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Confuorti C, Jaramillo M, Plante I. Hormonal regulation of miRNA during mammary gland development. Biol Open 2024; 13:bio060308. [PMID: 38712984 PMCID: PMC11190577 DOI: 10.1242/bio.060308] [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: 01/11/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
The mammary gland is a unique organ as most of its development occurs after birth through stages of proliferation, differentiation and apoptosis that are tightly regulated by circulating hormones and growth factors. Throughout development, hormonal cues induce the regulation of different pathways, ultimately leading to differential transcription and expression of genes involved in this process, but also in the activation or inhibition of post-transcriptional mechanisms of regulation. However, the role of microRNAs (miRNAs) in the different phases of mammary gland remodeling is still poorly understood. The objectives of this study were to analyze the expression of miRNA in key stages of mammary gland development in mice and to determine whether it could be associated with hormonal variation between stages. To do so, miRNAs were isolated from mouse mammary glands at stages of adulthood, pregnancy, lactation and involution, and sequenced. Results showed that 490, 473, 419, and 460 miRNAs are detected in adult, pregnant, lactating and involuting mice, respectively, most of them being common to all four groups, and 58 unique to one stage. Most genes could be divided into six clusters of expression, including two encompassing the highest number of miRNA (clusters 1 and 3) and showing opposite profiles of expression, reaching a peak at adulthood and valley at lactation, or showing the lowest expression at adulthood and peaking at lactation. GO and KEGG analyses suggest that the miRNAs differentially expressed between stages influence the expression of targets associated with mammary gland homeostasis and hormone regulation. To further understand the links between miRNA expression and hormones involved in mammary gland development, miRNAs were then sequenced in breast cells exposed to estradiol, progesterone, prolactin and oxytocin. Four, 38, 24 and 66 miRNAs were associated with progesterone, estradiol, prolactin, and oxytocin exposure, respectively. Finally, when looking at miRNAs modulated by the hormones, differentially expressed during mammary gland development, and having a pattern of expression that could be correlated with the relative levels of hormones known to be found in vivo, 16 miRNAs were identified as likely regulated by circulating hormones. Overall, our study brings a better understanding of the regulation of miRNAs throughout mammary gland development and suggests that there is a relationship between their expression and the main hormones involved in mammary gland development. Future studies will examine this role more in detail.
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Affiliation(s)
- Cameron Confuorti
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Maritza Jaramillo
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Isabelle Plante
- INRS, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
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2
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Pozovnikova MV, Leibova VB, Tulinova OV, Romanova EA, Dysin AP, Dementieva NV, Azovtseva AI, Sedykh SE. Comparison of miR-106b, miR-191, and miR-30d expression dynamics in milk with regard to its composition in Holstein and Ayrshire cows. Anim Biosci 2024; 37:965-981. [PMID: 38419530 PMCID: PMC11065953 DOI: 10.5713/ab.23.0427] [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: 10/18/2023] [Revised: 11/25/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE Milk composition varies considerably and depends on paratypical, genetic, and epigenetic factors. MiRNAs belong to the class of small non-coding RNAs; they are one of the key tools of epigenetic control because of their ability to regulate gene expression at the post-transcriptional level. We compared the relative expression levels of miR-106b, miR-191, and miR-30d in milk to demonstrate the relationship between the content of these miRNAs with protein and fat components of milk in Holstein and Ayrshire cattle. METHODS Milk fat, protein, and casein contents were determined in the obtained samples, as well as the content of the main fatty acids (g/100 g milk), including: saturated acids, such as myristic (C14:0), palmitic (C16:0), and stearic (C18:0) acids; monounsaturated acids, including oleic (C18:1) acid; as well as long-, medium- and short-chain, polyunsaturated, and trans fatty acids. Real-time stem-loop one-tube reverse transcription polymerase chain reaction with TaqMan probes was used to measure the miRNA expression levels. RESULTS The miRNA expression levels in milk samples were found to be decreased in the first two months in Holstein breed, and in the first four months in Ayrshire breed. Correlation analysis did not reveal any dependence between changes in the expression level of miRNA and milk fat content, but showed a multidirectional relationship with individual milk fatty acids. Positive associations between the expression levels of miR-106b and miR-30d and protein and casein content were found in the Ayrshire breed. Receiver operating characteristic curve analysis showed that miR-106b and miR-30d expression levels can cause changes in fatty acid and protein composition of milk in Ayrshire cows, whereas miR-106b expression level determines the fatty acid composition in Holsteins. CONCLUSION The data obtained in this study showed that miR-106b, miR-191, and miR-30d expression levels in milk samples have peculiarities associated with breed affiliation and the lactation period.
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Affiliation(s)
- Marina V. Pozovnikova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Viktoria B. Leibova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Olga V. Tulinova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Elena A. Romanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090,
Russia
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Mondal J, Pillarisetti S, Junnuthula V, Surwase SS, Hwang SR, Park IK, Lee YK. Extracellular vesicles and exosome-like nanovesicles as pioneering oral drug delivery systems. Front Bioeng Biotechnol 2024; 11:1307878. [PMID: 38260737 PMCID: PMC10800420 DOI: 10.3389/fbioe.2023.1307878] [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: 10/05/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
As extracellular vesicle (EV)-based nanotechnology has developed rapidly, it has made unprecedented opportunities for nanomedicine possible. EVs and exosome-like nanovesicles (ELNVs) are natural nanocarriers with unique structural, compositional, and morphological characteristics that provide excellent physical, chemical, and biochemical properties. In this literature, we examine the characteristics of EVs, including how they are administered orally and their therapeutic activity. According to the current examples of EVs and ELNVs for oral delivery, milk and plant EVs can exert therapeutic effects through their protein, nucleic acid, and lipid components. Furthermore, several methods for loading drugs into exosomes and targeting exosomes have been employed to investigate their therapeutic capability. Moreover, we discuss EVs as potential drug carriers and the potential role of ELNVs for disease prevention and treatment or as potential drug carriers in the future. In conclusion, the issues associated with the development of EVs and ELNVs from sources such as milk and plants, as well as concerns with standardized applications of these EVs, are discussed.
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Affiliation(s)
- Jagannath Mondal
- Department of Green Bioengineering, Korea National University of Transportation, Chungju, Republic of Korea
| | - Shameer Pillarisetti
- Department of Biomedical Sciences and Biomedical Science Graduate Program (BMSGP), Chonnam National University Medical School, Gwangju, Republic of Korea
| | | | - Sachin S. Surwase
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seung Rim Hwang
- College of Pharmacy, Chosun University, Gwangju, Republic of Korea
| | - In-Kyu Park
- Department of Biomedical Sciences and Biomedical Science Graduate Program (BMSGP), Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yong-kyu Lee
- Department of Green Bioengineering, Korea National University of Transportation, Chungju, Republic of Korea
- Department of Chemical and Biological Engineering, Korea National University of Transportation, Chungju, Republic of Korea
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Leroux C, Cuccato M, Pawłowski K, Cannizzo FT, Sacchi P, Pires JAA, Faulconnier Y. Milk fat miRNome changes in response to LPS challenge in Holstein cows. Vet Res 2023; 54:111. [PMID: 37993922 PMCID: PMC10666322 DOI: 10.1186/s13567-023-01231-4] [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: 11/10/2022] [Accepted: 09/02/2023] [Indexed: 11/24/2023] Open
Abstract
Mastitis is an inflammatory disease in dairy cows, causing economic losses and reducing animal welfare. In order to contribute for the discovery of early and noninvasive indicators, our objective was to determine the effects of a lipopolysaccharide (LPS) challenge on the microRNA profile (miRNome) of milk fat, using microarray analyses in cows. Cows were fed a lactation diet at ad libitum intake (n = 6). At 27 ± 3 days in milk, cows were injected with 50 µg of LPS Escherichia coli in one healthy rear mammary quarter. Milk samples were collected just before LPS challenge (LPS-) and 6.5 h after LPS challenge (LPS +) from the same cows. Microarray analysis was performed using customized 8 × 60 K ruminant miRNA microarrays to compare LPS- to LPS + miRNome. In silico functional analyses were performed using OmicsNet and Mienturnet software. MiRNome comparison between LPS- and LPS + identified 37 differentially abundant miRNAs (q-value ≤ 0.05). The predicted target genes of the 37 differentially abundant miRNAs are mostly involved in cell life including apoptosis, cell cycle, proliferation and differentiation and in gene expression processes. MiRNome analyses suggest that miRNAs profile is related to the inflammation response of the mammary gland. In conclusion, we demonstrated that milk fat might be an easy and rapid source of miRNAs that are potential indicators of early mastitis in cows.
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Affiliation(s)
- Christine Leroux
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122, Saint-Genès-Champanelle, France.
| | - Matteo Cuccato
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122, Saint-Genès-Champanelle, France
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Torino, Italy
| | - Karol Pawłowski
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122, Saint-Genès-Champanelle, France
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw Univeristy of Life Sciences, Nowoursynowska 159c, 02-776, Warsaw, Poland
| | - Francesca Tiziana Cannizzo
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Torino, Italy
| | - Paola Sacchi
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Torino, Italy
| | - José A A Pires
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122, Saint-Genès-Champanelle, France
| | - Yannick Faulconnier
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122, Saint-Genès-Champanelle, France
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Leduc A, Le Guillou S, Laloë D, Herve L, Laubier J, Poton P, Faulconnier Y, Pires J, Gele M, Martin P, Leroux C, Boutinaud M, Le Provost F. MiRNome variations in milk fractions during feed restrictions of different intensities in dairy cows. BMC Genomics 2023; 24:680. [PMID: 37957547 PMCID: PMC10641998 DOI: 10.1186/s12864-023-09769-5] [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: 06/14/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND In dairy cows, diet is one factor that can affect their milk production and composition. However, the effect of feed restriction on milk miRNome has not yet been described. Indeed, milk is the body fluid with the highest RNA concentration, which includes numerous microRNA. Its presence in the four different milk fractions, whole milk, fat globules, mammary epithelial cells and extracellular vesicles, is still poorly documented. This study aimed to describe the effects of different feed restrictions on the miRNome composition of different milk fractions. RESULTS Two feed restrictions were applied to lactating dairy cows, one of high intensity and one of moderate intensity. 2,896 mature microRNA were identified in the different milk fractions studied, including 1,493 that were already known in the bovine species. Among the 1,096 microRNA that were sufficiently abundant to be informative, the abundance of 1,027 of them varied between fractions: 36 of those were exclusive to one milk fraction. Feed restriction affected the abundance of 155 microRNA, with whole milk and milk extracellular vesicles being the most affected, whereas milk fat globules and exfoliated mammary epithelial cells were little or not affected at all. The high intensity feed restriction led to more microRNA variations in milk than moderate restriction. The target prediction of known microRNA that varied under feed restriction suggested the modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle, and stress responses. CONCLUSIONS This study highlighted that the miRNome of each milk fraction is specific, with mostly the same microRNA composition but with variations in abundance between fractions. These specific miRNomes were affected differently by feed restrictions, the intensity of which appeared to be a major factor modulating milk miRNomes. These findings offer opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows, which is affected by feed restrictions.
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Affiliation(s)
- A Leduc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
- Institut de L'Elevage, 75012, Paris, France
| | - S Le Guillou
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - D Laloë
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - L Herve
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - J Laubier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - P Poton
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Y Faulconnier
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - J Pires
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - M Gele
- Institut de L'Elevage, 75012, Paris, France
| | - P Martin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - C Leroux
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - M Boutinaud
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - F Le Provost
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France.
