Identification of the MicroRNA Repertoire in TLR-Ligand Challenged Bubaline PBMCs as a Model of Bacterial and Viral Infection

Singh, Jasdeep; Mukhopadhyay, C.S.; Kaur, Simarjeet; Malhotra, Purnima; Sethi, R. S.; Choudhary, Ratan K.

doi:10.1371/journal.pone.0156598

Cited by 13 publications

(13 citation statements)

References 45 publications

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“…Also, the mature and mature-star miRNA study can help detecting the most abundant change at 5`or 3`end or arm switching. Earlier, we have studied the expression of these miRNAs in TLR stimulated and non-stimulated PBMCs and recognized that some miRNAs were highly expressed while others were moderately expressed in both treatment and control groups [8]. This is the first report on experimental identification and validation of bubaline miRNAs.…”

Section: Panther Classification Of Mirna-target Gene Productsmentioning

confidence: 82%

“…However, reports on the empirical identification of miRNAs in livestock are limited. Available literature on RNAi-related works in the "black-gold" livestock-species Buffalo (Bubalus bubalis) is not available, except for the single research paper from our laboratory [8], where a total of 290 miRNAs were identified in bubaline-PBMCs out of which 130 were categorized as 'putative novel miRNAs'.…”

Section: Introductionmentioning

confidence: 99%

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Discovery of isomiRs in PBMCs of diseased vis-à-vis healthy Indian water buffaloes

Dhanoa

Singh

et al. 2019

ExRNA

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Background: MicroRNA isoforms are the variants of a canonical miRNA-sequence with alteration at the 3`or 5t ermini due to addition, deletion and/or substitution of nucleotide. The present study aims at identifying the isomiRs of the expressed miRNAs in peripheral blood mononuclear cells (PBMCs) of diseased vis-à-vis healthy buffaloes, vis-à-vis exploring the molecular pathways of the predicted target genes of the isomiRs/miRNAs. Four groups of experimental animals (adult, male or female) were included in the study: a) Brucellosis (Murrah breed), b) Paratuberculosis or Johne's disease (Murrah breed); c) Brucellosis (Nili-Ravi breed) and d) control group of healthy buffaloes of the Murrah breed. The small RNA (sRNA) samples, extracted from PBMCs of each of the four groups, pooled into four samples and then were subjected to next-generation sequencing (Ion-Torrent PGM™ platform). Results: The NGS data were analyzed using the miRanalyzer tool and R-programming to identify the differentially expressed (up and down-regulated (fold change ratio > 2)) miRNAs (exhibiting isomiRs and uniquely expressed miRNAs having isomiRs) of each of the three disease-groups as compared to the healthy-Murrah group. The target genes of these selected differentially and uniquely expressed miRNA & isomiRs were predicted using three different online tools (TargetScan, PicTar, and miRDB). These target genes were analyzed to determine their role in systems biology. We identified 153, 125 and 139 isomiR-exhibiting miRNAs that were common in those three experimental groups (healthy vs. Brucellosis-Murrah, Johne's disease-Murrah, and Brucellosis-Nili-Ravi, respectively). Gene ontology and pathway analyses of the target genes (Panther classification system) yielded several biological hits. Functional classification of the target genes indicated that these target genes were involved in different systems biology related functions like molecular binding, enzyme modulation, signal modulation, etc. The specificity of function was varying in the three experimental groups. Conclusion: We are presenting the first report on the identification of isomiRs and functional classification of the target genes in water buffaloes. The results revealed that isomiRs may be involved in the biological processes and can be used in disease diagnosis.

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Section: Panther Classification Of Mirna-target Gene Productsmentioning

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Discovery of isomiRs in PBMCs of diseased vis-à-vis healthy Indian water buffaloes

Dhanoa

Singh

et al. 2019

ExRNA

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“…They found that the abundantly expressed miRNAs include bta-miR-103, bta-miR-19b, -191 -29b, -15a, -19a, -30d, -30b-5p and members of the let family (let 7a-5p, let 7g and let 7f) in LPS-and CpG-treated and control samples, while bta-miR-21-5p was highly expressed in LPS-treated PBMCs only. 20 In our sequencing libraries, four Figure 5. Quantitative PCR was performed to verify expressions of the five miRNAs (ssc-miR-122, ssc-miR-129b, ssc-miR-152, ssc-miR-17-5p and ssc-miR-144) in RNA sequencing.…”

