microenvironment Alterations in Ductal Carcinoma In Situ and Invasive Breast Cancer Pathologies by Multiplexed Spatial Proteomics. Int J Mol Sci 2024; 25:6748. [PMID: 38928454 PMCID: PMC11203487 DOI: 10.3390/ijms25126748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Ductal carcinoma in situ (DCIS) is a heterogeneous breast disease that remains challenging to treat due to its unpredictable progression to invasive breast cancer (IBC). Contemporary literature has become increasingly focused on extracellular matrix (ECM) alterations with breast cancer progression. However, the spatial regulation of the ECM proteome in DCIS has yet to be investigated in relation to IBC. We hypothesized that DCIS and IBC present distinct ECM proteomes that could discriminate between these pathologies. Tissue sections of pure DCIS, mixed DCIS-IBC, or pure IBC (n = 22) with detailed pathological annotations were investigated by multiplexed spatial proteomics. Across tissues, 1,005 ECM peptides were detected in pathologically annotated regions and their surrounding extracellular microenvironments. A comparison of DCIS to IBC pathologies demonstrated 43 significantly altered ECM peptides. Notably, eight fibrillar collagen peptides could distinguish with high specificity and sensitivity between DCIS and IBC. Lesion-targeted proteomic imaging revealed heterogeneity of the ECM proteome surrounding individual DCIS lesions. Multiplexed spatial proteomics reported an invasive cancer field effect, in which DCIS lesions in closer proximity to IBC shared a more similar ECM profile to IBC than distal counterparts. Defining the ECM proteomic microenvironment provides novel molecular insights relating to DCIS and IBC.
Collapse
Affiliation(s)
- Taylor S. Hulahan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Elizabeth N. Wallace
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, USA;
| | - Robert B. West
- Department of Pathology Clinical, Stanford University, Stanford, CA 94305, USA;
| | - Jeffrey R. Marks
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - E. Shelley Hwang
- Department of Surgery, Duke University, Durham, NC 27710, USA; (J.R.M.); (E.S.H.)
| | - Richard R. Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA; (T.S.H.); (E.N.W.); (R.R.D.)
| |
Collapse
|
21
|
Vacher M, Canovas R, Laws SM, Doecke JD. A comprehensive multi-omics analysis reveals unique signatures to predict Alzheimer's disease. FRONTIERS IN BIOINFORMATICS 2024; 4:1390607. [PMID: 38962175 PMCID: PMC11219798 DOI: 10.3389/fbinf.2024.1390607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 07/05/2024] Open
Abstract
Background Complex disorders, such as Alzheimer's disease (AD), result from the combined influence of multiple biological and environmental factors. The integration of high-throughput data from multiple omics platforms can provide system overviews, improving our understanding of complex biological processes underlying human disease. In this study, integrated data from four omics platforms were used to characterise biological signatures of AD. Method The study cohort consists of 455 participants (Control:148, Cases:307) from the Religious Orders Study and Memory and Aging Project (ROSMAP). Genotype (SNP), methylation (CpG), RNA and proteomics data were collected, quality-controlled and pre-processed (SNP = 130; CpG = 83; RNA = 91; Proteomics = 119). Using a diagnosis of Mild Cognitive Impairment (MCI)/AD combined as the target phenotype, we first used Partial Least Squares Regression as an unsupervised classification framework to assess the prediction capabilities for each omics dataset individually. We then used a variation of the sparse generalized canonical correlation analysis (sGCCA) to assess predictions of the combined datasets and identify multi-omics signatures characterising each group of participants. Results Analysing datasets individually we found methylation data provided the best predictions with an accuracy of 0.63 (95%CI = [0.54-0.71]), followed by RNA, 0.61 (95%CI = [0.52-0.69]), SNP, 0.59 (95%CI = [0.51-0.68]) and proteomics, 0.58 (95%CI = [0.51-0.67]). After integration of the four datasets, predictions were dramatically improved with a resulting accuracy of 0.95 (95% CI = [0.89-0.98]). Conclusion The integration of data from multiple platforms is a powerful approach to explore biological systems and better characterise the biological signatures of AD. The results suggest that integrative methods can identify biomarker panels with improved predictive performance compared to individual platforms alone. Further validation in independent cohorts is required to validate and refine the results presented in this study.
Collapse
Affiliation(s)
- Michael Vacher
- The Australian eHealth Research Centre, CSIRO Health and Biosecurity, Kensington, WA, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Rodrigo Canovas
- The Australian eHealth Research Centre, CSIRO Health and Biosecurity, Parkville, VIC, Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - James D. Doecke
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- The Australian eHealth Research Centre, CSIRO Health and Biosecurity, Herston, QLD, Australia
| |
Collapse
|
22
|
Bechtold MA, Lin Y, Miller ML, Prieto JM, Frederick CE, Bennett LL, Peterson ME, Simpson KW, Loftus JP. Serum metabolome analysis in hyperthyroid cats before and after radioactive iodine therapy. PLoS One 2024; 19:e0305271. [PMID: 38857299 PMCID: PMC11164369 DOI: 10.1371/journal.pone.0305271] [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: 02/14/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
Hyperthyroidism is the most common feline endocrinopathy. In hyperthyroid humans, untargeted metabolomic analysis identified persistent metabolic derangements despite achieving a euthyroid state. Therefore, we sought to define the metabolome of hyperthyroid cats and identify ongoing metabolic changes after treatment. We prospectively compared privately-owned hyperthyroid cats (n = 7) admitted for radioactive iodine (I-131) treatment and euthyroid privately-owned control (CON) cats (n = 12). Serum samples were collected before (T0), 1-month (T1), and three months after (T3) I-131 therapy for untargeted metabolomic analysis by MS/MS. Hyperthyroid cats (T0) had a distinct metabolic signature with 277 significantly different metabolites than controls (70 increased, 207 decreased). After treatment, 66 (T1 vs. CON) and 64 (T3 vs. CON) metabolite differences persisted. Clustering and data reduction analysis revealed separate clustering of hyperthyroid (T0) and CON cats with intermediate phenotypes after treatment (T1 & T3). Mevalonate/mevalonolactone and creatine phosphate were candidate biomarkers with excellent discrimination between hyperthyroid and healthy cats. We found several metabolic derangements (e.g., decreased carnitine and α-tocopherol) do not entirely resolve after achieving a euthyroid state after treating hyperthyroid cats with I-131. Further investigation is warranted to determine diagnostic and therapeutic implications for candidate biomarkers and persistent metabolic abnormalities.
Collapse
Affiliation(s)
- Molly A. Bechtold
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Yimei Lin
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Meredith L. Miller
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Jennifer M. Prieto
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Carol E. Frederick
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Lucinda L. Bennett
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Mark E. Peterson
- Animal Endocrine Clinic, New York, New York, United States of America
| | - Kenneth W. Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - John P. Loftus
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| |
Collapse
|
23
|
Rashidi A, Ebadi M, Rehman TU, Elhusseini H, Kazadi D, Halaweish H, Khan MH, Hoeschen A, Cao Q, Luo X, Kabage AJ, Lopez S, Ramamoorthy S, Holtan SG, Weisdorf DJ, Khoruts A, Staley C. Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis. CANCER RESEARCH COMMUNICATIONS 2024; 4:1454-1466. [PMID: 38767452 PMCID: PMC11164016 DOI: 10.1158/2767-9764.crc-24-0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect. SIGNIFICANCE Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.
Collapse
Affiliation(s)
- Armin Rashidi
- Clinical Research Division, Fred Hutchinson Cancer Center; and Division of Oncology, University of Washington, Seattle, Washington
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Maryam Ebadi
- Department of Radiation Oncology, University of Washington and Fred Hutchinson Cancer Center, Seattle, Washington
| | - Tauseef U. Rehman
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Heba Elhusseini
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - David Kazadi
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Hossam Halaweish
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Mohammad H. Khan
- Department of Surgery, University of Minnesota, Minneapolis, Minnesota
| | - Andrea Hoeschen
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Qing Cao
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Xianghua Luo
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Amanda J. Kabage
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Sharon Lopez
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | | | - Shernan G. Holtan
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Daniel J. Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Alexander Khoruts
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Minnesota, Minneapolis, Minnesota
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota
| | | |
Collapse
|
24
|
Ravichandran S, Sood R, Das I, Dong T, Figueroa JD, Yang J, Finger N, Vaughan A, Vora P, Selvaraj K, Labus JS, Gupta A. Early life adversity impacts alterations in brain structure and food addiction in individuals with high BMI. Sci Rep 2024; 14:13141. [PMID: 38849441 PMCID: PMC11161480 DOI: 10.1038/s41598-024-63414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
Obesity and food addiction are associated with distinct brain signatures related to reward processing, and early life adversity (ELA) also increases alterations in these same reward regions. However, the neural mechanisms underlying the effect of early life adversity on food addiction are unknown. Therefore, the aim of this study was to examine the interactions between ELA, food addiction, and brain morphometry in individuals with obesity. 114 participants with high body mass index (BMI) underwent structural MRIs, and completed several questionnaires (e.g., Yale Food Addiction Scale (YFAS), Brief Resilience Scale (BRS), Early Traumatic Inventory (ETI)). Freesurfer 6 was applied to generate the morphometry of brain regions. A multivariate pattern analysis was used to derive brain morphometry patterns associated with food addiction. General linear modeling and mediation analyses were conducted to examine the effects of ELA and resilience on food addiction in individuals with obesity. Statistical significance was determined at a level of p < 0.05. High levels of ELA showed a strong association between reward control brain signatures and food addiction (p = 0.03). Resilience positively mediated the effect of ELA on food addiction (B = 0.02, p = 0.038). Our findings suggest that food addiction is associated with brain signatures in motivation and reward processing regions indicative of dopaminergic dysregulation and inhibition of cognitive control regions. These mechanistic variabilities along with early life adversity suggest increased vulnerability to develop food addiction and obesity in adulthood, which can buffer by the neuroprotective effects of resilience, highlighting the value of incorporating cognitive appraisal into obesity therapeutic regimens.