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Ma T, Meng Z, Ghaffari M, Lv J, Xin H, Zhao Q. Characterization and profiling of the microRNA in small extracellular vesicles isolated from goat milk samples collected during the first week postpartum. JDS COMMUNICATIONS 2023; 4:507-512. [PMID: 38045901 PMCID: PMC10692291 DOI: 10.3168/jdsc.2022-0369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/06/2023] [Indexed: 12/05/2023]
Abstract
Colostrum contains nutrients, immunoglobulins, and various bioactive compounds such as microRNA (miRNA). Less is known about the temporal changes in miRNA profiles in ruminant milk samples during the first week postpartum. In this study, we characterized and compared the profiles of miRNA in the small extracellular vesicles (sEV) isolated from colostrum (CM, collected immediately after parturition, n = 8) and transition milk (TM, collected 7 d postpartum, n = 8) from eight 1-yr-old Guanzhong dairy goats with a milk yield of approximately 500 kg/year. A total of 192 unique sEV-associated miRNA (transcripts per million >1 at least 4 samples in either CM or TM) were identified in all samples. There were 29 miRNA uniquely identified in the TM samples while no miRNA was uniquely identified in the CM samples. The abundance of the top 10 miRNA accounted for 82.4% ± 4.0% (± SD) of the total abundance, with let-7 families (e.g., let-7a/b/c-5p) being predominant in all samples. The top 10 miRNA were predicted to target 1,008 unique genes that may regulate pathways such as focal adhesion, TGF-β signaling, and axon guidance. The expression patterns of EV miRNA were similar between the 2 sample groups, although the abundance of let-7c-5p and miR-30a-3p was higher, whereas that of let-7i-5p and miR-103-3p was lower in CM than in TM. In conclusion, the core miRNAome identified in the samples from CM and TM may play an important role in cell proliferation, bone homeostasis, and neuronal network formation in newborn goat kids. The lack of differential miRNA expression between the CM and TM samples may be due to a relatively short sampling interval in which diet composition, intake and health status of ewes, and environment were relatively stable.
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Affiliation(s)
- T. Ma
- Institute of Feed Research, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Z. Meng
- Inner Mongolia Academy of Agriculture and Animal Husbandry Sciences, Hohhot, 010030, China
| | - M.H. Ghaffari
- Institute of Animal Science, University of Bonn, Bonn, 53115, Germany
| | - J. Lv
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - H. Xin
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Q. Zhao
- Inner Mongolia Academy of Agriculture and Animal Husbandry Sciences, Hohhot, 010030, China
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Abou el qassim L, Martínez B, Rodríguez A, Dávalos A, López de las Hazas MC, Menéndez Miranda M, Royo LJ. Effects of Cow's Milk Processing on MicroRNA Levels. Foods 2023; 12:2950. [PMID: 37569218 PMCID: PMC10419269 DOI: 10.3390/foods12152950] [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: 07/05/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression and might resist adverse physicochemical conditions, which makes them potential biomarkers. They are being investigated as biomarkers of dairy production systems, based on the variations in their levels in raw milk depending on animal diet and management. Whether miRNA levels can serve as biomarkers for dairy products remains unclear, since technological or culinary treatments, such as fermentation, may alter their levels. Here, 10 cow dairy farms were sampled in Asturias (north-west Spain) and milk samples were subjected to microwave heating or used to produce yogurt or cheese. Total RNA was isolated from raw milk and three derived products, and levels of seven miRNAs, selected based on previous studies as possible milk production system biomarkers, were assessed by RT-qPCR. The treatments decreased levels of all miRNAs to some extent. These results also imply that cheesemaking increases the concentration of miRNAs in this product; raw milk and cheese supposedly may provide similar concentrations of miRNAs, higher than those of yogurt and microwaved milk. They also indicate that the content of certain miRNAs in raw milk cannot necessarily be extrapolated to other dairy products.
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Affiliation(s)
- Loubna Abou el qassim
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain;
| | - Beatriz Martínez
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (B.M.); (A.R.)
| | - Ana Rodríguez
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Spain; (B.M.); (A.R.)
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, 28049 Madrid, Spain; (A.D.); (M.-C.L.d.l.H.)
| | - María-Carmen López de las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM+CSIC, 28049 Madrid, Spain; (A.D.); (M.-C.L.d.l.H.)
| | - Mario Menéndez Miranda
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain;
| | - Luis J. Royo
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Spain;
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain
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Sánchez-Visedo A, Gallego-Martínez B, Royo LJ, Soldado A, Valledor M, Campo JC, Ferrero FJ, Costa-Fernández JM, Fernández-Argüelles MT. MNAzymes and gold nanoparticles as isothermal signal amplification strategy for visual detection of miRNA. Mikrochim Acta 2023; 190:292. [PMID: 37458796 PMCID: PMC10352400 DOI: 10.1007/s00604-023-05868-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/08/2023] [Indexed: 07/20/2023]
Abstract
MicroRNAs (miRNAs) represent a class of small noncoding RNAs that are considered a novel emerging class of disease biomarkers in a variety of afflictions. Sensitive detection of miRNA is typically achieved using hybridization-based methods coupled with genetic amplification techniques. Although their sensitivity has improved, amplification techniques often present erroneous results due to their complexity. In addition, the use of these techniques is usually linked to the application of protein enzymes, the activity of which is dependent on the temperature and pH of the medium. To address these drawbacks, an alternative genetic enzyme for the highly sensitive detection of miRNAs is proposed in this work. Multicomponent nucleic acid enzymes (MNAzymes), coupled with the use of DNA-functionalized gold nanoparticles (AuNPs), were used in this study to develop an isothermal signal amplification strategy for visual genetic detection. miR146a, a biomarker of bovine mastitis present in milk, was selected as a model analyte. The developed methodology is easily carried out in 80 min at 50 °C, generating a low visual limit of detection of 250 pM based on the observation of a color change. The methodology was successfully applied to the detection of miR146a in raw cow milk samples.
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Affiliation(s)
- Adrián Sánchez-Visedo
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain
| | - Borja Gallego-Martínez
- Health Research Institute of Asturias, ISPA, Avenida Hospital Universitario, s/n 33011, Oviedo, Asturias, Spain
| | - Luis José Royo
- Department of Functional Biology, Genetics, University of Oviedo, Avenida Julián Claveria, s/n 33006, Oviedo, Asturias, Spain
| | - Ana Soldado
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain
| | - Marta Valledor
- Department of Electrical, Electronic, Communications and Systems Engineering, University of Oviedo, Campus of Gijón, 33204, Gijón, Spain
| | - Juan Carlos Campo
- Department of Electrical, Electronic, Communications and Systems Engineering, University of Oviedo, Campus of Gijón, 33204, Gijón, Spain
| | - Francisco Javier Ferrero
- Department of Electrical, Electronic, Communications and Systems Engineering, University of Oviedo, Campus of Gijón, 33204, Gijón, Spain.
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain
| | - María Teresa Fernández-Argüelles
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain.
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Ojo OE, Hajek L, Johanns S, Pacífico C, Sener-Aydemir A, Ricci S, Rivera-Chacon R, Castillo-Lopez E, Reisinger N, Zebeli Q, Kreuzer-Redmer S. Evaluation of circulating microRNA profiles in blood as potential candidate biomarkers in a subacute ruminal acidosis cow model - a pilot study. BMC Genomics 2023; 24:333. [PMID: 37328742 DOI: 10.1186/s12864-023-09433-y] [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: 08/08/2022] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Subacute ruminal acidosis (SARA) is a metabolic disorder often observed in high-yielding dairy cows, that are fed diets high in concentrates. We hypothesized that circulating miRNAs in blood of cows could serve as potential candidate biomarkers to detect animals with metabolic dysbalances such as SARA. MicroRNAs (miRNAs) are a class of small non-coding RNAs, serving as regulators of a plethora of molecular processes. To test our hypothesis, we performed a pilot study with non-lactating Holstein-Friesian cows fed a forage diet (FD; 0% concentrate, n = 4) or a high-grain diet (HG; 65% concentrate, n = 4) to induce SARA. Comprehensive profiling of miRNA expression in plasma and leucocytes were performed by next generation sequencing (NGS). The success of our model to induce SARA was evaluated based on ruminal pH and was evidenced by increased time spent with a pH threshold of 5.8 for an average period of 320 min/d. RESULTS A total of 520 and 730 miRNAs were found in plasma and leucocytes, respectively. From these, 498 miRNAs were shared by both plasma and leucocytes, with 22 miRNAs expressed exclusively in plasma and 232 miRNAs expressed exclusively in leucocytes. Differential expression analysis revealed 10 miRNAs that were up-regulated and 2 that were down-regulated in plasma of cows when fed the HG diet. A total of 63 circulating miRNAs were detected exclusively in the plasma of cows with SARA, indicating that these animals exhibited a higher number and diversity of circulating miRNAs. Considering the total read counts of miRNAs expressed when fed the HG diet, differentially expressed miRNAs ( log2 fold change) and known function, we have identified bta-miR-11982, bta-miR-1388-5p, bta-miR-12034, bta-miR-2285u, and bta-miR-30b-3p as potential candidates for SARA-biomarker in cows by NGS. These were further subjected to validation using small RNA RT-qPCR, confirming the promising role of bta-miR-30b-3p and bta-miR-2285. CONCLUSION Our data demonstrate that dietary change impacts the release and expression of miRNAs in systemic circulation, which may modulate post-transcriptional gene expression in cows undergoing SARA. Particularly, bta-miR-30b-3p and bta-miR-2285 might serve as promising candidate biomarker predictive for SARA and should be further validated in larger cohorts.
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Affiliation(s)
- O E Ojo
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L Hajek
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Johanns
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - C Pacífico
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Biome Diagnostics GmbH, Vienna, Austria
| | - A Sener-Aydemir
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Ricci
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - R Rivera-Chacon
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - E Castillo-Lopez
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - N Reisinger
- DSM, BIOMIN Research Center, Tulln an Der Donau, Austria
| | - Q Zebeli
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
| | - S Kreuzer-Redmer
- Christian Doppler Laboratory for Innovative Gut Health Concepts of Livestock, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
- Nutrigenomics Unit, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria.
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10
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Ojo OE, Kreuzer-Redmer S. MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology. Vet Sci 2023; 10:vetsci10010057. [PMID: 36669058 PMCID: PMC9867202 DOI: 10.3390/vetsci10010057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The knowledge of how diet choices, dietary supplements, and feed intake influence molecular mechanisms in ruminant nutrition and physiology to maintain ruminant health, is essential to attain. In the present review, we focus on the role of microRNAs in ruminant health and disease; additionally, we discuss the potential of circulating microRNAs as biomarkers of disease in ruminants and the state of technology for their detection, also considering the major difficulties in the transition of biomarker development from bench to clinical practice. MicroRNAs are an inexhaustible class of endogenous non-protein coding small RNAs of 18 to 25 nucleotides that target either the 3' untranslated (UTR) or coding region of genes, ensuring a tight post-transcriptionally controlled regulation of gene expression. The development of new "omics" technologies facilitated a fresh perspective on the nutrition-to-gene relationship, incorporating more extensive data from molecular genetics, animal nutrition, and veterinary sciences. MicroRNAs might serve as important regulators of metabolic processes and may present the inter-phase between nutrition and gene regulation, controlled by the diet. The development of biomarkers holds the potential to revolutionize veterinary practice through faster disease detection, more accurate ruminant health monitoring, enhanced welfare, and increased productivity. Finally, we summarize the latest findings on how microRNAs function as biomarkers, how technological paradigms are reshaping this field of research, and how platforms are being used to identify novel biomarkers. Numerous studies have demonstrated a connection between circulating microRNAs and ruminant diseases such as mastitis, tuberculosis, foot-and-mouth disease, fasciolosis, and metabolic disorders. Therefore, the identification and analysis of a small number of microRNAs can provide crucial information about the stage of a disease, etiology, and prognosis.
