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Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C. A novel cross-species differential tumor classification method based on exosome-derived microRNA biomarkers established by human-dog lymphoid and mammary tumor cell lines' transcription profiles. Vet World 2022; 15:1163-1170. [PMID: 35765483 PMCID: PMC9210832 DOI: 10.14202/vetworld.2022.1163-1170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/17/2022] [Indexed: 11/22/2022] Open
Abstract
Background and Aim: Exosome-derived microRNA (miRNA) has been widely studied as a non-invasive candidate biomarker for tumor diagnosis in humans and dogs. Its application, however, was primarily focused on intraspecies usage for individual tumor type diagnosis. This study aimed to gain insight into its application as a cross-species differential tumor diagnostic tool; we demonstrated the process of identifying and using exosome-derived miRNA as biomarkers for the classification of lymphoid and mammary tumor cell lines in humans and dogs. Materials and Methods: Exosome-derived miRNA sequencing data from B-cell lymphoid tumor cell lines (n=13), mammary tumor cell lines (n=8), and normal mammary epithelium cultures (n=4) were pre-processed in humans and dogs. F-test and rank product (RP) analyses were used to select candidate miRNA orthologs for tumor cell line classification. The classification was carried out using an optimized support vector machine (SVM) with various kernel classifiers, including linear SVM, polynomial SVM, and radial basis function SVM. The receiver operating characteristic and precision-recall curves were used to assess the performance of all models. Results: MIR10B, MIR21, and MIR30E were chosen as the candidate orthologs from a total of 236 human-dog miRNA orthologs (p≤0.01, F-test score ≥10, and RP score ≤10). Their use of polynomial SVM provided the best performance in classifying samples from various tumor cell lines and normal epithelial culture. Conclusion: The study successfully demonstrated a method for identifying and utilizing candidate human-dog exosome-derived miRNA orthologs for differential tumor cell line classification. Such findings shed light on a novel non-invasive tumor diagnostic tool that could be used in both human and veterinary medicine in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Denis Puthier
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
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Le Guillou S, Leduc A, Laubier J, Barbey S, Rossignol MN, Lefebvre R, Marthey S, Laloë D, Le Provost F. Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities. Sci Rep 2019; 9:20345. [PMID: 31889100 PMCID: PMC6937266 DOI: 10.1038/s41598-019-56690-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
The concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.
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Affiliation(s)
- S Le Guillou
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - A Leduc
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Laubier
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - S Barbey
- INRA, UE0326, Domaine expérimental du Pin-au-Haras, Exmes, France
| | - M-N Rossignol
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - R Lefebvre
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - S Marthey
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - D Laloë
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - F Le Provost
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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Chokeshaiusaha K, Puthier D, Nguyen C, Sudjaidee P, Sananmuang T. Factor Analysis for Bicluster Acquisition (FABIA) revealed vincristine-sensitive transcript pattern of canine transmissible venereal tumors. Heliyon 2019; 5:e01558. [PMID: 31193204 PMCID: PMC6520609 DOI: 10.1016/j.heliyon.2019.e01558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/25/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
Chemotherapeutic treatment for Canine transmissible venereal tumor (CTVT) commonly relies on vincristine administration. Since the treatment outcomes can vary among CTVT cases, gaining insight into the tumor cell mechanisms influencing vincristine's potency should render veterinarians novel knowledge to enhance its therapeutic effect. This study aimed to attain such knowledge from a meta-analysis of CTVT mRNA sequencing (mRNA-seq) transcriptome data using Factor Analysis for Bicluster Acquisition (FABIA) biclustering. FABIA biclustering identified 459 genes consistently expressed among mRNA-seq transcription profiling of CTVT samples regressed by vincristine. These genes were also differentially expressed from those of progressive CTVT (FDR ≤ 0.001). Enrichment analysis illustrated the affiliation of these genes with "Antigen presentation" and "Lysosome" GO terms (FDR ≤ 0.05). Several genes in "Lysosome" term involved 5 cell mechanisms-antigen presentation, autophagy, cell-adhesion, lysosomal membrane permeabilization (LMP), and PI3K/mTOR signaling. This study integrated FABIA biclustering in CTVT transcriptome analysis to gain insight into cell mechanisms responsible for vincristine-sensitive characteristics of the tumor, in order to identify new molecular targets augmenting therapeutic effect of vincristine. Interestingly, the analysis indicated LMP targeting by lysosome destabilizing agent-siramesine as the promising vincristine's enhancer for future study. As far as we know, this is the first canine tumor transcriptomic meta-analysis applying FABIA biclustering for the betterment of future CTVT therapy. This study hereby provided an interesting manifestation to acquire such knowledge in other canine neoplasia.
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Affiliation(s)
- K. Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - D. Puthier
- Aix Marseille Univ, TAGC INSERM UMR 1090, Marseille, France
| | - C. Nguyen
- Aix Marseille Univ, TAGC INSERM UMR 1090, Marseille, France
| | - P. Sudjaidee
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - T. Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
- Corresponding author.
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Benmoussa A, Provost P. Milk MicroRNAs in Health and Disease. Compr Rev Food Sci Food Saf 2019; 18:703-722. [PMID: 33336926 DOI: 10.1111/1541-4337.12424] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 02/06/2023]
Abstract
MicroRNAs are small noncoding RNAs responsible for regulating 40% to 60% of gene expression at the posttranscriptional level. The discovery of circulating microRNAs in several biological fluids opened the path for their study as biomarkers and long-range cell-to-cell communication mediators. Their transfer between individuals in the case of blood transfusion, for example, and their high enrichment in milk have sparked the interest for microRNA transfer through diet, especially from mothers to infants during breastfeeding. The extension of such paradigm led to the study of milk microRNAs in the case of cow or goat milk consumption in adults. Here we provide a comprehensive critical review of the key findings surrounding milk microRNAs in human, cow, and goat milk among other species. We discuss the data on their biological properties, their use as disease biomarkers, their transfer between individuals or species, and their putative or verified functions in health and disease of infants and adult consumers. This work is based on all the literature available and integrates all the results, theories, debates, and validation studies available so far on milk microRNAs and related areas of investigations. We critically discuss the limitations and outline future aspects and avenues to explore in this rapidly growing field of research that could impact public health through infant milk formulations or new therapies. We hope that this comprehensive review of the literature will provide insight for all teams investigating milk RNAs' biological activities and help ensure the quality of future reports.
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Affiliation(s)
- Abderrahim Benmoussa
- CHUQ Research Center/CHUL, 2705 Blvd Laurier, Quebec, QC, G1V 4G2, Canada.,Dept. of Microbiology-Infectious Disease and Immunity and Faculty of Medicine, Univ. Laval, Quebec, QC, G1V 0A6, Canada
| | - Patrick Provost
- CHUQ Research Center/CHUL, 2705 Blvd Laurier, Quebec, QC, G1V 4G2, Canada.,Dept. of Microbiology-Infectious Disease and Immunity and Faculty of Medicine, Univ. Laval, Quebec, QC, G1V 0A6, Canada
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