Collapse
Affiliation(s)
- Soumya Ravichandran
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
- UC San Diego School of Medicine, University of California, San Diego, USA
| | - Riya Sood
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Isha Das
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Tien Dong
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
- Goodman Luskin Microbiome Center, University of California, Los Angeles, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
- David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Johnny D Figueroa
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, USA
| | - Jennifer Yang
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
- Goodman Luskin Microbiome Center, University of California, Los Angeles, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Nicholas Finger
- David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Allison Vaughan
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Priten Vora
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Katie Selvaraj
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Jennifer S Labus
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA
- Goodman Luskin Microbiome Center, University of California, Los Angeles, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA
| | - Arpana Gupta
- Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, Los Angeles, USA.
- Goodman Luskin Microbiome Center, University of California, Los Angeles, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, The Obesity and Ingestive Behavior Program, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California, 10833 Le Conte Avenue, Center for Health Sciences 42-210, Los Angeles, CA, 90095, USA.
- David Geffen School of Medicine, University of California, Los Angeles, USA.
| |
Collapse
|
25
|
Yang X, Huang J, Peng J, Wang P, Wong FS, Wang R, Wang D, Wen L. Gut microbiota from B-cell-specific TLR9-deficient NOD mice promote IL-10 + Breg cells and protect against T1D. Front Immunol 2024; 15:1413177. [PMID: 38903498 PMCID: PMC11187306 DOI: 10.3389/fimmu.2024.1413177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of insulin-producing β cells. Toll-like receptor 9 (TLR9) plays a role in autoimmune diseases, and B cell-specific TLR9 deficiency delays T1D development. Gut microbiota are implicated in T1D, although the relationship is complex. However, the impact of B cell-specific deficiency of TLR9 on intestinal microbiota and the impact of altered intestinal microbiota on the development of T1D are unclear. Objectives This study investigated how gut microbiota and the intestinal barrier contribute to T1D development in B cell-specific TLR9-deficient NOD mice. Additionally, this study explored the role of microbiota in immune regulation and T1D onset. Methods The study assessed gut permeability, gene expression related to gut barrier integrity, and gut microbiota composition. Antibiotics depleted gut microbiota, and fecal samples were transferred to germ-free mice. The study also examined IL-10 production, Breg cell differentiation, and their impact on T1D development. Results B cell-specific TLR9-deficient NOD mice exhibited increased gut permeability and downregulated gut barrier-related gene expression. Antibiotics restored gut permeability, suggesting microbiota influence. Altered microbiota were enriched in Lachnospiraceae, known for mucin degradation. Transferring this microbiota to germ-free mice increased gut permeability and promoted IL-10-expressing Breg cells. Rag-/- mice transplanted with fecal samples from Tlr9 fl/fl Cd19-Cre+ mice showed delayed diabetes onset, indicating microbiota's impact. Conclusion B cell-specific TLR9 deficiency alters gut microbiota, increasing gut permeability and promoting IL-10-expressing Breg cells, which delay T1D. This study uncovers a link between TLR9, gut microbiota, and immune regulation in T1D, with implications for microbiota-targeted T1D therapies.
Collapse
Affiliation(s)
- Xin Yang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Juan Huang
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Jian Peng
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Pai Wang
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
- Department of Gastrocolorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - F. Susan Wong
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine (TCM) Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wen
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| |
Collapse
|
26
|
Vianello E, Ambrogi F, Kalousová M, Badalyan J, Dozio E, Tacchini L, Schmitz G, Zima T, Tsongalis GJ, Corsi-Romanelli MM. Circulating perturbation of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) is associated to cardiac remodeling and NLRP3 inflammasome in cardiovascular patients with insulin resistance risk. Exp Mol Pathol 2024; 137:104895. [PMID: 38703553 DOI: 10.1016/j.yexmp.2024.104895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 05/06/2024]
Abstract
Lipidome perturbation occurring during meta-inflammation is associated to left ventricle (LV) remodeling though the activation of the NLRP3 inflammasome, a key regulator of chronic inflammation in obesity-related disorders. Little is known about phosphatidylcholine (PC) and phosphatidylethanolamine (PE) as DAMP-induced NLRP3 inflammasome. Our study is aimed to evaluate if a systemic reduction of PC/PE molar ratio can affect NLRP3 plasma levels in cardiovascular disease (CVD) patients with insulin resistance (IR) risk. Forty patients from IRCCS Policlinico San Donato were enrolled, and their blood samples were drawn before heart surgery. LV geometry measurements were evaluated by echocardiography and clinical data associated to IR risk were collected. PC and PE were quantified by ESI-MS/MS. Circulating NLRP3 was quantified by an ELISA assay. Our results have shown that CVD patients with IR risk presented systemic lipid impairment of PC and PE species and their ratio in plasma was inversely associated to NLRP3 levels. Interestingly, CVD patients with IR risk presented LV changes directly associated to increased levels of NLRP3 and a decrease in PC/PE ratio in plasma, highlighting the systemic effect of meta-inflammation in cardiac response. In summary, PC and PE can be considered bioactive mediators associated to both the NLRP3 and LV changes in CVD patients with IR risk.
Collapse
Affiliation(s)
- Elena Vianello
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Experimental Laboratory for Research on Organ Damage Biomarkers, IRCCS Istituto Auxologico Italiano, Italy.
| | - Federico Ambrogi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy; IRCCS Policlinico San Donato, San Donato Milanese, Italy
| | - Marta Kalousová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and Prague General University Hospital, Prague, Czech Republic
| | - Julietta Badalyan
- Scuola di Specializzazione in Statistica Sanitaria e Biometria, Università Degli Studi Di Milano, Milan, Italy
| | - Elena Dozio
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Experimental Laboratory for Research on Organ Damage Biomarkers, IRCCS Istituto Auxologico Italiano, Italy
| | - Lorenza Tacchini
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Experimental Laboratory for Research on Organ Damage Biomarkers, IRCCS Istituto Auxologico Italiano, Italy
| | - Gerd Schmitz
- Department of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Tomáš Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and Prague General University Hospital, Prague, Czech Republic
| | - Gregory J Tsongalis
- Dartmouth-Hitchcock Medical Center, Department of Pathology and Laboratory Medicine, Lebanon, NH, USA
| | - Massimiliano M Corsi-Romanelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Department of Experimental and Clinical Pathology, IRCCS Istituto Auxologico Italiano, Milan, Italy
| |
Collapse
|
27
|
Lane RE, Korbie D, Khanna KK, Mohamed A, Hill MM, Trau M. Defining the relationship between cellular and extracellular vesicle (EV) content in breast cancer via an integrative multi-omic analysis. Proteomics 2024; 24:e2300089. [PMID: 38168906 DOI: 10.1002/pmic.202300089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024]
Abstract
Much recent research has been dedicated to exploring the utility of extracellular vesicles (EVs) as circulating disease biomarkers. Underpinning this work is the assumption that the molecular cargo of EVs directly reflects the originating cell. Few attempts have been made, however, to empirically validate this on the -omic level. To this end, we have performed an integrative multi-omic analysis of a panel of breast cancer cell lines and corresponding EVs. Whole transcriptome analysis validated that the cellular transcriptome remained stable when cultured cells are transitioned to low serum or serum-free medium for EV collection. Transcriptomic profiling of the isolated EVs indicated a positive correlation between transcript levels in cells and EVs, including disease-associated transcripts. Analysis of the EV proteome verified that HER2 protein is present in EVs, however neither the estrogen (ER) nor progesterone (PR) receptor proteins are detected regardless of cellular expression. Using multivariate analysis, we derived an EV protein signature to infer cellular patterns of ER and HER2 expression, though the ER protein could not be directly detected. Integrative analyses affirmed that the EV proteome and transcriptome captured key phenotypic hallmarks of the originating cells, supporting the potential of EVs for non-invasive monitoring of breast cancers.