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11
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Differences in the microRNAs Levels of Raw Milk from Dairy Cattle Raised under Extensive or Intensive Production Systems. Vet Sci 2022; 9:vetsci9120661. [PMID: 36548822 PMCID: PMC9783024 DOI: 10.3390/vetsci9120661] [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: 09/16/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Studying microRNA (miRNAs) in certain agri-food products is attractive because (1) they have potential as biomarkers that may allow traceability and authentication of such products; and (2) they may reveal insights into the products' functional potential. The present study evaluated differences in miRNAs levels in fat and cellular fractions of tank milk collected from commercial farms which employ extensive or intensive dairy production systems. We first sequenced miRNAs in three milk samples from each production system, and then validated miRNAs whose levels in the cellular and fat fraction differed significantly between the two production systems. To accomplish this, we used quantitative PCR with both fractions of tank milk samples from another 20 commercial farms. Differences in miRNAs were identified in fat fractions: overall levels of miRNAs, and, specifically, the levels of bta-mir-215, were higher in intensive systems than in extensive systems. Bovine mRNA targets for bta-miR-215 and their pathway analysis were performed. While the causes of these miRNAs differences remain to be elucidated, our results suggest that the type of production system could affect miRNAs levels and potential functionality of agri-food products of animal origin.
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12
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Mecocci S, Trabalza-Marinucci M, Cappelli K. Extracellular Vesicles from Animal Milk: Great Potentialities and Critical Issues. Animals (Basel) 2022; 12:ani12233231. [PMID: 36496752 PMCID: PMC9740508 DOI: 10.3390/ani12233231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Other than representing the main source of nutrition for newborn mammals, milk delivers a sophisticated signaling system from mother to child that promotes postnatal health. The bioactive components transferred through the milk intake are important for the development of the newborn immune system and include oligosaccharides, lactoferrin, lysozyme, α-La, and immunoglobulins. In the last 15 years, a pivotal role in this mother-to-child exchange has been attributed to extracellular vesicles (EVs). EVs are micro- and nanosized structures enclosed in a phospholipidic double-layer membrane that are produced by all cell types and released in the extracellular environment, reaching both close and distant cells. EVs mediate the intercellular cross-talk from the producing to the receiving cell through the transfer of molecules contained within them such as proteins, antigens, lipids, metabolites, RNAs, and DNA fragments. The complex cargo can induce a wide range of functional modulations in the recipient cell (i.e., anti-inflammatory, immunomodulating, angiogenetic, and pro-regenerative modulations) depending on the type of producing cells and the stimuli that these cells receive. EVs can be recovered from every biological fluid, including blood, urine, bronchoalveolar lavage fluid, saliva, bile, and milk, which is one of the most promising scalable vesicle sources. This review aimed to present the state-of-the-art of animal-milk-derived EV (mEV) studies due to the exponential growth of this field. A focus on the beneficial potentialities for human health and the issues of studying vesicles from milk, particularly for the analytical methodologies applied, is reported.
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13
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Oyelami FO, Usman T, Suravajhala P, Ali N, Do DN. Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases. Pathogens 2022; 11:pathogens11091009. [PMID: 36145441 PMCID: PMC9501195 DOI: 10.3390/pathogens11091009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tahir Usman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, Kerala, India
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Duy N. Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: ; Tel.: +1-9029578789
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14
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Leroux C, Pawlowski K, Billa PA, Pires JA, Faulconnier Y. Milk fat globules as a source of microRNAs for mastitis detection. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Ahmed F, Tamma M, Pathigadapa U, Reddanna P, Yenuganti VR. Drug Loading and Functional Efficacy of Cow, Buffalo, and Goat Milk-Derived Exosomes: A Comparative Study. Mol Pharm 2022; 19:763-774. [PMID: 35195427 DOI: 10.1021/acs.molpharmaceut.1c00182] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Quite recently, milk exosomes have been recognized as efficient drug delivery systems owing to their biocompatibility and easy availability for scale-up technologies. However, there are no reports of comparative studies with regards to drug delivery by milk exosomes derived from different species. In this study, we isolated and characterized milk exosomes of cow, buffalo, and goat by various techniques and tried to understand their drug loading capacity and functional efficiency in HepG2, HCT116, and A549 cells by using doxorubicin. Doxorubicin was loaded to milk exosomes by three methods, that is, incubation, saponin treatment, and sonication. The isolated exosomes were found to be spherical with a size of <200 nm and displayed specific markers, namely, CD81, HSP70, HSC70, and miRNAs. Drug loading studies revealed that goat milk exosomes had the highest loading capacity across all three methods. Doxorubicin-encapsulated goat milk exosomes resulted in the inhibition of cell viability, with low IC50 values in HepG2, HCT-116, and A549 cells. Doxorubicin-encapsulated goat exosomes displayed better IC50 values than cow and buffalo milk-derived counterparts. In line with this, the ability of doxorubicin-encapsulated goat milk exosomes to induce apoptosis in HepG2 and HCT-116 cells was higher than that of cow and buffalo milk exosomes and free doxorubicin. Furthermore, unbound goat milk exosomes significantly reduced cell viability as compared to cow and buffalo milk exosomes. The transepithelial transport assay shows that doxorubicin-loaded milk exosomes transport doxorubicin efficiently as compared to free doxorubicin in vitro. Doxorubicin released from milk exosomes shows a biphasic release pattern, burst release followed by sustained release. These observations are important in light of the emerging importance of milk-derived exosomes as drug carriers to treat cancers.
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Affiliation(s)
- Farhan Ahmed
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Mounipriya Tamma
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Umamaheswari Pathigadapa
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Pallu Reddanna
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Vengala Rao Yenuganti
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
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16
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Gutman-Ido E, Reif S, Musseri M, Schabes T, Golan-Gerstl R. Oxytocin Regulates the Expression of Selected Colostrum-derived microRNAs. J Pediatr Gastroenterol Nutr 2022; 74:e8-e15. [PMID: 34371509 DOI: 10.1097/mpg.0000000000003277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVE The highly expressed microRNAs (miRNAs) in milk are known as beneficial miRNAs, such as mir148a-3p, which is related to immune system development and disease prevention. There is a need to study their expression and secretion regulatory mechanism in breast milk. We hypothesize that oxytocin can be involved in the regulation of expression and secretion of milk-derived miRNAs. METHODS Initially, oxytocin's effect on miRNA expression in human mammary cells was analyzed. Secondly, the expression of selected miRNAs in mothers' colostrum treated or not with oxytocin before, during, or after labor was compared. MiRNA expression was analyzed by quantitative real-time PCR. RESULTS The expression of miR-148a was significantly upregulated, and miR-320 downregulated in oxytocin-treated mammary cells as well as their secreted extracellular vesicles to the media, compared with untreated cells. MiR-148a was found to be upregulated, and miR-320 was downregulated in the human colostrum of exogenous oxytocin-treated mothers. Moreover, miR-320 was highly expressed compared with miR-148a in the colostrum of mothers that did not receive exogenous oxytocin. In contrast, in the milk of mothers who received exogenous oxytocin, the expression of miRNA-148-3p was highly expressed compared with miR-320. CONCLUSIONS This study shows that oxytocin modulates the expression of main milk-derived miRNAs. Our findings provide a novel insight into oxytocin's role in milk composition by regulating miRNA expression. Our results implicate that oxytocin increases miRNA expression in mammary epithelial cells and human milk, affecting human milk composition and may contribute to further infant health.
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Affiliation(s)
| | - Shimon Reif
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mirit Musseri
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Talia Schabes
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Regina Golan-Gerstl
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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17
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The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep. Noncoding RNA 2021; 7:ncrna7040078. [PMID: 34940759 PMCID: PMC8708473 DOI: 10.3390/ncrna7040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.
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18
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Transcriptomic Characterization of Cow, Donkey and Goat Milk Extracellular Vesicles Reveals Their Anti-Inflammatory and Immunomodulatory Potential. Int J Mol Sci 2021; 22:ijms222312759. [PMID: 34884564 PMCID: PMC8657891 DOI: 10.3390/ijms222312759] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 02/06/2023] Open
Abstract
Milk extracellular vesicles (mEVs) seem to be one of the main maternal messages delivery systems. Extracellular vesicles (EVs) are micro/nano-sized membrane-bound structures enclosing signaling molecules and thus acting as signal mediators between distant cells and/or tissues, exerting biological effects such as immune modulation and pro-regenerative activity. Milk is also a unique, scalable, and reliable source of EVs. Our aim was to characterize the RNA content of cow, donkey, and goat mEVs through transcriptomic analysis of mRNA and small RNA libraries. Over 10,000 transcripts and 2000 small RNAs were expressed in mEVs of each species. Among the most represented transcripts, 110 mRNAs were common between the species with cow acting as the most divergent. The most represented small RNA class was miRNA in all the species, with 10 shared miRNAs having high impact on the immune regulatory function. Functional analysis for the most abundant mRNAs shows epigenetic functions such as histone modification, telomere maintenance, and chromatin remodeling for cow; lipid catabolism, oxidative stress, and vitamin metabolism for donkey; and terms related to chemokine receptor interaction, leukocytes migration, and transcriptional regulation in response to stress for goat. For miRNA targets, shared terms emerged as the main functions for all the species: immunity modulation, protein synthesis, cellular cycle regulation, transmembrane exchanges, and ion channels. Moreover, donkey and goat showed additional terms related to epigenetic modification and DNA maintenance. Our results showed a potential mEVs immune regulatory purpose through their RNA cargo, although in vivo validation studies are necessary.
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In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets. Sci Rep 2021; 11:19580. [PMID: 34599210 PMCID: PMC8486775 DOI: 10.1038/s41598-021-98639-9] [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: 02/01/2021] [Accepted: 09/03/2021] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis. Some polymorphisms have been studied in various livestock species from the perspective of pathology or production traits. To target variants that could be the causal variants of dairy traits, genetic variants of microRNAs expressed in the mammary gland or present in milk and localized in dairy quantitative trait loci (QTLs) were investigated in bovine, caprine, and ovine species. In this study, a total of 59,124 (out of 28 millions), 13,427 (out of 87 millions), and 4761 (out of 38 millions) genetic variants in microRNAs expressed in the mammary gland or present in milk were identified in bovine, caprine, and ovine species, respectively. A total of 4679 of these detected bovine genetic variants are located in dairy QTLs. In caprine species, 127 genetic variants are localized in dairy QTLs. In ovine species, no genetic variant was identified in dairy QTLs. This study leads to the detection of microRNA genetic variants of interest in the context of dairy production, taking advantage of whole genome data to identify microRNA genetic variants expressed in the mammary gland and localized in dairy QTLs.
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20
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Wijenayake S, Eisha S, Tawhidi Z, Pitino MA, Steele MA, Fleming AS, McGowan PO. Comparison of methods for pre-processing, exosome isolation, and RNA extraction in unpasteurized bovine and human milk. PLoS One 2021; 16:e0257633. [PMID: 34591894 PMCID: PMC8483318 DOI: 10.1371/journal.pone.0257633] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
Milk is a highly complex, heterogeneous biological fluid that contains non-nutritive, bioactive extracellular vesicles called exosomes. Characterization of milk-derived exosomes (MDEs) is challenging due to the lack of standardized methods that are currently being used for milk pre-processing, storage, and exosome isolation. In this study, we tested: 1) three pre-processing methods to remove cream, fat, cellular debris, and casein proteins from bovine milk to determine whether pre-processing of whole milk prior to long-term storage improves MDE isolations, 2) the suitability of two standard exosome isolation methods for MDE fractionation, and 3) four extraction protocols for obtaining high quality RNA from bovine and human MDEs. MDEs were characterized via Transmission Electron Microscopy (TEM), Nanoparticle Tracking Analysis (NTA), and western immunoblotting for CD9, CD63, and Calnexin protein markers. We also present an optimized method of TEM sample preparation for MDEs. Our results indicate that: 1) Removal of cream and fat globules from unpasteurized bovine milk, prior to long-term storage, improves the MDE yield but not purity, 2) Differential ultracentrifugation (DUC) combined with serial filtration is better suited for bovine MDE isolation compared to ExoQuick (EQ) combined with serial filtration, however both methods were comparable for human milk, and 3) TRIzol LS is better suited for RNA extraction from bovine MDEs isolated by EQ and DUC methods. 4) TRIzol LS, TRIzol+RNA Clean and Concentrator, and TRIzol LS+RNA Clean and Concentrator methods can be used for RNA extractions from human MDEs isolated by EQ, yet the TRIzol LS method is better suited for human MDEs isolated by DUC. The QIAzol + miRNeasy Mini Kit produced the lowest RNA yield for bovine and human MDEs.