Section: Discussionmentioning

confidence: 99%

Analysis of microRNA expression profiles in porcine PBMCs after LPS stimulation

Zhang

Huang

et al. 2020

Innate Immun

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In the present study, we used microRNA (miRNA) sequencing to discover and explore the expression profiles of known and novel miRNAs in 1000 ng/ml LPS stimulated for 8 h vis-à-vis non-stimulated (i.e. control) PBMCs isolated from the blood of healthy pigs. A total of 291 known miRNAs were bio-computationally identified in porcine PBMCs, and 228 novel miRNAs (not enlisted in the swine mirBase) were identified. Among these miRNAs, ssc-miR-148a-3p, ssc-let-7g, ssc-let-7f, 3_8760, ssc-miR-26a, ssc-miR-451, ssc-miR-21, ssc-miR-30d, ssc-miR-99a and ssc-miR-103 were the top 10 most abundant miRNAs in porcine PBMCs. Through miRNA differential analysis combined with quantitative PCR, we found the expressions of ssc-miR-122, ssc-miR-129b, ssc-miR-17-5p and ssc-miR-152 were significantly changed in porcine PBMCs after LPS stimulation. Furthermore, targets prediction and function analysis indicated a significant enrichment in gene ontology functional categories related to diseases, immunity and inflammation. In conclusion, this study on profiling of miRNAs expressed in LPS-stimulated PBMCs provides an important reference point for future studies on regulatory roles of miRNAs in porcine immune system.

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“…Recently our lab explored the differentially expressed miRNAs in PBMCs culture, obtained from blood of Indian water buffaloes, challenged with ligands of toll like receptors viz. LPS, poly I:C, and CpG ODN to mimic the microbial infections and identified 160 mature and 130 novel miRNAs [58].…”

Section: Discussionmentioning

confidence: 99%

MicroRNA expression profiling in PBMCs of Indian water Buffalo (Bubalus bubalis) infected with Brucella and Johne’s disease

Singh

Dhanoa

Choudhary

et al. 2020

ExRNA

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Background: MicroRNAs play key roles in host-pathogen-interactions and disease pathogenesis. Our aim was to characterize the differentially expressed miRNAs in the blood cells of diseased (Brucellosis-positive, Johne's diseasepositive) and healthy-water buffaloes. The pooled small-RNA samples of each group were sequenced on Ion Torrent Personal Genome Machine (PGM) sequencer and the data were analyzed for differential expression. Results: Here we identified 274 known miRNAs with bovine homologs and 36 novel mature-star miRNAs from the sequnces of small RNA libraries. Overall 195 miRNAs were common to all the three groups. Certain miRNAs such as bta-miR-21-5p, −26a, −29a/b, −30d − 103, − 140, − 150, − 191, − 374, − 1434-5p,-1260b, − 2484 and let-7 members were abundantly expressed in diseased groups. Bta-miR-1434-5p, − 188, −200c were up-regulated (> 1.5 folds) while bta-miR-27a-5p, −34b and-2285x were down-regulated (> 100 folds) in Brucellosis group. In Johne's Disease group, only 3 miRNAs (bta-miR-1434-5p, − 2340 and − 2484) were up-regulated (> 1.5 folds). The functional classification of miRNA target genes into gene ontology (GO) terms indicated their involvement in innate immunity and cellular process of disease pathogenesis. Expression profile of four differentially expressed miRNAs (bta-miR-9-5p, − 677, − 331-3p and − 2440) and eight predicted target-genes were validated through reverse transcriptase qPCR. Conclusion: This study provides a valuable frame of reference for elucidation of regulatory roles of miRNAs associated with disease pathogenesis in water buffaloes as well as identification of miRNA biomarkers for disease diagnosis and treatment.

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Identification of the MicroRNA Repertoire in TLR-Ligand Challenged Bubaline PBMCs as a Model of Bacterial and Viral Infection

Cited by 13 publications

References 45 publications

Discovery of isomiRs in PBMCs of diseased vis-à-vis healthy Indian water buffaloes

Discovery of isomiRs in PBMCs of diseased vis-à-vis healthy Indian water buffaloes

Analysis of microRNA expression profiles in porcine PBMCs after LPS stimulation

MicroRNA expression profiling in PBMCs of Indian water Buffalo (Bubalus bubalis) infected with Brucella and Johne’s disease

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