Collapse
Affiliation(s)
- Rebecca E Lane
- Australian Institute for Bioengineering and Nanotechnology, Centre for Personalised Nanomedicine, The University of Queensland, St Lucia, Queensland, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology, Centre for Personalised Nanomedicine, The University of Queensland, St Lucia, Queensland, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology, Centre for Personalised Nanomedicine, The University of Queensland, St Lucia, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
28
|
Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nat Ecol Evol 2024; 8:1140-1153. [PMID: 38622362 DOI: 10.1038/s41559-024-02398-5] [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: 08/02/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024]
Abstract
Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.
Collapse
Affiliation(s)
- Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Marquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josefa Cruz
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Xavier Franch-Marro
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | - Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Marcela Nouzova
- Institute of Parasitology, CAS, České Budějovice, Czech Republic
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia; Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Fernando G Noriega
- Biology and BSI, Florida International University, Miami, FL, USA
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | | | - Caroline B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Karl R Wotton
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Isabel Almudi
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - David Martin
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| |
Collapse
|
29
|
Checcucci E, De Cillis S, Alladio E, Piramide F, Volpi G, Granato S, Zamengo D, Bignante G, Amparore D, Piana A, Manfredi M, Vallariello E, Stura I, Di Dio M, Autorino R, Porpiglia F, Fiori C. Ten-year functional and oncological outcomes of a prospective randomized controlled trial comparing laparoscopic versus robot-assisted radical prostatectomy. Prostate 2024; 84:832-841. [PMID: 38572570 DOI: 10.1002/pros.24702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/28/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND Among prostate cancer (PCa) treatment options, mini-invasive surgical approaches have gained a wide diffusion in the last decades. The aim of this study was to present oncological, functional, and quality of life data after 10 years of follow-up of a prospective randomized controlled trial (RCT) (ISRCTN11552140) comparing robot-assisted radical prostatectomy (RARP) versus laparoscopic radical prostatectomy (LRP) for the treatment of PCa. METHODS Patients with localized PCa were randomized to undergo LRP or RARP between January 2010 and January 2011. Functional (continence and potency) and oncological (prostate-specific antigen, biochemical recurrence [BCR] and BCR-free survival [BCRFS]) variables were evaluated. BCRFS curves were estimated by the Kaplan-Meier method and compared using the log-rank test. Machine learning partial least square-discriminant analysis (PLS-DA) was used to identify the variables characterizing more the patients who underwent RARP or LRP. RESULTS Seventy-five of the originally enrolled 120 patients remained on follow-up for 10 years; 40 (53%) underwent RARP and 35 (47%) LRP. Continence and potency recovery rates did not show significant differences (p = 0.068 and p = 0.56, respectively), despite a Δ12% for continence and Δ8% for potency in favor of the robotic approach. However, the quality of continence (in terms of International Consultation on Incontinence Questionnaire-Short Form [ICIQ-SF] score) and erection (in terms of International Index of Erectile Function-5 [IIEF-5] score) was significantly better after 10 years in the robotic group (p = 0.02 and p < 0.001). PLS-DA revealed that LRP was characterized by the worst functional-related outcomes analyzing the entire follow-up period. Four (10%) and six (17%) patients experienced BCR in RARP and LRP groups, respectively (p = 0.36), with an overall 10-year BCR-free survival of 88% and 78% (p = 0.16). CONCLUSIONS Comparable continence and potency rates were observed between RARP and LRP after a 10-year follow-up. However, the RARP group exhibited superior totally dry rate and erection quality. No difference in terms of oncological outcomes was found.
Collapse
Affiliation(s)
- Enrico Checcucci
- Department of Surgery, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Sabrina De Cillis
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | | | - Federico Piramide
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Gabriele Volpi
- Department of Surgery, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Stefano Granato
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Davide Zamengo
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Gabriele Bignante
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Daniele Amparore
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Alberto Piana
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Matteo Manfredi
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | | | - Ilaria Stura
- Department of Public Health and Pediatric Sciences, School of Medicine, University of Turin, Turin, Italy
| | - Michele Di Dio
- Division of Urology, Department of Surgery, SS Annunziata Hospital, Cosenza, Italy
| | | | - Francesco Porpiglia
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| | - Cristian Fiori
- Division of Urology, Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Italy
| |
Collapse
|
30
|
Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
Collapse
Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| |
Collapse
|
31
|
Casaro S, Prim JG, Gonzalez TD, Cunha F, Bisinotto RS, Chebel RC, Santos JEP, Nelson CD, Jeon SJ, Bicalho RC, Driver JP, Galvão KN. Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis. Anim Microbiome 2024; 6:30. [PMID: 38802977 PMCID: PMC11131188 DOI: 10.1186/s42523-024-00314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days postpartum, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine microbiome and metabolome data to advance the understanding of the uterine environment in dairy cows that develop metritis. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine microbiome and metabolome were evaluated individually, and then integrated using network analyses. RESULTS The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows that did and did not develop metritis. Omics integration was performed between 6 significant bacteria genera and 153 significant metabolites on the day of metritis diagnosis. Integration was not performed at calving because there were no significant differences in the uterine microbiome. A total of 3 bacteria genera (i.e. Fusobacterium, Porphyromonas, and Bacteroides) were strongly correlated with 49 metabolites on the day of metritis diagnosis. Seven of the significant metabolites at calving were among the 49 metabolites strongly correlated with opportunistic pathogenic bacteria on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, opportunistic pathogenic bacteria overgrowth, tissue damage and inflammation, immune evasion, and immune dysregulation. CONCLUSIONS The data integration presented herein helps advance the understanding of the uterine environment in dairy cows with metritis. The identified metabolites may provide a competitive advantage to the main uterine pathogens Fusobacterium, Porphyromonas and Bacteroides, and may be promising targets for future interventions aiming to reduce opportunistic pathogenic bacteria growth in the uterus.
Collapse
Affiliation(s)
- S Casaro
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, USA
| | - J G Prim
- Department of Clinical Sciences, Auburn University, Auburn, AL, USA
| | - T D Gonzalez
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, USA
| | - F Cunha
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, USA
| | - R S Bisinotto
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, USA
| | - R C Chebel
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, USA
| | - J E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
- D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - C D Nelson
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - S J Jeon
- Department of Veterinary Biomedical Sciences, Long Island University, Brookville, NY, USA
| | - R C Bicalho
- FERA Diagnostics and Biologicals, College Station, TX, USA
| | - J P Driver
- Division of Animals Sciences, University of Missouri, Columbia, MO, USA
| | - Klibs N Galvão
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, USA.
- D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
32
|
Sun J, Guo H, Zhang S, Nie Y, Zhou S, Zeng Y, Sun Y. Machine learning-based integration develops an immunogenic cell death-derived lncRNA signature for predicting prognosis and immunotherapy response in lung adenocarcinoma. Sci Rep 2024; 14:11724. [PMID: 38778157 PMCID: PMC11111459 DOI: 10.1038/s41598-024-62569-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/19/2024] [Indexed: 05/25/2024] Open
Abstract
Accumulating evidence demonstrates that lncRNAs are involved in the regulation of the immune microenvironment and early tumor development. Immunogenic cell death occurs mainly through the release or increase of tumor-associated antigen and tumor-specific antigen, exposing "danger signals" to stimulate the body's immune response. Given the recent development of immunotherapy in lung adenocarcinoma, we explored the role of tumor immunogenic cell death-related lncRNAs in lung adenocarcinoma for prognosis and immunotherapy benefit, which has never been uncovered yet. Based on the lung adenocarcinoma cohorts from the TCGA database and GEO database, the study developed the immunogenic cell death index signature by several machine learning algorithms and then validated the signature for prognosis and immunotherapy benefit of lung adenocarcinoma patients, which had a more stable performance compared with published signatures in predicting the prognosis, and demonstrated predictive value for benefiting from immunotherapy in multiple cohorts of multiple cancers, and also guided the utilization of chemotherapy drugs.