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Affiliation(s)
- Sanoji Wijenayake
- Center for Environmental Epigenetics and Development, Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Shafinaz Eisha
- Center for Environmental Epigenetics and Development, Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zoya Tawhidi
- Center for Environmental Epigenetics and Development, Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Michael A. Pitino
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael A. Steele
- Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada
| | - Alison S. Fleming
- Department of Psychology, University of Toronto, Mississauga, Mississauga, Ontario, Canada
| | - Patrick O. McGowan
- Center for Environmental Epigenetics and Development, Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Keel BN, Lindholm-Perry AK, Oliver WT, Wells JE, Jones SA, Rempel LA. Characterization and comparative analysis of transcriptional profiles of porcine colostrum and mature milk at different parities. BMC Genom Data 2021; 22:25. [PMID: 34376140 PMCID: PMC8353812 DOI: 10.1186/s12863-021-00980-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Porcine milk is a complex fluid, containing a myriad of immunological, biochemical, and cellular components, made to satisfy the nutritional requirements of the neonate. Whole milk contains many different cell types, including mammary epithelial cells, neutrophils, macrophages, and lymphocytes, as well nanoparticles, such as milk exosomes. To-date, only a limited number of livestock transcriptomic studies have reported sequencing of milk. Moreover, those studies focused only on sequencing somatic cells as a proxy for the mammary gland with the goal of investigating differences in the lactation process. Recent studies have indicated that RNA originating from multiple cell types present in milk can withstand harsh environments, such as the digestive system, and transmit regulatory molecules from maternal to neonate. Transcriptomic profiling of porcine whole milk, which is reflective of the combined cell populations, could help elucidate these mechanisms. To this end, total RNA from colostrum and mature milk samples were sequenced from 65 sows at differing parities. A stringent bioinformatic pipeline was used to identify and characterize 70,841 transcripts. RESULTS The 70,841 identified transcripts included 42,733 previously annotated transcripts and 28,108 novel transcripts. Differential gene expression analysis was conducted using a generalized linear model coupled with the Lancaster method for P-value aggregation across transcripts. In total, 1667 differentially expressed genes (DEG) were identified for the milk type main effect, and 33 DEG were identified for the milk type x parity interaction. Several gene ontology (GO) terms related to immune response were significant for the milk type main effect, supporting the well-known fact that immunoglobulins and immune cells are transferred to the neonate via colostrum. CONCLUSIONS This is the first study to perform global transcriptome analysis from whole milk samples in sows from different parities. Our results provide important information and insight into synthesis of milk proteins and innate immunity and potential targets for future improvement of swine lactation and piglet development.
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Affiliation(s)
- Brittney N Keel
- USDA-ARS Roman L Hruska US Meat Animal Research Center, Clay Center, NE, 68933, USA.
| | | | - William T Oliver
- USDA-ARS Roman L Hruska US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - James E Wells
- USDA-ARS Roman L Hruska US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Shuna A Jones
- USDA-ARS Roman L Hruska US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Lea A Rempel
- USDA-ARS Roman L Hruska US Meat Animal Research Center, Clay Center, NE, 68933, USA
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Kleinjan M, van Herwijnen MJ, Libregts SF, van Neerven RJ, Feitsma AL, Wauben MH. Regular Industrial Processing of Bovine Milk Impacts the Integrity and Molecular Composition of Extracellular Vesicles. J Nutr 2021; 151:1416-1425. [PMID: 33768229 DOI: 10.1093/jn/nxab031] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/13/2020] [Accepted: 01/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bovine milk contains extracellular vesicles (EVs), which act as mediators of intercellular communication by regulating the recipients' cellular processes via their selectively incorporated bioactive molecules. Because some of these EV components are evolutionarily conserved, EVs present in commercial milk might have the potential to regulate cellular processes in human consumers. OBJECTIVES Because commercial milk is subjected to industrial processing, we investigated its effect on the number and integrity of isolated milk EVs and their bioactive components. For this, we compared EVs isolated from raw bovine milk with EVs isolated from different types of commercial milk, including pasteurized milk, either homogenized or not, and ultra heat treated (UHT) milk. METHODS EVs were separated from other milk components by differential centrifugation, followed by density gradient ultracentrifugation. EVs from different milk types were compared by single-particle high-resolution fluorescence-based flow cytometry to determine EV numbers, Cryo-electron microscopy to visualize EV integrity and morphology, western blot analysis to investigate EV-associated protein cargo, and RNA analysis to assess total small RNA concentration and milk-EV-specific microRNA expression. RESULTS In UHT milk, we could not detect intact EVs. Interestingly, although pasteurization (irrespective of homogenization) did not affect mean ± SD EV numbers (3.4 × 108 ± 1.2 × 108-2.8 × 108 ± 0.3 × 107 compared with 3.1 × 108 ± 1.2 × 108 in raw milk), it affected EV integrity and appearance, altered their protein signature, and resulted in a loss of milk-EV-associated RNAs (from 40.2 ± 3.4 ng/μL in raw milk to 17.7 ± 5.4-23.3 ± 10.0 mg/μL in processed milk, P < 0.05). CONCLUSIONS Commercial milk, that has been heated by either pasteurization or UHT, contains fewer or no intact EVs, respectively. Although most EVs seemed resistant to pasteurization based on particle numbers, their integrity was affected and their molecular composition was altered. Thus, the possible transfer of bioactive components via bovine milk EVs to human consumers is likely diminished or altered in heat-treated commercial milk.
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Affiliation(s)
- Marije Kleinjan
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Martijn Jc van Herwijnen
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Sten Fwm Libregts
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rj Joost van Neerven
- FrieslandCampina, Amersfoort, Netherlands.,Cell Biology and Immunology, Wageningen University, Wageningen, Netherlands
| | | | - Marca Hm Wauben
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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23
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Leroux C, Chervet ML, German JB. Perspective: Milk microRNAs as Important Players in Infant Physiology and Development. Adv Nutr 2021; 12:1625-1635. [PMID: 34022770 PMCID: PMC8483967 DOI: 10.1093/advances/nmab059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/08/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Evolutionary selective pressure on lactation has resulted in milk that provides far more than simply essential nutrients, delivering a complex repertoire of agents from hormones to intact cells. Human infants are born with low barrier integrity of their gut, which means that many of the complex biopolymer components of milk enter and circulate in lymph and blood, reaching organs throughout the body. Due to this state of gut maturation, all components of milk are potentially part of the crosstalk between mother and infants. This article highlights the functions of milk's complex biopolymers, more specifically the potential role of microRNAs (miRNAs) contained in extracellular vesicles in human milk. miRNAs are key effectors in the regulation of many biological processes during early-age development, and consequently milk-sourced miRNAs must be considered to provide unique biological assets to the infant during breastfeeding. This article interprets the evidence of the potential action of human milk miRNAs on infant development, taking into account their abundance in milk based on the literature and current knowledge. Human milk miRNAs appear to influence lipid and glucose metabolism, gut maturation, neurogenesis, and immunity. We also show growing evidence that human milk miRNAs are epigenetic modulators that play a pivotal role in the regulation of tissue-specific gene expression throughout life. Furthermore, this article addresses the ongoing debate regarding the potential influence of human milk miRNAs on viral infection as a new research area. This article highlights that these bioactive molecules are now being incorporated into our overall understanding of nutrient needs for healthy infant development, preparing each individual infant to succeed as a healthy and protected adult throughout its life. In essence, miRNAs are a new language in the Rosetta stone of health that is mammalian lactation.
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Affiliation(s)
| | - Mathilde Lea Chervet
- Foods for Health Institute, Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - J Bruce German
- Foods for Health Institute, Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
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24
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Hue-Beauvais C, Faulconnier Y, Charlier M, Leroux C. Nutritional Regulation of Mammary Gland Development and Milk Synthesis in Animal Models and Dairy Species. Genes (Basel) 2021; 12:genes12040523. [PMID: 33916721 PMCID: PMC8067096 DOI: 10.3390/genes12040523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 12/16/2022] Open
Abstract
In mammals, milk is essential for the growth, development, and health. Milk quantity and quality are dependent on mammary development, strongly influenced by nutrition. This review provides an overview of the data on nutritional regulations of mammary development and gene expression involved in milk component synthesis. Mammary development is described related to rodents, rabbits, and pigs, common models in mammary biology. Molecular mechanisms of the nutritional regulation of milk synthesis are reported in ruminants regarding the importance of ruminant milk in human health. The effects of dietary quantitative and qualitative alterations are described considering the dietary composition and in regard to the periods of nutritional susceptibly. During lactation, the effects of lipid supplementation and feed restriction or deprivation are discussed regarding gene expression involved in milk biosynthesis, in ruminants. Moreover, nutrigenomic studies underline the role of the mammary structure and the potential influence of microRNAs. Knowledge from three lactating and three dairy livestock species contribute to understanding the variety of phenotypes reported in this review and highlight (1) the importance of critical physiological stages, such as puberty gestation and early lactation and (2) the relative importance of the various nutrients besides the total energetic value and their interaction.
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Affiliation(s)
- Cathy Hue-Beauvais
- INRAE, AgroParisTech, GABI, University of Paris-Saclay, F-78350 Jouy-en-Josas, France;
- Correspondence:
| | - Yannick Faulconnier
- INRAE, VetAgro Sup, UMR Herbivores, University of Clermont Auvergne, F-63122 Saint-Genès-Champanelle, France; (Y.F.); (C.L.)
| | - Madia Charlier
- INRAE, AgroParisTech, GABI, University of Paris-Saclay, F-78350 Jouy-en-Josas, France;
| | - Christine Leroux
- INRAE, VetAgro Sup, UMR Herbivores, University of Clermont Auvergne, F-63122 Saint-Genès-Champanelle, France; (Y.F.); (C.L.)
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25
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Melnik BC. Lifetime Impact of Cow's Milk on Overactivation of mTORC1: From Fetal to Childhood Overgrowth, Acne, Diabetes, Cancers, and Neurodegeneration. Biomolecules 2021; 11:404. [PMID: 33803410 PMCID: PMC8000710 DOI: 10.3390/biom11030404] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
The consumption of cow's milk is a part of the basic nutritional habits of Western industrialized countries. Recent epidemiological studies associate the intake of cow's milk with an increased risk of diseases, which are associated with overactivated mechanistic target of rapamycin complex 1 (mTORC1) signaling. This review presents current epidemiological and translational evidence linking milk consumption to the regulation of mTORC1, the master-switch for eukaryotic cell growth. Epidemiological studies confirm a correlation between cow's milk consumption and birthweight, body mass index, onset of menarche, linear growth during childhood, acne vulgaris, type 2 diabetes mellitus, prostate cancer, breast cancer, hepatocellular carcinoma, diffuse large B-cell lymphoma, neurodegenerative diseases, and all-cause mortality. Thus, long-term persistent consumption of cow's milk increases the risk of mTORC1-driven diseases of civilization. Milk is a highly conserved, lactation genome-controlled signaling system that functions as a maternal-neonatal relay for optimized species-specific activation of mTORC1, the nexus for regulation of eukaryotic cell growth, and control of autophagy. A deeper understanding of milk´s impact on mTORC1 signaling is of critical importance for the prevention of common diseases of civilization.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Am Finkenhügel 7a, D-49076 Osnabrück, Germany
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26
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Hao ZY, Wang JQ, Luo YL, Liu X, Li SB, Zhao ML, Jin XY, Shen JY, Ke N, Song YZ, Qiao LR. Deep small RNA-Seq reveals microRNAs expression profiles in lactating mammary gland of 2 sheep breeds with different milk performance. Domest Anim Endocrinol 2021; 74:106561. [PMID: 33035848 DOI: 10.1016/j.domaniend.2020.106561] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
Micro ribonucleic acid (miRNA) is a type of noncoding RNA, and it has been revealed to play important roles in the activity of the mammary gland (MG) in some species. However, the function of miRNAs in MG of sheep is poorly understood. In the study, Gansu Alpine Merino (GAM; n = 9) and Small-tailed Han sheep (STH; n = 9) with different milk production traits were investigated. Microstructures and the expression profile of miRNAs of MG tissues at peak lactation were studied. Mature alveolar lumens of MG in appearance were larger in STH than GAM. The expression levels of CSN2 and the content of rough endoplasmic reticulum were also higher in STH ewes than GAM ewes. A total of 124 mature miRNAs were expressed, and 18 of these were differentially expressed between the 2 breeds. The KEGG analysis results showed that the targeted genes of differentially expressed miRNAs were mainly involved in some metabolic pathways and signaling pathways related to MG development, milk protein, and fat synthesis. The findings in the study can improve our understanding of the roles of miRNAs in the development and lactation of MG in sheep.
