Placental expression of RNU44, RNU48 and miR-16-5p: stability and relations with fetoplacental growth

Kochhar, P.; Dwarkanath, Pratibha; Ravikumar, Gayatri; Thomas, Annie; Crasta, Julian; Thomas, Tinku; Kurpad, Anura V; Mukhopadhyay, Arpita

doi:10.1038/s41430-021-01003-3

Cited by 5 publications

(3 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To identify the stability of expression of the 4 potential reference genes ( ACTB, PPIB, YWHAZ , and GAPDH ) in PBMCs from all study samples and separately in NGT and T2DM groups, the raw Ct values were assessed using the RefFinder tool 36 . The raw Ct values were directly imported into the RefFinder tool, which takes into account the stability rankings generated by four algorithms: GeNORM 37 , 38 , NormFinder 39 , BestKeeper 40 , and delta Ct 41 to provide a comprehensive stability ranking to the potential reference genes 36 , 42 . The stability of the 4 potential reference genes, examined using the RefFinder tool, for all samples (n = 86), NGT (n = 47), and T2DM (n = 39) groups is depicted in Fig.…”

Section: Resultsmentioning

confidence: 99%

Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients

Hazarika

Nongkhlaw

Mukhopadhyay

2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

Reference genes are obligatory for accurate normalization of mRNA transcript levels across samples and experimental conditions in Real Time-polymerase chain reaction (qRT-PCR) based quantitative gene expression assays. Selection of stably expressed reference genes is therefore crucial for ensuring reproducibility of such assays. However, there is a complete dearth of data on stability of commonly used reference genes in Peripheral Blood Mononuclear Cells (PBMCs) from Type 2 diabetes mellitus (T2DM) patients. We have evaluated the gene expression stability of 4 widely used reference genes (Beta-actin, ACTB; Peptidylprolyl Isomerase B, PPIB; Tyrosine 3 Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Zeta, YWHAZ; and Glyceraldehyde-3-Phosphate Dehydrogenase, GAPDH); in PBMCs from 39 T2DM patients and 47 normoglycemic (NGT) subjects. ACTB and YWHAZ were found to be the most stable genes in PBMCs from T2DM patients and therefore, can be recommended as suitable reference genes in similar contexts. GAPDH and PPIB expressions were not stable in PBMCs from T2DM patients. On using ACTB and YWHAZ as reference genes for measuring relative expression of GAPDH and PPIB in these subjects, relative GAPDH expression was found to be significantly lower in female T2DM patients, compared to female NGT subjects [GAPDH relative normalization unit (RNU): female T2DM (n = 19), median (Q1, Q3): 9.0 (8.1, 9.9); female NGT (n = 18): median (Q1, Q3): 10.1 (9.1, 11.0); P = 0.034]. Dysregulation of GAPDH in PBMCs from female T2DM patients could be associated with sex-specific differences in pathogenesis and outcomes of T2DM.

show abstract

Section: Resultsmentioning

confidence: 99%

Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients

Hazarika

Nongkhlaw

Mukhopadhyay

2023

Sci Rep

Self Cite

View full text Add to dashboard Cite

show abstract

“…RNU44 is encoded by the intron of growth arrest specific 5 (GAS5) gene. As a snoRNA, its performance as reference gene for quantification of miRNA had been demonstrated in a series of human physiological and pathological conditions, including fetoplacental growth [ 35 , 36 ], cartilage development [ 37 ], osteoblast differentiation [ 38 ], immunoglobulin A nephropathy [ 39 ], and tumors (pituitary tumors [ 40 ], prostate tumors [ 41 ], kidney cancer [ 42 ], and breast cancer [ 43 ]). Meanwhile, RNU44 has also shown to be associated with certain tumors [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of RNU44 as an Endogenous Reference Gene for Normalizing Cell-Free RNA in Tuberculosis