Collapse
Affiliation(s)
- Jiazheng Sun
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hehua Guo
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Respiratory Medicine, The First People's Hospital of Jiangxia District, Wuhan, China
| | - Siyu Zhang
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yalan Nie
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sirui Zhou
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yalu Sun
- Department of Rehabilitation Medicine, Affiliated Hospital of Jining Medical University, Jining, China.
| |
Collapse
|
33
|
Nagel M, Niestroj M, Bansal R, Fleck D, Lampert A, Stopkova R, Stopka P, Ben-Shaul Y, Spehr M. Deciphering the chemical language of inbred and wild mouse conspecific scents. eLife 2024; 12:RP90529. [PMID: 38747258 PMCID: PMC11095937 DOI: 10.7554/elife.90529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
In most mammals, conspecific chemosensory communication relies on semiochemical release within complex bodily secretions and subsequent stimulus detection by the vomeronasal organ (VNO). Urine, a rich source of ethologically relevant chemosignals, conveys detailed information about sex, social hierarchy, health, and reproductive state, which becomes accessible to a conspecific via vomeronasal sampling. So far, however, numerous aspects of social chemosignaling along the vomeronasal pathway remain unclear. Moreover, since virtually all research on vomeronasal physiology is based on secretions derived from inbred laboratory mice, it remains uncertain whether such stimuli provide a true representation of potentially more relevant cues found in the wild. Here, we combine a robust low-noise VNO activity assay with comparative molecular profiling of sex- and strain-specific mouse urine samples from two inbred laboratory strains as well as from wild mice. With comprehensive molecular portraits of these secretions, VNO activity analysis now enables us to (i) assess whether and, if so, how much sex/strain-selective 'raw' chemical information in urine is accessible via vomeronasal sampling; (ii) identify which chemicals exhibit sufficient discriminatory power to signal an animal's sex, strain, or both; (iii) determine the extent to which wild mouse secretions are unique; and (iv) analyze whether vomeronasal response profiles differ between strains. We report both sex- and, in particular, strain-selective VNO representations of chemical information. Within the urinary 'secretome', both volatile compounds and proteins exhibit sufficient discriminative power to provide sex- and strain-specific molecular fingerprints. While total protein amount is substantially enriched in male urine, females secrete a larger variety at overall comparatively low concentrations. Surprisingly, the molecular spectrum of wild mouse urine does not dramatically exceed that of inbred strains. Finally, vomeronasal response profiles differ between C57BL/6 and BALB/c animals, with particularly disparate representations of female semiochemicals.
Collapse
Affiliation(s)
- Maximilian Nagel
- Department of Chemosensation, Institute for Biology II, RWTH Aachen UniversityAachenGermany
| | - Marco Niestroj
- Department of Chemosensation, Institute for Biology II, RWTH Aachen UniversityAachenGermany
| | - Rohini Bansal
- Department of Medical Neurobiology, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - David Fleck
- Department of Chemosensation, Institute for Biology II, RWTH Aachen UniversityAachenGermany
| | - Angelika Lampert
- Institute of Neurophysiology, Uniklinik RWTH Aachen UniversityAachenGermany
- Research Training Group 2416 MultiSenses – MultiScales, RWTH Aachen UniversityAachenGermany
| | - Romana Stopkova
- BIOCEV group, Department of Zoology, Faculty of Science, Charles UniversityPragueCzech Republic
| | - Pavel Stopka
- BIOCEV group, Department of Zoology, Faculty of Science, Charles UniversityPragueCzech Republic
| | - Yoram Ben-Shaul
- Department of Medical Neurobiology, Institute for Medical Research Israel Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Marc Spehr
- Department of Chemosensation, Institute for Biology II, RWTH Aachen UniversityAachenGermany
- Research Training Group 2416 MultiSenses – MultiScales, RWTH Aachen UniversityAachenGermany
| |
Collapse
|
34
|
Nováková S, Baranovičová E, Hatoková Z, Beke G, Pálešová J, Záhumenská R, Baďurová B, Janíčková M, Strnádel J, Halašová E, Škovierová H. Comparison of Various Extraction Approaches for Optimized Preparation of Intracellular Metabolites from Human Mesenchymal Stem Cells and Fibroblasts for NMR-Based Study. Metabolites 2024; 14:268. [PMID: 38786745 PMCID: PMC11122815 DOI: 10.3390/metabo14050268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Metabolomics has proven to be a sensitive tool for monitoring biochemical processes in cell culture. It enables multi-analysis, clarifying the correlation between numerous metabolic pathways. Together with other analysis, it thus provides a global view of a cell's physiological state. A comprehensive analysis of molecular changes is also required in the case of mesenchymal stem cells (MSCs), which currently represent an essential portion of cells used in regenerative medicine. Reproducibility and correct measurement are closely connected to careful metabolite extraction, and sample preparation is always a critical point. Our study aimed to compare the efficiencies of four harvesting and six extraction methods. Several organic reagents (methanol, ethanol, acetonitrile, methanol-chloroform, MTBE) and harvesting approaches (trypsinization vs. scraping) were tested. We used untargeted nuclear magnetic resonance spectroscopy (NMR) to determine the most efficient method for the extraction of metabolites from human adherent cells, specifically human dermal fibroblasts adult (HDFa) and dental pulp stem cells (DPSCs). A comprehensive dataset of 29 identified and quantified metabolites were determined to possess statistically significant differences in the abundances of several metabolites when the cells were detached mechanically to organic solvent compared to when applying enzymes mainly in the classes of amino acids and peptides for both types of cells. Direct scraping to organic solvent is a method that yields higher abundances of determined metabolites. Extraction with the use of different polar reagents, 50% and 80% methanol, or acetonitrile, mostly showed the same quality. For both HDFa and DPSC cells, the MTBE method, methanol-chloroform, and 80% ethanol extractions showed higher extraction efficiency for the most identified and quantified metabolites Thus, preparation procedures provided a cell sample processing protocol that focuses on maximizing extraction yield. Our approach may be useful for large-scale comparative metabolomic studies of human mesenchymal stem cell samples.
Collapse
Affiliation(s)
- Slavomíra Nováková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Eva Baranovičová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Zuzana Hatoková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Gábor Beke
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia;
| | - Janka Pálešová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Romana Záhumenská
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Bibiána Baďurová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Mária Janíčková
- Department of Stomatology and Maxillofacial Surgery, University Hospital in Martin and JFM CU, Kollárova 2, 036 01 Martin, Slovakia;
| | - Ján Strnádel
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Erika Halašová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| | - Henrieta Škovierová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava (JFM CU), Malá Hora 4C, 036 01 Martin, Slovakia; (S.N.); (Z.H.); (J.P.); (R.Z.); (J.S.); (E.H.); (H.Š.)
| |
Collapse
|
35
|
Chen S, Pu K, Wang Y, Su Y, Qiu J, Wang X, Guo K, Hu J, Wei H, Wang H, Wei X, Chen Y, Lin W, Ni W, Lin Y, Chen J, Lai SKM, Ng KM. Hierarchical superstructure aerogels for in situ biofluid metabolomics. NANOSCALE 2024; 16:8607-8617. [PMID: 38602354 DOI: 10.1039/d3nr05895f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
High-throughput biofluid metabolomics analysis for screening life-threatening diseases is urgently needed. However, the high salt content of biofluid samples, which introduces severe interference, can greatly limit the analysis throughput. Here, a new 3-D interconnected hierarchical superstructure, namely a "plasmonic gold-on-silica (Au/SiO2) double-layered aerogel", integrating distinctive features of an upper plasmonic gold aerogel with a lower inert silica aerogel was successfully developed to achieve in situ separation and storage of inorganic salts in the silica aerogel, parallel enrichment of metabolites on the surface of the functionalized gold aerogel, and direct desorption/ionization of enriched metabolites by the photo-excited gold aerogel for rapid, sensitive, and comprehensive metabolomics analysis of human serum/urine samples. By integrating all these unique advantages into the hierarchical aerogel, multifunctional properties were introduced in the SALDI substrate to enable its effective utilization in clinical metabolomics for the discovery of reliable metabolic biomarkers to achieve unambiguous differentiation of early and advanced-stage lung cancer patients from healthy individuals. This study provides insight into the design and application of superstructured nanomaterials for in situ separation, storage, and photoexcitation of multi-components in complex biofluid samples for sensitive analysis.
Collapse
Affiliation(s)
- Siyu Chen
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
| | - Keyuan Pu
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
| | - Yue Wang
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
| | - Yang Su
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
| | - Jiamin Qiu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, China
| | - Xin Wang
- The Cancer Hospital of Shantou University Medical College, Guangdong, 515031, China.
| | - Kunbin Guo
- The Cancer Hospital of Shantou University Medical College, Guangdong, 515031, China.
| | - Jun Hu
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
| | - Huiwen Wei
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
| | - Hongbiao Wang
- The Cancer Hospital of Shantou University Medical College, Guangdong, 515031, China.
| | - Xiaolong Wei
- The Cancer Hospital of Shantou University Medical College, Guangdong, 515031, China.
| | - Yuping Chen
- The Cancer Hospital of Shantou University Medical College, Guangdong, 515031, China.
| | - Wen Lin
- The Cancer Hospital of Shantou University Medical College, Guangdong, 515031, China.
| | - Wenxiu Ni
- Department of Medicinal Chemistry, Shantou University Medical College, Guangdong, 515041, China
- Chemistry and Chemical Engineering Guangdong Laboratory, Guangdong, 515063, China
| | - Yan Lin
- The Second Affiliated Hospital of Shantou University Medical College, Guangdong, 515041, China
| | - Jiayang Chen
- Instrumental Analysis & Testing Centre, Shantou University, Guangdong, 515063, China
| | - Samuel Kin-Man Lai
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Units 1503-1511, 15/F., Building 17 W, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Kwan-Ming Ng
- Department of Chemistry and Key Laboratory for Preparation and Application of Ordered Structural Materials of Guangdong Province, Shantou University, Guangdong, 515063, China.