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Affiliation(s)
- Z Y Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - J Q Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Y L Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - X Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - S B Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - M L Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - X Y Jin
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - J Y Shen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - N Ke
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Y Z Song
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - L R Qiao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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27
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Zeng B, Chen T, Luo JY, Zhang L, Xi QY, Jiang QY, Sun JJ, Zhang YL. Biological Characteristics and Roles of Noncoding RNAs in Milk-Derived Extracellular Vesicles. Adv Nutr 2020; 12:1006-1019. [PMID: 33080010 PMCID: PMC8166544 DOI: 10.1093/advances/nmaa124] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/21/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) have diverse roles in the transport of proteins, lipids, and nucleic acids between cells, and they serve as mediators of intercellular communication. Noncoding RNAs (ncRNAs) that are present in EVs, including microRNAs, long noncoding RNAs, and circular RNAs, have been found to participate in complex networks of interactions and regulate a wide variety of genes in animals. Milk is an important source of nutrition for humans and other mammals. Evidence suggests that milk-derived EVs contain abundant ncRNAs, which are stable and can be transported to the offspring and other consumers. Current data suggest a strong link between milk EV ncRNAs and many biological processes, and these ncRNAs have been drawing increasing attention and might play an epigenetic regulatory role in recipients, though further research is still necessary to understand their precise roles. The present review introduces basic information about milk EV ncRNAs, summarizes their expression profiles, biological characteristics, and functions based on current knowledge, and discusses their biological roles, indeterminate issues, and perspectives. Our goal is to provide a deeper understanding of the physiological effects of milk EV ncRNAs on offspring and to provide a reference for future research in this field.
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Affiliation(s)
- Bin Zeng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun-Yi Luo
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lin Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qian-Yun Xi
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qing-Yan Jiang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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28
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Pawlowski K, Lago-Novais D, Bevilacqua C, Mobuchon L, Crapart N, Faulconnier Y, Boby C, Carvalho G, Martin P, Leroux C. Different miRNA contents between mammary epithelial cells and milk fat globules: a random or a targeted process? Mol Biol Rep 2020; 47:8259-8264. [PMID: 32909217 DOI: 10.1007/s11033-020-05787-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs present in milk-derived extracellular vesicles and milk fat globules (MFG). Nucleic acid content between the lactating mammary tissue (MT) and MFG are quite similar but discrepancies exist in their miRNA content. Our objective was to identify the origin of these discrepancies, and to evaluate the existence of a possible mechanism sorting miRNAs that will or will not be exported from the mammary epithelial cells (MECs) in bovine MFG. miR-125b-5p, miR-126-3p, miR-141-3p, and miR-204-5p, chosen on the basis of their abundance in the MT, were quantified using RT-qPCR in lactating cow MT, MFG, and laser capture-microdissected MECs. Two miRNAs (miR-125b-5p and miR-141-3p) were detected in the MT as well as in MFG and MECs. miR-204-5p was detected only in the MT, suggesting that it is very likely expressed in a cell type other than MECs. miR-126-3p was detected both in the MT and in MECs but not in MFG, suggesting a targeting mechanism for miRNAs in MECs. These results highlights differences in miRNA content between MECs and MFG may be due to a possibly not random mechanism for loading MFG with miRNA cargos that could involve a variable distribution in MECs or a sorting mechanism.
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Affiliation(s)
- Karol Pawlowski
- UMR1213 Herbivores, INRAE, Université Clermont-Auvergne, VetAgro Sup, 63122, Saint Genès Champanelle, France.,Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Warsaw, Poland
| | - Daiane Lago-Novais
- UMR1213 Herbivores, INRAE, Université Clermont-Auvergne, VetAgro Sup, 63122, Saint Genès Champanelle, France.,Programa de Pós Graduação em Zootecnia, Universidade Federal da Bahia (UFBA), Av. Adhemar de Barros 500, CEP 40170-110, Salvador, BA, Brazil
| | - Claudia Bevilacqua
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, INRAE, 78350, Jouy-en-Josas, France.,Plateforme @BRIDGE, INRAE, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Lenha Mobuchon
- UMR1213 Herbivores, INRAE, Université Clermont-Auvergne, VetAgro Sup, 63122, Saint Genès Champanelle, France.,UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, INRAE, 78350, Jouy-en-Josas, France
| | - Nicolas Crapart
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, INRAE, 78350, Jouy-en-Josas, France.,Plateforme @BRIDGE, INRAE, Domaine de Vilvert, 78350, Jouy-en-Josas, France.,Excilone, 78990, Elancourt, France
| | - Yannick Faulconnier
- UMR1213 Herbivores, INRAE, Université Clermont-Auvergne, VetAgro Sup, 63122, Saint Genès Champanelle, France
| | - Céline Boby
- UMR1213 Herbivores, INRAE, Université Clermont-Auvergne, VetAgro Sup, 63122, Saint Genès Champanelle, France
| | - Gleidson Carvalho
- Programa de Pós Graduação em Zootecnia, Universidade Federal da Bahia (UFBA), Av. Adhemar de Barros 500, CEP 40170-110, Salvador, BA, Brazil
| | - Patrice Martin
- UMR1313 Génétique Animale et Biologie Intégrative, AgroParisTech, Université Paris-Saclay, INRAE, 78350, Jouy-en-Josas, France
| | - Christine Leroux
- UMR1213 Herbivores, INRAE, Université Clermont-Auvergne, VetAgro Sup, 63122, Saint Genès Champanelle, France.
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29
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Zandi E, Ayatollahi Mehrgardi A, Esmailizadeh A. Mammary tissue transcriptomic analysis for construction of integrated regulatory networks involved in lactogenesis of Ovis aries. Genomics 2020; 112:4277-4287. [PMID: 32693106 DOI: 10.1016/j.ygeno.2020.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/19/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
The mammary gland experiences vast changes between the onset of lactation and pregnancy. This remodeling involves different functions such as lactation that is controlled by innumerable regulators and various gene networks which are still not completely understood. MicroRNAs (miRNAs) are one of the important non-coding gene regulators which control an extensive range of biological processes. Thus, exploring miRNAs functions is important for solving gene regulation complexity. The main purpose in the present study is to identify the various gene regulative integrated networks involved in lactation progress in mammary gland. We analyzed ovine mammary tissue data sets which included expression profiles of mRNA (genes) and miRNAs related to six ewes in different days of lactation and nutritional treatments. We combined two different types of information: the network that is module inference by mRNAs (RNA-seq data), miRNAs and transcription factors (TFs) expression matrix and prediction of targets via computational methods. To discover the miRNAs regulatory function, 134 modules were predicted by using gene expression data and 14 TFs and 20 miRNAs were allocated to these predicted modules. By applying this integrated computation-based method, 38 miRNA-modules and 35 TF-module interactions were identified from ovine mammary tissue data during lactogenesis. A lot of these modules were involved in lipid and protein metabolism, as well as steroids and vitamin biosynthesis, which would play key roles in mammary tissue and lactation development. These results present new information about the regulatory procedures at the miRNAs and TF levels throughout lactation.
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Affiliation(s)
- Elmira Zandi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran; Yong Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
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30
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Marina H, Reverter A, Gutiérrez-Gil B, Alexandre PA, Porto-Neto LR, Suárez-Vega A, Li Y, Esteban-Blanco C, Arranz JJ. Gene Networks Driving Genetic Variation in Milk and Cheese-Making Traits of Spanish Assaf Sheep. Genes (Basel) 2020; 11:genes11070715. [PMID: 32605032 PMCID: PMC7397207 DOI: 10.3390/genes11070715] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 02/04/2023] Open
Abstract
Most of the milk produced by sheep is used for the production of high-quality cheese. Consequently, traits related to milk coagulation properties and cheese yield are economically important to the Spanish dairy industry. The present study aims to identify candidate genes and their regulators related to 14 milk and cheese-making traits and to develop a low-density panel of markers that could be used to predict an individual's genetic potential for cheese-making efficiency. In this study, we performed a combination of the classical genome-wide association study (GWAS) with a stepwise regression method and a pleiotropy analysis to determine the best combination of the variants located within the confidence intervals of the potential candidate genes that may explain the greatest genetic variance for milk and cheese-making traits. Two gene networks related to milk and cheese-making traits were created using the genomic relationship matrices built through a stepwise multiple regression approach. Several co-associated genes in these networks are involved in biological processes previously found to be associated with milk synthesis and cheese-making efficiency. The methodology applied in this study enabled the selection of a co-association network comprised of 374 variants located in the surrounding of genes showing a potential influence on milk synthesis and cheese-making efficiency.
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Affiliation(s)
- Héctor Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Pâmela Almeida Alexandre
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Aroa Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Yutao Li
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, Queensland 4067, Australia; (A.R.); (P.A.A.); (L.R.P.-N.); (Y.L.)
| | - Cristina Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
| | - Juan-José Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain; (H.M.); (B.G.-G.); (A.S.-V.); (C.E.-B.)
- Correspondence: ; Tel.: +34-987-291-470
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31
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Jakubek P, Cieślewicz J, Bartoszek A. MicroRNAs as novel bioactive components of human breastmilk. POSTEP HIG MED DOSW 2020. [DOI: 10.5604/01.3001.0014.1434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are short, non-coding oligonucleotides that regulate gene expression at the post-transcriptional level. These small molecules participate in the control of various cellular processes and signalling pathways. Since 2010 microRNAs have been recognized as a new bioactive component of breastmilk, which is an exceptionally rich source of these oligonucleotides. In infants fed with breastmilk, microRNAs are involved in the growth and proper development as well as maturation of the immune system. It has been demonstrated that microRNAs are resistant to harsh conditions during in vitro digestion in simulated gastrointestinal tract of a newborn and, therefore, may be absorbed by the intestinal cells. Protection against RNase activity and low pH is provided by exosomes, which are carriers of microRNAs in skim milk or by fat globules and milk cells. It has been reported that, in contrast to human milk, infant formulas contain only a few microRNAs, which have been derived from other organisms, such as cow or soy. It may be presumed that supplementing infant formulas with microRNAs identical
with those which occur naturally in breastmilk may constitute a new way of designing
artificial substitutes for human breastmilk.