et al. 2022

Open Forum Infectious Diseases

View full text Add to dashboard Cite

Background Normalization of cell-free RNA (cf-RNA) concentration can be affected by variable experimental conditions and thus impact the performance of their diagnostic potential. Our study aimed to identify appropriate endogenous reference genes for cf-RNA biomarker evaluation in the diagnosis of tuberculosis (TB). Methods Subjects consisting of patients with TB with and without malignancy, patients with pneumonia, and healthy controls were recruited. Candidate reference genes were screened and identified by literature reviewing and RNA-Seq analysis. Expression levels of the candidate genes were determined by reverse-transcription real-time quantitative polymerase chain reaction in plasma from patients with TB and healthy controls. The stability of gene expression was assessed by geNorm, NormFinder, BestKeeper, the Comparative Delta Ct method, and RefFinder. Differential expression of 2 small RNAs (sRNAs) encoding by genome of Mycobacterium tuberculosis in plasma of patients with TB were determined by both absolute quantification and relative quantification with candidate reference genes. Results According to the stability ranking analyzed with the 5 computational programs, the top 4 candidates—miR-93, RNU44, miR-16, and glyceraldehyde 3-phosphate dehydrogenase—were used to normalize the transcript levels of 2 mycobacterial sRNAs, MTS2823 and MTS1338, which were observed to have higher copy numbers in the plasma of patients with TB. Normalization with RNU44 displayed significantly higher levels of the 2 M tuberculosis sRNAs in the patients’ plasma than those of healthy controls. Conclusions RNU44 was demonstrated as a proper endogenous gene for cf-RNA normalization in TB diagnosis.

show abstract

“…Up to now, aberrant expression of regulatory miRNAs has been associated with the initiation and progression of various pathological processes ( 37 – 39 ). Recent evidence also highlights their regulatory roles in human fetoplacental growth ( 40 – 43 ). Some of them, such as miR-214 and miR-378, have also regulated the Hh signaling pathway ( 44 – 46 ).…”

Section: Introductionmentioning

confidence: 99%

WNT5A, β‑catenin and SUFU expression patterns, and the significance of microRNA deregulation in placentas with intrauterine growth restriction

et al. 2022

View full text Add to dashboard Cite

Placental insufficiency is a common cause of intrauterine growth restriction (IUGR). It affects ~10% of pregnancies and increases fetal and neonatal morbidity and mortality. Although Wnt and Hh pathways are crucial for embryonic development and placentation, their role in the pathology of IUGR is still not sufficiently explored. The present study analyzed the expression of positive regulators of the Wnt pathway, WNT5A and β-catenin, and the expression of the Hh pathway negative regulator suppressor of fused (SUFU). Immunohistochemical and reverse transcription-quantitative PCR (RT-qPCR) assays were performed on 34 IUGR and 18 placental tissue samples from physiologic singleton-term pregnancies. Epigenetic mechanisms of SUFU gene regulation were also investigated by methylation-specific PCR analysis of its promoter and RT-qPCR analysis of miR-214-3p and miR-378a-5p expression. WNT5A protein expression was higher in endothelial cells of placental villi from IUGR compared with control tissues. That was also the case for β-catenin protein expression in trophoblasts and endothelial cells and SUFU protein expression in trophoblasts from IUGR placentas. The SUFU gene promoter remained unmethylated in all tissue samples, while miR-214-3p and miR-378a-5p were downregulated in IUGR. The present results suggested altered Wnt and Hh signaling in IUGR. DNA methylation did not appear to be a mechanism of SUFU regulation in the pathogenesis of IUGR, but its expression could be regulated by miRNA targeting.

show abstract

Placental expression of RNU44, RNU48 and miR-16-5p: stability and relations with fetoplacental growth

Cited by 5 publications

References 36 publications

Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients

Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients

Identification of RNU44 as an Endogenous Reference Gene for Normalizing Cell-Free RNA in Tuberculosis

WNT5A, β‑catenin and SUFU expression patterns, and the significance of microRNA deregulation in placentas with intrauterine growth restriction

Contact Info

Product

Resources

About