- Chemistry and Chemical Engineering Guangdong Laboratory, Guangdong, 515063, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Units 1503-1511, 15/F., Building 17 W, Hong Kong Science Park, New Territories, Hong Kong, China
| |
Collapse
|
36
|
Suh YS, Lee J, George J, Seol D, Jeong K, Oh SY, Bang C, Jun Y, Kong SH, Lee HJ, Kim JI, Kim WH, Yang HK, Lee C. RNA expression of 6 genes from metastatic mucosal gastric cancer serves as the global prognostic marker for gastric cancer with functional validation. Br J Cancer 2024; 130:1571-1584. [PMID: 38467827 PMCID: PMC11059174 DOI: 10.1038/s41416-024-02642-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/08/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Molecular analysis of advanced tumors can increase tumor heterogeneity and selection bias. We developed a robust prognostic signature for gastric cancer by comparing RNA expression between very rare early gastric cancers invading only mucosal layer (mEGCs) with lymph node metastasis (Npos) and those without metastasis (Nneg). METHODS Out of 1003 mEGCs, all Npos were matched to Nneg using propensity scores. Machine learning approach comparing Npos and Nneg was used to develop prognostic signature. The function and robustness of prognostic signature was validated using cell lines and external datasets. RESULTS Extensive machine learning with cross-validation identified the prognostic classifier consisting of four overexpressed genes (HDAC5, NPM1, DTX3, and PPP3R1) and two downregulated genes (MED12 and TP53), and enabled us to develop the risk score predicting poor prognosis. Cell lines engineered to high-risk score showed increased invasion, migration, and resistance to 5-FU and Oxaliplatin but maintained sensitivity to an HDAC inhibitor. Mouse models after tail vein injection of cell lines with high-risk score revealed increased metastasis. In three external cohorts, our risk score was identified as the independent prognostic factor for overall and recurrence-free survival. CONCLUSION The risk score from the 6-gene classifier can successfully predict the prognosis of gastric cancer.
Collapse
Affiliation(s)
- Yun-Suhk Suh
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Jieun Lee
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Donghyeok Seol
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Kyoungyun Jeong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung-Young Oh
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Chanmi Bang
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Yukyung Jun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, South Korea
| | - Seong-Ho Kong
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Hyuk-Joon Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
| | - Han-Kwang Yang
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Surgery, Seoul National University Hospital, Seoul, South Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
| |
Collapse
|
37
|
Sun J, Guo H, Nie Y, Zhou S, Zeng Y, Sun Y. Deciphering the heterogeneity dominated by tumor-associated macrophages for survival prognostication and prediction of immunotherapy response in lung adenocarcinoma. Sci Rep 2024; 14:9276. [PMID: 38653742 DOI: 10.1038/s41598-024-60132-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024] Open
Abstract
Tumor-associated macrophages (TAMs) are a specific subset of macrophages that reside inside the tumor microenvironment. The dynamic interplay between TAMs and tumor cells plays a crucial role in the treatment response and prognosis of lung adenocarcinoma (LUAD). The study aimed to examine the association between TAMs and LUAD to advance the development of targeted strategies and immunotherapeutic approaches for treating this type of lung cancer. The study employed single-cell mRNA sequencing data to characterize the immune cell composition of LUAD and delineate distinct subpopulations of TAMs. The "BayesPrism" and "Seurat" R packages were employed to examine the association between these subgroups and immunotherapy and clinical features to identify novel immunotherapy biomarkers. Furthermore, a predictive signature was generated to forecast patient prognosis by examining the gene expression profile of immunotherapy-associated TAMs subsets and using 104 machine-learning techniques. A comprehensive investigation has shown the existence of a hitherto unidentified subgroup of TAMs known as RGS1 + TAMs, which has been found to have a strong correlation with the efficacy of immunotherapy and the occurrence of tumor metastasis in LUAD patients. CD83 was identified CD83 as a distinct biomarker for the expression of RGS1 + TAMs, showcasing its potential utility as an indicator for immunotherapeutic interventions. Furthermore, the prognostic capacity of the RTMscore signature, encompassing three specific mRNA (NR4A2, MMP14, and NPC2), demonstrated enhanced robustness when contrasted against the comprehensive collection of 104 features outlined in the published study. CD83 has potential as an immunotherapeutic biomarker. Meanwhile, The RTMscore signature established in the present study might be beneficial for survival prognostication.
Collapse
Affiliation(s)
- Jiazheng Sun
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hehua Guo
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yalan Nie
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sirui Zhou
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yalu Sun
- Affiliated Hospital of Jining Medical University, Jining, China.
| |
Collapse
|
38
|
Fomina P, Femenias A, Tafintseva V, Freitag S, Sulyok M, Aledda M, Kohler A, Krska R, Mizaikoff B. Prediction of Deoxynivalenol Contamination in Wheat via Infrared Attenuated Total Reflection Spectroscopy and Multivariate Data Analysis. ACS FOOD SCIENCE & TECHNOLOGY 2024; 4:895-904. [PMID: 38660051 PMCID: PMC11037394 DOI: 10.1021/acsfoodscitech.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
The climate crisis further exacerbates the challenges for food production. For instance, the increasingly unpredictable growth of fungal species in the field can lead to an unprecedented high prevalence of several mycotoxins, including the most important toxic secondary metabolite produced by Fusarium spp., i.e., deoxynivalenol (DON). The presence of DON in crops may cause health problems in the population and livestock. Hence, there is a demand for advanced strategies facilitating the detection of DON contamination in cereal-based products. To address this need, we introduce infrared attenuated total reflection (IR-ATR) spectroscopy combined with advanced data modeling routines and optimized sample preparation protocols. In this study, we address the limited exploration of wheat commodities to date via IR-ATR spectroscopy. The focus of this study was optimizing the extraction protocol for wheat by testing various solvents aligned with a greener and more sustainable analytical approach. The employed chemometric method, i.e., sparse partial least-squares discriminant analysis, not only facilitated establishing robust classification models capable of discriminating between high vs low DON-contaminated samples adhering to the EU regulatory limit of 1250 μg/kg but also provided valuable insights into the relevant parameters shaping these models.
Collapse
Affiliation(s)
- Polina Fomina
- Institute
of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89075 Ulm, Germany
| | - Antoni Femenias
- Institute
of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89075 Ulm, Germany
| | - Valeria Tafintseva
- Faculty
of Science and Technology, Norwegian University
of Life Sciences, Drøbakveien 31, 1432 Ås, Norway
| | - Stephan Freitag
- University
of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology
IFA-Tulln, Institute of Bioanalytics and
Agro-Metabolomics, Konrad
Lorenzstr. 20, A-3430 Tulln, Austria
| | - Michael Sulyok
- University
of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology
IFA-Tulln, Institute of Bioanalytics and
Agro-Metabolomics, Konrad
Lorenzstr. 20, A-3430 Tulln, Austria
| | - Miriam Aledda
- Faculty
of Science and Technology, Norwegian University
of Life Sciences, Drøbakveien 31, 1432 Ås, Norway
| | - Achim Kohler
- Faculty
of Science and Technology, Norwegian University
of Life Sciences, Drøbakveien 31, 1432 Ås, Norway
| | - Rudolf Krska
- University
of Natural Resources and Life Sciences, Vienna, Department of Agrobiotechnology
IFA-Tulln, Institute of Bioanalytics and
Agro-Metabolomics, Konrad
Lorenzstr. 20, A-3430 Tulln, Austria
- Institute
for Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, BT9 5DL Belfast, Northern Ireland
| | - Boris Mizaikoff
- Institute
of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89075 Ulm, Germany
- Hahn-Schickard, Sedanstraße 14, 89077 Ulm, Germany
| |
Collapse
|
39
|
Gindri M, Ithurbide M, Pires J, Rupp R, Puillet L, Friggens NC. Responses of selected plasma metabolites to a two-day nutritional challenge of goats divergently selected for functional longevity. J Dairy Sci 2024:S0022-0302(24)00723-9. [PMID: 38608949 DOI: 10.3168/jds.2023-23908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/02/2024] [Indexed: 04/14/2024]
Abstract
Understanding the extent to which genetics × environment plays a role in shaping individual strategies to environmental challenges is of considerable interest for future selection of more resilient animals. Accordingly, the objective of this study was to evaluate the metabolic responses to a nutritional challenge of goats divergently selected for functional longevity based on plasma metabolites and the repeatability of these responses across 2 experimental farms and years. We carried out 6 different experimental trials from years 2018 to 2022 (4 trials on site Bourges (2018-21) and 2 trials (2021-22) on site Grignon) in which 267 first kidding goats, daughters of Alpine bucks divergently selected for functional longevity, longevity plus (n = 137), and longevity minus (n = 130), were exposed to a 2-d nutritional challenge in early lactation. The experiments consisted of a 5 or 7-d control period (pre-challenge) on a standard lactation diet followed by a 2-d nutritional challenge with straw-only feeding and then a 7 or 10-d recovery period on a standard lactation diet, for site Bourges and Grignon, respectively. During the challenge plasma metabolite composition was recorded daily. Linear mixed-effects models were used to analyze all traits, considering the individual as a random effect and the 2x2 treatments (i.e., genetic line and year nested in site) and litter size as fixed effects. The linear mixed-effects model using a piecewise arrangement was used to analyze the response/recovery profiles to the nutritional challenge. Random parameters estimated for each individual, using the mixed-effects models without the fixed effects of genetic line, were used in a Sparse Partial Least Square Discriminant Analysis (sPLS-DA) to compare the goat metabolism response to the challenge on a multivariate scale. The plasma metabolites, glucose, β-hydroxybutyrate (BHB), and nonesterified fatty acids (NEFA), and urea concentrations responded to the 2-d nutritional challenge. Selection for functional longevity did not affect plasma glucose, NEFA, BHB, and urea response/recoveries to a 2-d nutritional challenge. However, site, trial, and litter size affected these responses. Moreover, the plasma metabolites seem not to fully recover to prechallenge levels after the recovery phase. The sPLS-DA analysis did not discriminate between the 2 longevity lines. We observed meaningful between-individuals' variability in plasma BHB, especially on the prechallenge and rate of response and rate of recovery from the 2-d nutritional challenge (CV = 26.2%, 36.1%, and 41.2%, repeatability = 0.749, 0.322, and 0.741, respectively). Plasma NEFA recovery from challenge also demonstrated high between-individuals' variability (CV = 16.4%, repeatability = 0.323). Selection for functional longevity did not affect plasma metabolites responses to a 2-d nutritional challenge in dairy goats. Plasma NEFA and BHB response/recovery presented high between-individuals' variability, indicating individual adaptative characteristics to nutritional challenges not related to the environmental conditions but to inherent individual characteristics.