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Affiliation(s)
- Patrycja Jakubek
- Katedra Chemii, Technologii i Biotechnologii Żywności, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Joanna Cieślewicz
- Katedra Chemii, Technologii i Biotechnologii Żywności, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
| | - Agnieszka Bartoszek
- Katedra Chemii, Technologii i Biotechnologii Żywności, Wydział Chemiczny, Politechnika Gdańska, Gdańsk
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Yu X, Fang X, Gao M, Mi J, Zhang X, Xia L, Zhao Z, Albrecht E, Maak S, Yang R. Isolation and Identification of Bovine Preadipocytes and Screening of MicroRNAs Associated with Adipogenesis. Animals (Basel) 2020; 10:ani10050818. [PMID: 32397360 PMCID: PMC7278844 DOI: 10.3390/ani10050818] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/24/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Promoting fat deposition in beef cattle has been a focus of modern animal breeding research. However, previous researchers have not examined the mechanism of adipogenesis in much detail. MicroRNAs (miRNAs) are small noncoding RNAs that play a pivotal role in adipogenesis. In this study, to explore the molecular regulatory mechanism of adipocyte differentiation and formation, bovine preadipocytes were isolated and induced into adipocytes, and then the expression patterns of miRNAs between preadipocytes and adipocytes were detected through RNA sequencing. Deep sequence analysis has identified 78, 71, and 48 novel miRNAs and 497, 491, and 524 known miRNAs in the preadipocytes, and 44, 54, and 47 novel miRNAs and 519, 522, and 504 known miRNAs in the adipocytes. Among the annotated miRNAs, 131 bovine miRNAs were upregulated in adipocytes, and 119 bovine miRNAs were downregulated in adipocytes, such as bta-miR-3604, bta-miR-23b-3p, bta-miR-26a, and bta-miR-129-3p. Bovine target gene prediction results of these miRNAs show that numerous genes are associated with lipid metabolism. These results can provide both technical support and a research basis for promoting bovine adipocyte fat deposition. Abstract The elucidation of the mechanisms of preadipocyte differentiation and fat accumulation in adipocytes is a major work in beef cattle breeding. As important post-transcriptional regulators, microRNAs (miRNAs) take part in cell proliferation, differentiation, apoptosis, and fat metabolism through binding seed sites of targeting mRNAs. The aim of this study was to isolate and identify bovine preadipocytes and screen miRNAs associated with adipogenesis. Bovine preadipocytes were isolated from subcutaneous fatty tissue and induced to differentiate into adipocytes. Verification of preadipocytes and adipocytes was performed by qRT-PCR (real-time quantitative reverse transcription PCR), Oil Red O staining, and immunofluorescence staining. Total RNA was extracted for small RNA sequencing. The sequencing data showed that 131 miRNAs were highly expressed in adipocytes, and 119 miRNAs were highly expressed in preadipocytes. Stem–loop qPCR (stem–loop quantitative real-time PCR) results showed that the expression patterns of 11 miRNAs were consistent with the sequencing results (miR-149-5p, miR-24-3p, miR-199a-5p, miR-33a, etc.). According to KEGG pathway and Gene Ontology (GO) analyses, multiple predicted target genes were associated with lipid metabolism. In summary, this study provides a protocol of isolating bovine preadipocytes and screening various differently expressed miRNAs during preadipocyte differentiation.
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Affiliation(s)
- Xiang Yu
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
| | - Xibi Fang
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
| | - Ming Gao
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
| | - Jiaqi Mi
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
| | - Xiuqi Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
| | - Lixin Xia
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
| | - Zhihui Zhao
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, Guangdong Province, China;
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (E.A.); (S.M.)
| | - Steffen Maak
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (E.A.); (S.M.)
| | - Runjun Yang
- College of Animal Sciences, Jilin University, Changchun 130062, Jilin Province, China; (X.Y.); (X.F.); (M.G.); (J.M.); (X.Z.); (L.X.)
- Correspondence:
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Wang L, Shi Z, Wang X, Mu S, Xu X, Shen L, Li P. Protective effects of bovine milk exosomes against oxidative stress in IEC-6 cells. Eur J Nutr 2020; 60:317-327. [PMID: 32328746 DOI: 10.1007/s00394-020-02242-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 03/27/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Bovine milk exosomes, which are enriched with microRNAs (miRNAs) and proteins, regulate immune response and growth. In the present study, we aimed to assess the protective effects of bovine milk exosomes against oxidative stress of intestinal crypt epithelial cells (IEC-6). METHODS Bovine milk exosomes were isolated and characterized. To assess the protective effects of exosomes, IEC-6 cells were pretreated with exosomes, followed by H2O2. Cell viability and levels of superoxide dismutase (SOD), malondialdehyde (MDA), glutathione peroxidase (GPX), reactive oxidative species (ROS), and lactate dehydrogenase (LDH) were measured. The expression levels of nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase 1 (Ho1) genes, and miR-146a, miR-155, and the HO-1 protein were also determined. RESULTS The isolated bovine milk exosome were positive for CD63 and CD9 expression. The exosomes were approximately circular and had a diameter of about 67.23 nm. Pretreatment of IEC-6 cells with bovine milk exosomes enhanced cell viability; increased SOD and GPX activities; and reduced LDH, ROS, and MDA levels after H2O2 challenge. Further analysis showed that exosome pretreatment increased intracellular miR-146a and miR-155 levels. Exosome pretreatment inhibited the elevation of Nrf2 and Ho1 gene expression induced by H2O2, but promoted HO-1 protein expression. CONCLUSION The results indicated that bovine milk exosomes exerted protective effects against oxidative stress in IEC-6 cells.
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Affiliation(s)
- Lanfang Wang
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China.
| | - Zhexi Shi
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Xinyan Wang
- The People's Hospital of Zhaoyuan City, Zhaoyuan, 265400, Shandong Province, China
| | - Shu Mu
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Xiaoyan Xu
- Research Center for Translational Medicine at Shanghai East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Li Shen
- Department of Pathogen Biology, Tongji University School of Medicine, Shanghai, 200092, China
| | - Ping Li
- Research Center for Translational Medicine at Shanghai East Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
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Sánchez-Visedo A, Gallego B, Royo LJ, Soldado A, Valledor M, Ferrero FJ, Campo JC, Costa-Fernández JM, Fernández-Argüelles MT. Visual detection of microRNA146a by using RNA-functionalized gold nanoparticles. Mikrochim Acta 2020; 187:192. [PMID: 32124045 DOI: 10.1007/s00604-020-4148-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/26/2020] [Indexed: 01/07/2023]
Abstract
Gold nanoparticles of different sizes have been synthesized and surface-functionalized with selected RNA probes in order to develop a rapid, low-cost and sensitive method for detection of microRNA146a (miR146a). The strategy is based on the change of colour that can be observed visually after aggregation of the RNA modified-gold nanoparticles (AuNPs) in presence of miR146a. Experimental conditions have been carefully selected in order to obtain a good sensitivity that allows to perform visual detection of microRNA at the nM level, achieving a detection limit of 5 nM. Good repeatability and selectivity versus other sequences that only differ from miR146a in 3 bases was achieved. miR146a has been described as one of the main microRNA involved in the immune response of bovine mastitis, being expressed in tissue, blood and milk samples. The method was successfully applied to the detection of miR146a in raw cow milk samples. The present scheme constitutes a rapid and low-cost alternative to perform highly sensitive detection of microRNA without the need of instrumentation and amplification steps for the early detection of bovine mastitis in the agrofood industry. Graphical abstract Schematic representation of the assay based on aggregation of RNA-modified gold nanoparticles (blue) in presence of microRNA146a generating a dark blue spot onto a solid support, versus a pink spot observed in absence of miR146a due to dispersed gold nanoparticles (red).
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Affiliation(s)
- Adrián Sánchez-Visedo
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - Borja Gallego
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - Luis José Royo
- Department of Animal Nutrition, Grassland and Forages, Regional Institute for Research and Agro-Food Development (SERIDA), Carretera Oviedo S/N, 33300, Villaviciosa (Asturias), Spain.
| | - Ana Soldado
- Department of Animal Nutrition, Grassland and Forages, Regional Institute for Research and Agro-Food Development (SERIDA), Carretera Oviedo S/N, 33300, Villaviciosa (Asturias), Spain
| | - Marta Valledor
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus Gijón, 33204, Gijón, Spain
| | - Francisco Javier Ferrero
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus Gijón, 33204, Gijón, Spain
| | - Juan Carlos Campo
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus Gijón, 33204, Gijón, Spain
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - María Teresa Fernández-Argüelles
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain.
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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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36
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Lai YC, Lai YT, Rahman MM, Chen HW, Husna AA, Fujikawa T, Ando T, Kitahara G, Koiwa M, Kubota C, Miura N. Bovine milk transcriptome analysis reveals microRNAs and RNU2 involved in mastitis. FEBS J 2019; 287:1899-1918. [PMID: 31663680 DOI: 10.1111/febs.15114] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 07/09/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022]
Abstract
Mastitis is a common inflammatory infectious disease in dairy cows. To understand the microRNA (miRNA) expression profile changes during bovine mastitis, we undertook a genome-wide miRNA study of normal milk and milk that tested positive on the California mastitis test for bovine mastitis (CMT+). Twenty-five miRNAs were differentially expressed (23 miRNAs upregulated and two downregulated) during bovine mastitis relative to their expression in normal milk. Upregulated mature miR-1246 probably derived from a U2 small nuclear RNA rather than an miR-1246 precursor. The significantly upregulated miRNA precursors and RNU2 were significantly enriched on bovine chromosome 19, which is homologous to human chromosome 17. A gene ontology analysis of the putative mRNA targets of the significantly upregulated miRNAs showed that these miRNAs were involved in binding target mRNA transcripts and regulating target gene expression, and a Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the upregulated miRNAs were predominantly related to cancer and immune system pathways. Three novel miRNAs were associated with bovine mastitis and were relatively highly expressed in milk. We confirmed that one of the novel mastitis-related miRNAs was significantly upregulated using a digital PCR system. The differentially expressed miRNAs were involved in human cancers, infections, and immune-related diseases. The genome-wide analysis of miRNA profiles in this study provides insight into bovine mastitis and inflammatory diseases. DATABASES: The miRNAseq generated for this study can be found in the Sequence Read Archive (SRA) under BioProject Number PRJNA421075 and SRA Study Number SRP126134 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA421075).
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Affiliation(s)
- Yu-Chang Lai
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | | | - Md Mahfuzur Rahman
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Japan
| | - Hui-Wen Chen
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,Joint Graduate School of Veterinary Medicine, Kagoshima University, Japan
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Japan
| | - Takuro Fujikawa
- The United Graduate School of Veterinary Science, Yamaguchi University, Japan.,Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Takaaki Ando
- Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Go Kitahara
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Japan
| | - Masateru Koiwa
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Chikara Kubota
- Laboratory of Veterinary Theriogenology, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
| | - Naoki Miura
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Japan
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An Optimized Method of RNA Isolation from Goat Milk Somatic Cells for Transcriptomic Analysis. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The goat (Capra hircus) is a perfect animal model for analyzing the transcriptome of milk somatic cells (MSCs), as sufficient numbers of somatic cells in goat milk, i.e., exfoliated epithelial cells, can be obtained using noninvasive methods. RNA integrity and purity are the first and most important parameters qualifying samples for transcriptomic tests and next-generation sequencing, as RNA quality influences experimental results. The aim of this study was to optimize a method for obtaining high-quality RNA from goat MSCs, irrespective of effects like breed, lactation stage, health status (e.g., with or without small ruminant lentivirus [SRLV] infection), or number of somatic cells. Milk samples were obtained from goats of two Polish breeds in various lactation stages and in different parities, and from goats infected and not infected with SRLV. Altogether, 412 MSC samples were examined: 206 using method A with fenozol and 206 using method B with QIAzol. Though the overall purity (measured as absorbance ratios at 260 nm/280 nm and 260 nm/230 nm) of the RNA material was comparable, the average yield of RNA isolated using method A was 11.9 µg, while method B’s average yield was 29.9 µg. Moreover, method B resulted in good quality RNA suitable for transcriptome analysis. Results were confirmed by RT-qPCR, using 18S rRNA and RPLP0 as the reference genes. The application of our modified treatment method was successful in obtaining high-integrity samples for transcriptomic or next-generation sequencing analysis. Using a 400 mL milk sample cooled in ice directly after milking, securing the cooling chain process from milking to MSC isolation, and applying method B to isolate RNA, we obtained good RNA quality irrespective of the goats’ breed, lactation stage, parity, milk yield, SRLV infection, and even milk yield and number of somatic cells in milk.