Collapse
Affiliation(s)
- M Gindri
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
| | - M Ithurbide
- GenPhySE, Université de Toulouse, INRAE, Institut National Polytechnique de Toulouse, École Nationale Vétérinaire de Toulouse, Castanet Tolosan, 31320, France
| | - J Pires
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - R Rupp
- GenPhySE, Université de Toulouse, INRAE, Institut National Polytechnique de Toulouse, École Nationale Vétérinaire de Toulouse, Castanet Tolosan, 31320, France
| | - L Puillet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
| | - N C Friggens
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France.
| |
Collapse
|
40
|
Schmidt N, Van Den Ham K, Bower L, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton P. Susceptibility to febrile malaria is associated with an inflammatory gut microbiome. RESEARCH SQUARE 2024:rs.3.rs-3974068. [PMID: 38645126 PMCID: PMC11030534 DOI: 10.21203/rs.3.rs-3974068/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with Plasmodium falciparum is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following Plasmodium infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. The fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., Ruminococcus gauvreauii, Ruminococcus torques, Dorea formicigenerans, Dorea longicatena, Lachnoclostridium phocaeense and Lachnoclostridium sp. YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., Anaerobutyricum hallii, Blautia producta and Sellimonas intestinalis). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.
Collapse
|
41
|
Petersen MC, Smith GI, Palacios HH, Farabi SS, Yoshino M, Yoshino J, Cho K, Davila-Roman VG, Shankaran M, Barve RA, Yu J, Stern JH, Patterson BW, Hellerstein MK, Shulman GI, Patti GJ, Klein S. Cardiometabolic characteristics of people with metabolically healthy and unhealthy obesity. Cell Metab 2024; 36:745-761.e5. [PMID: 38569471 PMCID: PMC11025492 DOI: 10.1016/j.cmet.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/06/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
There is considerable heterogeneity in the cardiometabolic abnormalities associated with obesity. We evaluated multi-organ system metabolic function in 20 adults with metabolically healthy obesity (MHO; normal fasting glucose and triglycerides, oral glucose tolerance, intrahepatic triglyceride content, and whole-body insulin sensitivity), 20 adults with metabolically unhealthy obesity (MUO; prediabetes, hepatic steatosis, and whole-body insulin resistance), and 15 adults who were metabolically healthy lean. Compared with MUO, people with MHO had (1) altered skeletal muscle biology (decreased ceramide content and increased expression of genes involved in BCAA catabolism and mitochondrial structure/function); (2) altered adipose tissue biology (decreased expression of genes involved in inflammation and extracellular matrix remodeling and increased expression of genes involved in lipogenesis); (3) lower 24-h plasma glucose, insulin, non-esterified fatty acids, and triglycerides; (4) higher plasma adiponectin and lower plasma PAI-1 concentrations; and (5) decreased oxidative stress. These findings provide a framework of potential mechanisms responsible for MHO and the metabolic heterogeneity of obesity. This study was registered at ClinicalTrials.gov (NCT02706262).
Collapse
Affiliation(s)
- Max C Petersen
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA; Division of Endocrinology, Metabolism, and Lipid Research, Washington University in St. Louis, St. Louis, MO, USA
| | - Gordon I Smith
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA
| | - Hector H Palacios
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA
| | - Sarah S Farabi
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA; Goldfarb School of Nursing at Barnes-Jewish College, St. Louis, MO, USA
| | - Mihoko Yoshino
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA
| | - Jun Yoshino
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA; Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Victor G Davila-Roman
- Cardiovascular Imaging and Clinical Research Core Laboratory, Cardiovascular Division, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Ruteja A Barve
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Jinsheng Yu
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Jennifer H Stern
- Division of Endocrinology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Bruce W Patterson
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Gerald I Shulman
- Departments of Internal Medicine and Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Samuel Klein
- Center for Human Nutrition, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
42
|
Biada I, Ibáñez-Escriche N, Blasco A, Casto-Rebollo C, Santacreu MA. Microbiome composition as a potential predictor of longevity in rabbits. Genet Sel Evol 2024; 56:25. [PMID: 38565991 PMCID: PMC10986140 DOI: 10.1186/s12711-024-00895-6] [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: 06/30/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Longevity and resilience are two fundamental traits for more sustainable livestock production. These traits are closely related, as resilient animals tend to have longer lifespans. An interesting criterion for increasing longevity in rabbit could be based on the information provided by its gut microbiome. The gut microbiome is essential for regulating health and plays crucial roles in the development of the immune system. The aim of this research was to investigate if animals with different longevities have different microbial profiles. We sequenced the 16S rRNA gene from soft faeces from 95 does. First, we compared two maternal rabbit lines with different longevities; a standard longevity maternal line (A) and a maternal line (LP) that was founded based on longevity criteria: females with a minimum of 25 parities with an average prolificacy per parity of 9 or more. Second, we compared the gut microbiota of two groups of animals from line LP with different longevities: females that died/were culled with two parities or less (LLP) and females with more than 15 parities (HLP). RESULTS Differences in alpha and beta diversity were observed between lines A and LP, and a partial least square discriminant analysis (PLS-DA) showed a high prediction accuracy (> 91%) of classification of animals to line A versus LP (146 amplicon sequence variants (ASV)). The PLS-DA also showed a high prediction accuracy (> 94%) to classify animals to the LLP and HLP groups (53 ASV). Interestingly, some of the most important taxa identified in the PLS-DA were common to both comparisons (Akkermansia, Christensenellaceae R-7, Uncultured Eubacteriaceae, among others) and have been reported to be related to resilience and longevity. CONCLUSIONS Our results indicate that the first parity gut microbiome profile differs between the two rabbit maternal lines (A and LP) and, to a lesser extent, between animals of line LP with different longevities (LLP and HLP). Several genera were able to discriminate animals from the two lines and animals with different longevities, which shows that the gut microbiome could be used as a predictive factor for longevity, or as a selection criterion for these traits.
Collapse
Affiliation(s)
- Iliyass Biada
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Maria A Santacreu
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| |
Collapse
|
43
|
Muñoz Hoyos L, Anisha WP, Meng C, Kleigrewe K, Dawid C, Hückelhoven R, Stam R. Untargeted metabolomics reveals PTI-associated metabolites. PLANT, CELL & ENVIRONMENT 2024; 47:1224-1237. [PMID: 38164085 DOI: 10.1111/pce.14794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Plants employ a multilayered immune system to combat pathogens. In one layer, recognition of Pathogen- or Microbe-Associated Molecular Patterns or elicitors, triggers a cascade that leads to defence against the pathogen and Pattern Triggered Immunity. Secondary or specialised metabolites (SMs) are expected to play a role, because they are potentially anti-fungal compounds. Tomato (Solanum lycopersicum) plants inoculated with Alternaria solani s.l. show symptoms of infection after inoculation. Plants inoculated with Alternaria alternata remain symptomless. We hypothesised that pattern-triggered induction of resistance related metabolites in tomato contributes to the resistance against A. alternata. We compared the metabolomic profile (metabolome) of tomato after treatments with A. alternata, A. solani and the fungal elicitor chitin, and identified SMs involved in early defence of tomato plants. We revealed differential metabolome fingerprints. The composition of A. alternata and chitin induced metabolomes show larger overlap with each other than with the A. solani induced metabolome. We identify 65 metabolites possibly associated with PTI in tomato plants, including NAD and trigonelline. We confirm that trigonelline inhibits fungal growth in vitro at physiological concentrations. Thus, a true pattern-triggered, chemical defence is mounted against A. alternata, which contains anti-fungal compounds that could be interesting for crop protection strategies.