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Billa PA, Faulconnier Y, Ye T, Chervet M, Le Provost F, Pires JAA, Leroux C. Deep RNA-Seq reveals miRNome differences in mammary tissue of lactating Holstein and Montbéliarde cows. BMC Genomics 2019; 20:621. [PMID: 31362707 PMCID: PMC6668132 DOI: 10.1186/s12864-019-5987-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
Background Genetic polymorphisms are known to influence milk production and composition. However, the genomic mechanisms involved in the genetic regulation of milk component synthesis are not completely understood. MicroRNAs (miRNAs) regulate gene expression. Previous research suggests that the high developmental potential of the mammary gland may depend in part on a specific miRNA expression pattern. The objective of the present study was to compare the mammary gland miRNomes of two dairy cow breeds, Holstein and Montbéliarde, which have different mammogenic potentials that are related to differences in dairy performance. Results Milk, fat, protein, and lactose yields were lower in Montbéliarde cows than in Holstein cows. We detected 754 distinct miRNAs in the mammary glands of Holstein (n = 5) and Montbéliarde (n = 6) midlactating cows using RNA-Seq technology, among which 738 were known and 16 were predicted miRNAs. The 25 most abundant miRNAs accounted for 90.6% of the total reads. The comparison of their abundances in the mammary glands of Holstein versus Montbéliarde cows identified 22 differentially expressed miRNAs (Padj ≤ 0.05). Among them, 11 presented a fold change ≥2, and 2 (miR-100 and miR-146b) were highly expressed. Among the most abundant miRNAs, miR-186 is known to inhibit cell proliferation and epithelial-to-mesenchymal transition. Data mining showed that 17 differentially expressed miRNAs with more than 20 reads were involved in the regulation of mammary gland plasticity. Several of them may potentially target mRNAs involved in signaling pathways (such as mTOR) and lipid metabolism, thereby indicating that they could influence milk composition. Conclusion We found differences in the mammary gland miRNomes of two dairy cattle breeds. These differences suggest a potential role for miRNAs in mammary gland plasticity and milk component synthesis, both of which are related to milk production and composition. Further research is warranted on the genetic regulation of miRNAs and their role in milk synthesis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5987-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- P A Billa
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - Y Faulconnier
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - T Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67404, Illkirch, France
| | - M Chervet
- Department of Food Science & Technology, University of California Davis, Davis, CA, USA
| | - F Le Provost
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, F-78352, France
| | - J A A Pires
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France
| | - C Leroux
- Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, UMR1213 Herbivores, F-63122, Saint-Genès-Champanelle, France. .,Department of Food Science & Technology, University of California Davis, Davis, CA, USA.
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Sequence-based GWAS, network and pathway analyses reveal genes co-associated with milk cheese-making properties and milk composition in Montbéliarde cows. Genet Sel Evol 2019; 51:34. [PMID: 31262251 PMCID: PMC6604208 DOI: 10.1186/s12711-019-0473-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/07/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Milk quality in dairy cattle is routinely assessed via analysis of mid-infrared (MIR) spectra; this approach can also be used to predict the milk's cheese-making properties (CMP) and composition. When this method of high-throughput phenotyping is combined with efficient imputations of whole-genome sequence data from cows' genotyping data, it provides a unique and powerful framework with which to carry out genomic analyses. The goal of this study was to use this approach to identify genes and gene networks associated with milk CMP and composition in the Montbéliarde breed. RESULTS Milk cheese yields, coagulation traits, milk pH and contents of proteins, fatty acids, minerals, citrate, and lactose were predicted from MIR spectra. Thirty-six phenotypes from primiparous Montbéliarde cows (1,442,371 test-day records from 189,817 cows) were adjusted for non-genetic effects and averaged per cow. 50 K genotypes, which were available for a subset of 19,586 cows, were imputed at the sequence level using Run6 of the 1000 Bull Genomes Project (comprising 2333 animals). The individual effects of 8.5 million variants were evaluated in a genome-wide association study (GWAS) which led to the detection of 59 QTL regions, most of which had highly significant effects on CMP and milk composition. The results of the GWAS were further subjected to an association weight matrix and the partial correlation and information theory approach and we identified a set of 736 co-associated genes. Among these, the well-known caseins, PAEP and DGAT1, together with dozens of other genes such as SLC37A1, ALPL, MGST1, SEL1L3, GPT, BRI3BP, SCD, GPAT4, FASN, and ANKH, explained from 12 to 30% of the phenotypic variance of CMP traits. We were further able to identify metabolic pathways (e.g., phosphate and phospholipid metabolism and inorganic anion transport) and key regulator genes, such as PPARA, ASXL3, and bta-mir-200c that are functionally linked to milk composition. CONCLUSIONS By using an approach that integrated GWAS with network and pathway analyses at the whole-genome sequence level, we propose candidate variants that explain a substantial proportion of the phenotypic variance of CMP traits and could thus be included in genomic evaluation models to improve milk CMP in Montbéliarde cows.
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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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Gebreyesus G, Buitenhuis AJ, Poulsen NA, Visker MHPW, Zhang Q, van Valenberg HJF, Sun D, Bovenhuis H. Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition. BMC Genomics 2019; 20:178. [PMID: 30841852 PMCID: PMC6404302 DOI: 10.1186/s12864-019-5573-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 02/28/2019] [Indexed: 01/23/2023] Open
Abstract
Background The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analytical techniques. Combining multi-population datasets can enhance the power of GWAS enabling detection of genomic region explaining medium to low proportions of the genetic variation. GWAS often detect broader genomic regions containing several positional candidate genes making it difficult to untangle the causative candidates. Post-GWAS analyses with data on pathways, ontology and tissue-specific gene expression status might allow prioritization among positional candidate genes. Results Multi-population GWAS for 16 FA traits quantified using gas chromatography (GC) in sample populations of the Chinese, Danish and Dutch Holstein with high-density (HD) genotypes detects 56 genomic regions significantly associated to at least one of the studied FAs; some of which have not been previously reported. Pathways and gene ontology (GO) analyses suggest promising candidate genes on the novel regions including OSBPL6 and AGPS on Bos taurus autosome (BTA) 2, PRLH on BTA 3, SLC51B on BTA 10, ABCG5/8 on BTA 11 and ALG5 on BTA 12. Novel genes in previously known regions, such as FABP4 on BTA 14, APOA1/5/7 on BTA 15 and MGST2 on BTA 17, are also linked to important FA metabolic processes. Conclusion Integration of multi-population GWAS and enrichment analyses enabled detection of several novel genomic regions, explaining relatively smaller fractions of the genetic variation, and revealed highly likely candidate genes underlying the effects. Detection of such regions and candidate genes will be crucial in understanding the complex genetic control of FA metabolism. The findings can also be used to augment genomic prediction models with regions collectively capturing most of the genetic variation in the milk FA traits. Electronic supplementary material The online version of this article (10.1186/s12864-019-5573-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- G Gebreyesus
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, P.O. Box 50, DK-8830, Tjele, Denmark. .,Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.
| | - A J Buitenhuis
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Blichers Allé 20, P.O. Box 50, DK-8830, Tjele, Denmark
| | - N A Poulsen
- Department of Food Science, Aarhus University, Blichers Allé 20, P.O. Box 50, DK-8830, Tjele, Denmark
| | - M H P W Visker
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Q Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H J F van Valenberg
- Dairy Science and Technology Group, Wageningen University and Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - D Sun
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H Bovenhuis
- Animal Breeding and Genomics, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
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Das PP, Krishnan G, Doley J, Bhattacharya D, Deb SM, Chakravarty P, Das PJ. Establishing gene Amelogenin as sex-specific marker in yak by genomic approach. J Genet 2019; 98:7. [PMID: 30945688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yak, an economically important bovine species considered as lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. Amelogenin is an essential protein for tooth enamel which eutherian mammals contain two copies in both X and Y chromosome each. In bovine, the deletion of a fragment of the nucleotide sequence in Y chromosome copy of exon 6 made Amelogenin an excellent sex-specific marker. Thus, an attempt was made to use the gene as an advanced molecular marker of sexing of the yak to improve breeding strategies and reproduction. The present study confirmed that the polymerase chain reaction amplification of the Amelogenin gene with a unique primer is useful in sex identification of the yak. The test is further refined with qPCR validation by quantifying the DNA copy number of the Amelogenin gene in male and female. We observed a high level of sequence polymorphisms of AMELX and AMELY in yak considered as novel identification. These tests can be further extended into several other specialized fields including forensics, meat production and processing, and quality control.
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Affiliation(s)
- P P Das
- Indian Council of Agricultural Research-National Research Centre on Yak, Dirang 790 101, India. ,
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43
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MicroRNA of whole milk samples are not suitable for pregnancy detection in cattle. Gene 2019; 692:17-21. [PMID: 30641211 DOI: 10.1016/j.gene.2018.12.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 11/23/2022]
Abstract
Common pregnancy detection methods in dairy cattle have limits in sensitivity and timing. Thus, we aimed at finding new early pregnancy biomarkers in milk. A previous study in milk cells and skim milk suggested the possible use of several miRNAs for this purpose. In order to make the sampling procedure more convenient for daily use and to include the milk fat into analysis, here, a similar study was repeated using whole fresh milk of days 4, 12, 18 and 21 of pregnancy and non-pregnant day-matched controls, respectively. The microRNAs (miRNAs) were extracted from milk samples and sequenced on a high throughput sequencer (RNAseq). Promising miRNAs were validated via RT-qPCR. Several miRNAs were significantly regulated and six miRNAs (bta-miR-221, bta-miR-223, bta-miR-93, bta-miR-200c, bta-miR-125b and the closely related bta-miR-15b) showed a continuous trend, similar as in the milk cells of the previous study. However, pregnant and cyclic animals could not be separated completely and RT-qPCR validation of the RNAseq data was unsuccessful. Thus, miRNA of bovine whole fresh milk samples failed to show suitability for early pregnancy diagnosis.
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Ibeagha-Awemu EM, Li R, Dudemaine PL, Do DN, Bissonnette N. Transcriptome Analysis of Long Non-Coding RNA in the Bovine Mammary Gland Following Dietary Supplementation with Linseed Oil and Safflower Oil. Int J Mol Sci 2018; 19:E3610. [PMID: 30445766 PMCID: PMC6274745 DOI: 10.3390/ijms19113610] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023] Open
Abstract
This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented with 5% LSO or 5% SFO) of 28 days. Mammary gland biopsies were collected from each animal on day-14 (D-14, control period), D+7 (early treatment period) and D+28 (late treatment period) and were subjected to RNA-Sequencing and subsequent bioinformatics analyses. Functional enrichment of lncRNA was performed via potential cis regulated target genes located within 50 kb flanking regions of lncRNAs and having expression correlation of >0.7 with mRNAs. A total of 4955 lncRNAs (325 known and 4630 novel) were identified which potentially cis targeted 59 and 494 genes in LSO and SFO treatments, respectively. Enrichments of cis target genes of lncRNAs indicated potential roles of lncRNAs in immune function, nucleic acid metabolism and cell membrane organization processes as well as involvement in Notch, cAMP and TGF-β signaling pathways. Thirty-two and 21 lncRNAs were differentially expressed (DE) in LSO and SFO treatments, respectively. Six genes (KCNF1, STARD13, BCL6, NXPE2, HHIPL2 and MMD) were identified as potential cis target genes of six DE lncRNAs. In conclusion, this study has identified lncRNAs with potential roles in mammary gland functions and potential candidate genes and pathways via which lncRNAs might function in response to LSO and SFA.