Collapse
Affiliation(s)
- Lina Muñoz Hoyos
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wan Petra Anisha
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chen Meng
- TUM School of Life Sciences, Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- TUM School of Life Sciences, Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Corinna Dawid
- TUM School of Life Sciences, Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Functional Phytometabolomics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Department of Phytopathology and Crop protection, Institute of Phytopathology, Kiel University, Kiel, Germany
| |
Collapse
|
44
|
Irnawati I, Windarsih A, Fadzillah NA, Rohman A, Nadia LOMH, Arlana S, Ruslin. The combination of Fourier-transform infrared spectroscopy with pattern recognition techniques for classification and discrimination of red snapper fish oils. J Adv Pharm Technol Res 2024; 15:99-103. [PMID: 38903555 PMCID: PMC11186539 DOI: 10.4103/japtr.japtr_401_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 06/22/2024] Open
Abstract
Fish oils are good sources for essential fatty acids such as omega-3 and omega-6 fatty acids needed to human growth. Indonesia is rich in fish species and among this, red snapper fish (Lutjanus sp.) can be extracted to get red snapper fish oils (RSFOs). The aim of this study was to classify and discriminate RSFO from different origins using Fourier-transform infrared (FTIR) spectra and pattern recognition techniques. All of the RSFO's FTIR spectra were very similar. The FTIR vibrations showed the presence of triglycerides as the main composition in fish oils. Principal component analysis (PCA) could separate the RSFO according to sample origin. Supervised pattern recognition of partial least square-discriminant analysis (PLS-DA) and sparse PLS-DA (sPLS-DA) successfully discriminated and classified different Lutjanus species of fish oils obtained from different origins. The vibration of functional groups at 1711, 1653, 1745, and 3012 per cm were considered for their important contributions in discriminating of Lutjanus species (variable importance in projection, variable importance in the projection score >1). Fish oils obtained from the same species were classified into the same class indicating similar chemical compositions. Among the three pattern recognition techniques used, sPLS-DA offers the best model for the discrimination and classification of Lutjanus fish oils. It can be concluded that FTIR spectroscopy in combination with the pattern recognition technique is the potential to be used for of fish oil authentication to verify the quality of the fish oils. It can be further developed as a rapid and effective method for fish oil authentication.
Collapse
Affiliation(s)
- Irnawati Irnawati
- Department of Analytical Chemistry and Medical Chemistry, Study Program of Pharmacy, Faculty of Pharmacy, Halu Oleo University, Kendari, Indonesia
| | - Anjar Windarsih
- Research Center for Food Technology and Processing, National Research and Innovation Agency, Yogyakarta, Indonesia
| | - Nurrulhidayah Ahmad Fadzillah
- International Institute for Halal Research and Training (INHART), International Islamic University Malaysia, Kuala Lumpur, Malaysia
| | - Abdul Rohman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Center of Excellence, Institute for Halal Industry and Systems, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - La Ode Muhammad Hazairin Nadia
- Department of Fisheries Product Technology, Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari, Indonesia
| | - Sofia Arlana
- Department of Analytical Chemistry and Medical Chemistry, Study Program of Pharmacy, Faculty of Pharmacy, Halu Oleo University, Kendari, Indonesia
| | - Ruslin
- Department of Analytical Chemistry and Medical Chemistry, Study Program of Pharmacy, Faculty of Pharmacy, Halu Oleo University, Kendari, Indonesia
| |
Collapse
|
45
|
Farah CS, Shearston K, Turner EC, Vacher M, Fox SA. Global gene expression profile of proliferative verrucous leukoplakia and its underlying biological disease mechanisms. Oral Oncol 2024; 151:106737. [PMID: 38408418 DOI: 10.1016/j.oraloncology.2024.106737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Proliferative verrucous leukoplakia (PVL) is a rare and enigmatic oral potentially malignant disorder which almost invariably results in oral squamous cell carcinoma (OSCC). The aims of this project were to use transcriptome profiling to characterise PVL gene expression patterns for biomarker identification and gain insight into the molecular aetiopathogenesis of PVL. METHODS Forty-three oral cavity mucosal biopsies from 32 patients with oral lesions clinically compatible with either PVL or non-PVL conventional oral leukoplakia (OLK) underwent transcriptome profiling by RNA sequencing. Data was analysed by hierarchical clustering, differential gene expression, functional enrichment and network analysis, sparse partial least squares discriminant analysis sPLS-DA, and immune cell phenotypic estimation. RESULTS We found 464 genes significantly differentially expressed at least 2-fold between PVL and non-PVL OLK (193 up and 271 down). HOX genes, including HOXA1 and HOXB7, keratin-associated proteins (KRTAPs) and olfactory receptor G proteins (OR) were significantly upregulated in PVL. Other upregulated genes in PVL included FOS, WNT16 and IFNA1. Pathway analysis showed that there was a significant downregulation of connective tissue signalling in PVL. Classifying multivariate models based upon 22 genes discriminated PVL from non-PVL OLK. Bioinformatic profiling showed that immune cell profiles in PVL and OLK were similar except that fibroblast markers were reduced in PVL. CONCLUSION These results demonstrate that PVL and conventional OLK are molecularly distinct with upregulation of many cancer-associated genes. They provide insight into the pathogenesis of PVL and show that biomarker based molecular diagnostics is feasible to discriminate and inform diagnosis and management.
Collapse
Affiliation(s)
- Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia; Central Queensland University, Rockhampton, Queensland, Australia; Genomics for Life, Milton, QLD, Australia.
| | - Kate Shearston
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia; UWA Dental School, University of Western Australia, Nedlands, WA, Australia.
| | - Emma C Turner
- UWA Dental School, University of Western Australia, Nedlands, WA, Australia; Special Needs Dental Unit, Royal Darwin Hospital, Tiwi, NT, Australia
| | - Michael Vacher
- The Australian eHealth Research Centre, CSIRO Health and Biosecurity, Kensington, WA, Australia.
| | - Simon A Fox
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia; UWA Dental School, University of Western Australia, Nedlands, WA, Australia.
| |
Collapse
|
46
|
Munk K, Ilina D, Ziemba L, Brader G, Molin EM. Holomics - a user-friendly R shiny application for multi-omics data integration and analysis. BMC Bioinformatics 2024; 25:93. [PMID: 38438871 PMCID: PMC10913680 DOI: 10.1186/s12859-024-05719-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
An organism's observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic and abiotic stressors, can significantly impact this complex biological system, influencing processes like growth, development and productivity. A comprehensive analysis of the entire biological system and its interactions is thus crucial to identify key components that support adaptation to stressors and to discover biomarkers applicable in breeding programs or disease diagnostics. Since the genomics era, several other 'omics' disciplines have emerged, and recent advances in high-throughput technologies have facilitated the generation of additional omics datasets. While traditionally analyzed individually, the last decade has seen an increase in multi-omics data integration and analysis strategies aimed at achieving a holistic understanding of interactions across different biological layers. Despite these advances, the analysis of multi-omics data is still challenging due to their scale, complexity, high dimensionality and multimodality. To address these challenges, a number of analytical tools and strategies have been developed, including clustering and differential equations, which require advanced knowledge in bioinformatics and statistics. Therefore, this study recognizes the need for user-friendly tools by introducing Holomics, an accessible and easy-to-use R shiny application with multi-omics functions tailored for scientists with limited bioinformatics knowledge. Holomics provides a well-defined workflow, starting with the upload and pre-filtering of single-omics data, which are then further refined by single-omics analysis focusing on key features. Subsequently, these reduced datasets are subjected to multi-omics analyses to unveil correlations between 2-n datasets. This paper concludes with a real-world case study where microbiomics, transcriptomics and metabolomics data from previous studies that elucidate factors associated with improved sugar beet storability are integrated using Holomics. The results are discussed in the context of the biological background, underscoring the importance of multi-omics insights. This example not only highlights the versatility of Holomics in handling different types of omics data, but also validates its consistency by reproducing findings from preceding single-omics studies.
Collapse
Affiliation(s)
- Katharina Munk
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Daria Ilina
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Lisa Ziemba
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Günter Brader
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Eva M Molin
- Center for Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria.
| |
Collapse
|
47
|
Wang X, Campuzano S, Guenne A, Mazéas L, Chapleur O. Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics. CHEMOSPHERE 2024; 351:141157. [PMID: 38218245 DOI: 10.1016/j.chemosphere.2024.141157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/22/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024]
Abstract
The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomics provides novel perspectives to study microbial processes and facilitates a more profound understanding at the metabolic level. The advanced statistical framework enables deciphering the complexity of large metabolomics data sets. More specifically, a series of lab-scale batch reactors were set up with different ammonia sources added. Samples of nine time points over the degradation were analyzed with liquid chromatography-mass spectrometry. A filtering procedure was applied to select the promising metabolomic peaks from 1262 peaks, followed by modeling their intensities across time. The metabolomic peaks with similar time profiles were clustered, evidencing the correlation of different biological processes. Differential analysis was performed to seek the differences in metabolite dynamics caused by different anions. Finally, tandem mass spectrometry and metabolite annotation provided further information on the molecular structure and possible metabolic pathways. For example, the consumption of 5-aminovaleric acid, a short-chain fatty acid obtained from l-lysine degradation, was slowed down by phosphates. Overall, by investigating the effect of anions on anaerobic digestion, our study demonstrated the effectiveness of metabolomics in providing detailed information in a set of samples from different experimental conditions. With the statistical framework, the approach enables capturing subtle differences in metabolite dynamics between samples while accounting for the differences caused by time variations.
Collapse
Affiliation(s)
- Xiaoqing Wang
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France
| | - Stephany Campuzano
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France
| | - Angéline Guenne
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France
| | - Laurent Mazéas
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France
| | - Olivier Chapleur
- Université Paris-Saclay, INRAE, PRocédés biOtechnologiques au Service de l'Environnement, 92761, Antony, France.
| |
Collapse
|
48
|
Li H, Wang X, Vinsky M, Manafiazar G, Fitzsimmons C, Li L, Li C. Analyses of plasma metabolites using a high performance four-channel CIL LC-MS method and identification of metabolites associated with enteric methane emissions in beef cattle. PLoS One 2024; 19:e0299268. [PMID: 38427676 PMCID: PMC10906882 DOI: 10.1371/journal.pone.0299268] [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: 08/31/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
Reducing enteric methane (one greenhouse gas) emissions from beef cattle not only can be beneficial in reducing global warming, but also improve efficiency of nutrient utilization in the production system. However, direct measurement of enteric methane emissions on individual cattle is difficult and expensive. The objective of this study was to detect plasma metabolites that are associated with enteric methane emissions in beef cattle. Average enteric methane emissions (CH4) per day (AVG_DAILYCH4) for each individual cattle were measured using the GreenFeed emission monitoring (GEM) unit system, and beef cattle with divergent AVG_DAILYCH4 from Angus (n = 10 for the low CH4 group and 9 for the high CH4 group), Charolais (n = 10 for low and 10 for = high), and Kinsella Composite (n = 10 for low and 10 for high) populations were used for plasma metabolite quantification and metabolite-CH4 association analyses. Blood samples of these cattle were collected near the end of the GEM system tests and a high performance four-channel chemical isotope labeling (CIL) liquid chromatography (LC) mass spectrometer (MS) method was applied to identify and quantify concentrations of metabolites. The four-channel CIL LC-MS method detected 4235 metabolites, of which 1105 were found to be significantly associated with AVG_DAILYCH4 by a t-test, while 1305 were significantly associated with AVG_DAILYCH4 by a regression analysis at p<0.05. Both the results of the t-test and regression analysis revealed that metabolites that were associated with enteric methane emissions in beef cattle were largely breed-specific whereas 4.29% to 6.39% CH4 associated metabolites were common across the three breed populations and 11.07% to 19.08% were common between two breed populations. Pathway analyses of the CH4 associated metabolites identified top enriched molecular processes for each breed population, including arginine and proline metabolism, arginine biosynthesis, butanoate metabolism, and glutathione metabolism for Angus; beta-alanine metabolism, pyruvate metabolism, glycolysis / gluconeogenesis, and citrate cycle (TCA cycle) for Charolais; phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arginine biosynthesis, and arginine and proline metabolism for Kinsella Composite. The detected CH4 associated metabolites and enriched molecular processes will help understand biological mechanisms of enteric methane emissions in beef cattle. The detected CH4 associated plasma metabolites will also provide valuable resources to further characterize the metabolites and verify their utility as biomarkers for selection of cattle with reduced methane emissions.
Collapse
Affiliation(s)
- Hongwei Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaohang Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Ghader Manafiazar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Animal Science and Aquaculture, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| |
Collapse
|
49
|
Neiva de Jesus J, Ribeiro Mesquita PR, Barbosa da Silva K, de Medeiros Rodrigues F, Lopes de Carvalho CA, Gomes da Costa J, Lima Aguiar CM. Volatile Organic Compounds from Offspring of Stingless Bee Sacrificed in Hygienic Behavior Test. Chem Biodivers 2024; 21:e202301641. [PMID: 38358043 DOI: 10.1002/cbdv.202301641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
This study shows the profile of volatile organic compounds (VOCs) from pupae and larvae of Melipona quadrifasciata anthidioides Lepeletier subjected to three death induction techniques for hygienic behavior (HB) studies: freezing in liquid nitrogen (LN2), freezing in a freezer (FRZ) and piercing of offspring with an entomological pin (PIN). The VOCs from larvae and pupae were obtained through headspace solid-phase microextraction and characterized using gas chromatography coupled to mass spectrometry. In addition, an HB test was performed on the colonies. The main classes of VOCs were hydrocarbons, terpenes and alcohols. Multivariate analysis was applied and showed that there was a separation in the compound profiles between the different treatments. The HB test in the colonies showed that 24 hours after the application of the techniques, the bees removed more dead larvae in LN2 treatment (83.5 %), while after 48 hours more larvae were removed in the LN2 and FRZ treatments (92.3 %). When compared to pupae removal, larvae removal was significantly faster in LN2.
Collapse
Affiliation(s)
- Jossimara Neiva de Jesus
- Agricultural Technological Center of the State of Bahia, Ondina, CEP, 40170-110, n° 967, Salvador, Bahia, Brazil
- Universidade Federal do Recôncavo da Bahia, CEP, 44380-000, n° 710, Cruz das Almas, Bahia, Brasil
| | | | - Kelly Barbosa da Silva
- Agricultural Technological Center of the State of Bahia, Ondina, CEP, 40170-110, n° 967, Salvador, Bahia, Brazil
| | | | | | - João Gomes da Costa
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Alimentos e Territórios, CEP, 57020-050, n° 348, Maceió, Alagoas, Brasil
| | | |
Collapse
|
50
|
Li W, Larsen A, Fregulia P. Investigating the impact of feed-induced, subacute ruminal acidosis on rumen epimural transcriptome and metatranscriptome in young calves at 8- and 17-week of age. Front Vet Sci 2024; 11:1328539. [PMID: 38455258 PMCID: PMC10918858 DOI: 10.3389/fvets.2024.1328539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
Introduction With the goal to maximize intake of high-fermentable diet needed to meet energy needs during weaning period, calves are at risk for ruminal acidosis. Using the calves from previously established model of feed-induced, ruminal acidosis in young calves, we aimed to investigate the changes in rumen epimural transcriptome and its microbial metatranscriptome at weaning (8-week) and post-weaning (17-week) in canulated (first occurred at 3 weeks of age) Holstein bull calves with feed-induced subacute ruminal acidosis. Methods Eight bull calves were randomly assigned to acidosis-inducing diet (Treated, n = 4; pelleted, 42.7% starch, 15.1% neutral detergent fiber [NDF], and 57.8% nonfiber carbohydrates), while texturized starter was fed as a control (Control, n = 4; 35.3% starch, 25.3% NDF, and 48.1% nonfiber carbohydrates) starting at 1 week through 17 weeks. Calves fed acidosis-inducing diet showed significantly less (p < 0.01) body weight over the course of the experiment, in addition to lower ruminal pH (p < 0.01) compared to the control group. Rumen epithelial (RE) tissues were collected at both 8 weeks (via biopsy) and 17 weeks (via euthanasia) and followed for whole transcriptome RNA sequencing analysis. Differentially expressed genes (DEGs) analysis was done using cufflinks2 (fold-change ≥2 and p < 0.05) between treated and control groups at 8-week of age, and between 8- and 17-week for the treated group. Results At 8-week of age, DEGs between treatment groups showed an enrichment of genes related to the response to lipopolysaccharide (LPS) (p < 0.005). The impact of prolonged, feed-induced acidosis was reflected by the decreased expression (p < 0.005) in genes involved in cell proliferation related pathways in the RE at 17-week of age in the treated group. Unique sets of discriminant microbial taxa were identified between 8-and 17-week calves in the treated group and the treatment groups at 8-week, indicating that active microbial community changes in the RE are an integral part of the ruminal acidosis development and progression.
Collapse
Affiliation(s)
- Wenli Li
- US Dairy Forage Research Center, USDA-Agricultural Research Service, Madison, WI, United States
| | - Anna Larsen
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Priscila Fregulia
- US Dairy Forage Research Center, USDA-Agricultural Research Service, Madison, WI, United States
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| |
Collapse
|