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Affiliation(s)
- Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
| | - Ran Li
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Pier-Luc Dudemaine
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
| | - Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC H9X 3V9, Canada.
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
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Do DN, Dudemaine PL, Fomenky BE, Ibeagha-Awemu EM. Integration of miRNA and mRNA Co-Expression Reveals Potential Regulatory Roles of miRNAs in Developmental and Immunological Processes in Calf Ileum during Early Growth. Cells 2018; 7:E134. [PMID: 30208606 PMCID: PMC6162677 DOI: 10.3390/cells7090134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/04/2023] Open
Abstract
This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the post-weaning period and miRNA expression characterized by miRNA sequencing, followed by functional analyses. A total of 388 miRNAs, including 81 novel miRNAs, were identified. A total of 220 miRNAs were differentially expressed (DE) between the two periods. The potential functions of DE miRNAs in ileum development were supported by significant enrichment of their target genes in gene ontology terms related to metabolic processes and transcription factor activities or pathways related to metabolism (peroxisomes), vitamin digestion and absorption, lipid and protein metabolism, as well as intracellular signaling. Integration of DE miRNAs and DE mRNAs revealed several DE miRNA-mRNA pairs with crucial roles in ileum development (bta-miR-374a-FBXO18, bta-miR-374a-GTPBP3, bta-miR-374a-GNB2) and immune function (bta-miR-15b-IKBKB). This is the first integrated miRNA-mRNA analysis exploring the potential roles of miRNAs in calf ileum growth and development during early life.
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Affiliation(s)
- Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- Department of Animal Science, McGill University, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada.
| | - Pier-Luc Dudemaine
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
| | - Bridget E Fomenky
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- Département de Sciences Animale, Université Laval, Quebec, QC G1V 0A6, Canada.
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
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Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C. An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles. Vet World 2018; 11:1203-1209. [PMID: 30410222 PMCID: PMC6200572 DOI: 10.14202/vetworld.2018.1203-1209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Aim: Milk is rich in miRNAs - the endogenous small non-coding RNA responsible for gene post-transcriptional silencing. Milk miRNAs were previously evidenced to affect consumer’s immune response. While most studies relied on a few well-characterized milk miRNAs to relate their immunoregulatory roles on target genes among mammals, this study introduced a procedure to predict the target genes based on overall milk miRNA expression profiles - the miRNome data of cow and human. Materials and Methods: Cow and human milk miRNome expression datasets of cow and human milk lipids at 2, 4, and 6 months of lactation periods were preprocessed and predicted for their target genes using TargetScanHuman. Enrichment analysis was performed using target genes to extract the immune-associated gene ontology (GO) terms shared between the two species. The genes within these terms with more than 50 different miRNAs of each species targeting were selected and reviewed for their immunological functions. Results: A total of 146 and 129 miRNAs were identified in cow and human milk with several miRNAs reproduced from other previous reports. Enrichment analysis revealed nine immune-related GO terms shared between cow and human (adjusted p≤0.01). There were 14 genes related to these terms with more than 50 miRNA genes of each species targeting them. These genes were evidenced for their major roles in lymphocyte stimulation and differentiation. Conclusion: A novel procedure to determine mutual immune-associated genes targeted by milk miRNAs was demonstrated using cow and human milk miRNome data. As far as we know, this was the 1st time that milk miRNA target genes had been identified based on such cross-species approach. Hopefully, the introduced strategy should hereby facilitate a variety of cross-species miRNA studies 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, Chonburi, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
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Co-Expression Network Analysis Identifies miRNA⁻mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites. Int J Mol Sci 2018; 19:ijms19092500. [PMID: 30149509 PMCID: PMC6164576 DOI: 10.3390/ijms19092500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/05/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNA) regulate mRNA networks to coordinate cellular functions. In this study, we constructed gene co-expression networks to detect miRNA modules (clusters of miRNAs with similar expression patterns) and miRNA–mRNA pairs associated with blood (triacylglyceride and nonesterified fatty acids) and milk (milk yield, fat, protein, and lactose) components and milk fatty acid traits following dietary supplementation of cows’ diets with 5% linseed oil (LSO) (n = 6 cows) or 5% safflower oil (SFO) (n = 6 cows) for 28 days. Using miRNA transcriptome data from mammary tissues of cows for co-expression network analysis, we identified three consensus modules: blue, brown, and turquoise, composed of 70, 34, and 86 miRNA members, respectively. The hub miRNAs (miRNAs with the most connections with other miRNAs) were miR-30d, miR-484 and miR-16b for blue, brown, and turquoise modules, respectively. Cell cycle arrest, and p53 signaling and transforming growth factor–beta (TGF-β) signaling pathways were the common gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched for target genes of the three modules. Protein percent (p = 0.03) correlated with the turquoise module in LSO treatment while protein yield (p = 0.003) and milk yield (p = 7 × 10−04) correlated with the turquoise model, protein and milk yields and lactose percent (p < 0.05) correlated with the blue module and fat percent (p = 0.04) correlated with the brown module in SFO treatment. Several fatty acids correlated (p < 0.05) with the blue (CLA:9,11) and brown (C4:0, C12:0, C22:0, C18:1n9c and CLA:10,12) modules in LSO treatment and with the turquoise (C14:0, C18:3n3 and CLA:9,11), blue (C14:0 and C23:0) and brown (C6:0, C16:0, C22:0, C22:6n3 and CLA:10,12) modules in SFO treatment. Correlation of miRNA and mRNA data from the same animals identified the following miRNA–mRNA pairs: miR-183/RHBDD2 (p = 0.003), miR-484/EIF1AD (p = 0.011) and miR-130a/SBSPON (p = 0.004) with lowest p-values for the blue, brown, and turquoise modules, respectively. Milk yield, protein yield, and protein percentage correlated (p < 0.05) with 28, 31 and 5 miRNA–mRNA pairs, respectively. Our results suggest that, the blue, brown, and turquoise modules miRNAs, hub miRNAs, miRNA–mRNA networks, cell cycle arrest GO term, p53 signaling and TGF-β signaling pathways have considerable influence on milk and blood phenotypes following dietary supplementation of dairy cows’ diets with 5% LSO or 5% SFO.
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48
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Cai W, Li C, Liu S, Zhou C, Yin H, Song J, Zhang Q, Zhang S. Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows. Front Genet 2018; 9:281. [PMID: 30105049 PMCID: PMC6077245 DOI: 10.3389/fgene.2018.00281] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential. In total, 31 lncRNAs and 18 novel genes were identified to be differentially expressed in high milk protein samples (HP) relative to low milk protein samples (LP), respectively. Differentially expressed lncRNAs were selected to predict target genes through bioinformatics analysis, followed by the integration of differentially expressed mRNA data, gene function, gene ontology (GO) and pathway, genome wide association study (GWAS) and quantitative trait locus (QTL) information, as well as network analysis to further characterize potential interactions. Several lncRNAs were found (such as XLOC_059976) that could be used as candidate markers for milk protein content prediction. This is the first study to perform global expression profiling of lncRNAs and mRNAs related to milk protein traits in dairy cows. These results provide important information and insights into the synthesis of milk proteins, and potential targets for the future improvement of milk quality.
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Affiliation(s)
- Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenghao Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Oliveira GB, Regitano LCA, Cesar ASM, Reecy JM, Degaki KY, Poleti MD, Felício AM, Koltes JE, Coutinho LL. Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle. BMC Genomics 2018; 19:126. [PMID: 29415651 PMCID: PMC5804041 DOI: 10.1186/s12864-018-4514-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology. The aim of this study was to identify differentially expressed (DE) miRNAs, regulatory candidate genes and co-expression networks related to intramuscular fat (IMF) deposition. To achieve this, we used mRNA and miRNA expression data from the Longissimus dorsi muscle of 30 Nelore steers with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF deposition. RESULTS Differential miRNA expression analysis between animals with extreme GEBV values for IMF identified six DE miRNAs (FDR 10%). Functional annotation of the target genes for these microRNAs indicated that the PPARs signaling pathway is involved with IMF deposition. Candidate regulatory genes such as SDHAF4, FBXO17, ALDOA and PKM were identified by partial correlation with information theory (PCIT), phenotypic impact factor (PIF) and regulatory impact factor (RIF) co-expression approaches from integrated miRNA-mRNA expression data. Two DE miRNAs (FDR 10%), bta-miR-143 and bta-miR-146b, which were upregulated in the Low IMF group, were correlated with regulatory candidate genes, which were functionally enriched for fatty acid oxidation GO terms. Co-expression patterns obtained by weighted correlation network analysis (WGCNA), which showed possible interaction and regulation between mRNAs and miRNAs, identified several modules related to immune system function, protein metabolism, energy metabolism and glucose catabolism according to in silico analysis performed herein. CONCLUSION In this study, several genes and miRNAs were identified as candidate regulators of IMF by analyzing DE miRNAs using two different miRNA-mRNA co-expression network methods. This study contributes to the understanding of potential regulatory mechanisms of gene signaling networks involved in fat deposition processes measured in muscle. Glucose metabolism and inflammation processes were the main pathways found in silico to influence intramuscular fat deposition in beef cattle in the integrative mRNA-miRNA co-expression analysis.
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Affiliation(s)
- Gabriella B. Oliveira
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - Aline S. M. Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - Karina Y. Degaki
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Mirele D. Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Andrezza M. Felício
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - James E. Koltes
- Department of Animal Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Luiz L. Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
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Chen Y, Wang J, Yang S, Utturkar S, Crodian J, Cummings S, Thimmapuram J, San Miguel P, Kuang S, Gribskov M, Plaut K, Casey T. Effect of high-fat diet on secreted milk transcriptome in midlactation mice. Physiol Genomics 2017; 49:747-762. [PMID: 29093195 DOI: 10.1152/physiolgenomics.00080.2017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
High-fat diet (HFD) during lactation alters milk composition and is associated with development of metabolic diseases in the offspring. We hypothesized that HFD affects milk microRNA (miRNA) and mRNA content, which potentially impact offspring development. Our objective was to determine the effect of maternal HFD on secreted milk transcriptome. To meet this objective, 4 wk old female ICR mice were divided into two treatments: control diet containing 10% kcal fat and HFD containing 60% kcal fat. After 4 wk on CD or HFD, mice were bred while continuously fed the same diets. On postnatal day 2 (P2), litters were normalized to 10 pups, and half the pups in each litter were cross-fostered between treatments. Milk was collected from dams on P10 and P12. Total RNA was isolated from milk fat fraction of P10 samples and used for mRNA-Seq and small RNA-Seq. P12 milk was used to determine macronutrient composition. After 4 wk of prepregnancy feeding HFD mice weighed significantly more than did the control mice. Lactose and fat concentration were significantly ( P < 0.05) higher in milk of HFD dams. Pup weight was significantly greater ( P < 0.05) in groups suckled by HFD vs. control dams. There were 25 miRNA and over 1,500 mRNA differentially expressed (DE) in milk of HFD vs. control dams. DE mRNA and target genes of DE miRNA enriched categories that were primarily related to multicellular organismal development. Maternal HFD impacts mRNA and miRNA content of milk, if bioactive nucleic acids are absorbed by neonate differences may affect development.
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Affiliation(s)
- Y. Chen
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - J. Wang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - S. Yang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - S. Utturkar
- Bioinformatics Core, Purdue University, West Lafayette, Indiana
| | - J. Crodian
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - S. Cummings
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - J. Thimmapuram
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - P. San Miguel
- Genomics Core at Purdue University, West Lafayette, Indiana
| | - S. Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - M. Gribskov
- Bioinformatics Core, Purdue University, West Lafayette, Indiana
| | - K. Plaut
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - T. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
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