Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids

Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction

Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.

Development of circulating microRNA-based biomarkers for medical decision-making: a friendly reminder of what should NOT be done

Circulating cell-free microRNAs (miRNAs) represent a major reservoir for biomarker discovery. Unfortunately, their implementation in clinical practice is limited due to a profound lack of reproducibility. The great technical variability linked to major pre-analytical and analytical caveats makes the interpretation of circulating cell-free miRNA data challenging and leads to inconsistent findings. Additional efforts directed to standardization are fundamental. Several well-established protocols are currently used by independent groups worldwide. Nonetheless, there are some specific aspects in specimen collection and processing, sample handling, miRNA quantification, and data analysis that should be considered to ensure reproducibility of results. Here, we have addressed this challenge using an alternative approach. We have highlighted and discussed common pitfalls that negatively impact the robustness of circulating miRNA quantification and their application for clinical decision-making. Furthermore, we provide a checklist usable by investigators to facilitate and ensure the control of the whole miRNA quantification and analytical process. We expect that these recommendations improve the reproducibility of findings, and ultimately, facilitate the incorporation of circulating miRNA profiles into clinical practice as the next generation of disease biomarkers.

Nasturtium officinale L. and metformin alleviate the estradiol- induced polycystic ovary syndrome with synergistic effects through modulation of Bax/Bcl-2/p53/caspase-3 signaling pathway and anti-inflammatory and anti-oxidative effects

Polycystic ovary syndrome (PCOS) is one of the most common causes of infertility in women, which is associated with metabolic, hereditary and hormonal disorders. The aim of this study was to evaluate the therapeutic effects of Nasturtium officinale L. (N. officinale) on biochemical and molecular parameters in estradiol-induced PCOS in rats. Seventy Wistar rats in 7 groups (n = 10) were randomly assigned to normal (NC), PCOS, metformin (MET - 300 mg/kg), N. officinale (50 and 100 mg/kg) and co-treatment with MET and N. officinale groups. After 21 days of treatment, biochemical parameters levels of estrogen, LH and FSH along with serum levels of (IL-6 and IL-1β cytokines) and serum antioxidant parameters (enzymatic activity of catalase and superoxide dismutase) were measured. Finally, by measuring the expression of apoptosis related genes (Bax/Bcl-2/p53/caspase-3) with the help of real-time PCR and the expression of p53 with the help of immunohistochemistry in ovarian cells. N. officinale modulates hormones through its hypothalamic-pituitary-gonadal pathway with its synergistic effects along with MET. Also, in co-treatment groups (MET and N. officinale), the activity of serum antioxidant enzymes increased and also the serum level of inflammatory cytokines decreased. N. officinale, along with MET, amplified the Bax/Bcl2/p53/caspase-3 pathways, which eventually increased the number of p53 positive cells. These findings indicate that N. officinale extract along with MET can improve the physiological function of the ovaries in PCOS-induced disorders. PRACTICAL APPLICATIONS: Polycystic ovary syndrome (PCOS) is one of the most common causes of infertility in women, which is associated with metabolic, hereditary and hormonal disorders. The extract of Nasturtium officinale L. was able to intensify mitochondrial apoptotic pathway in cystic follicles and prevent their formation. It seems that pro-drugs containing N. officinale along with effective commercial drugs in PCOS can help ovulation and fertility in woman with this disease.

Mesenchymal Stem Cell Exosomes Derived from Feline Adipose Tissue Enhance the Effects of Anti-Inflammation Compared to Fibroblasts-Derived Exosomes

Adipose tissue-derived mesenchymal stem cells (AD-MSCs) release extracellular vesicles such as exosomes, apoptotic bodies, and microparticles. In particular, exosomes are formed inside cells via multivesicular bodies (MVBs), thus their protein, DNA, and RNA content are similar to those of the parent cells. Exosome research is rapidly expanding, with an increase in the number of related publications observed in recent years; therefore, the function and application of MSC-derived exosomes could emerge as cell-free therapeutics. Exosomes have been isolated from feline AD-MSCs and feline fibroblast cell culture media using ultracentrifugation. Feline exosomes have been characterized by FACS, nanoparticle tracking analysis, and transmission electron microscopy imaging. Moreover, cytokine levels were detected by sandwich enzyme-linked immunosorbent assay in exosomes and LPS-induced THP-1 macrophages. The size of the isolated exosomes was that of a typical exosome, i.e., approximately 150 nm, and they expressed tetraspanins CD9 and CD81. The anti-inflammatory factor IL-10 was increased in feline AD-MSC-derived exosomes. However, pro-inflammatory factors such as IL-1β, IL-8, IL-2, RANTES, and IFN-gamma were significantly decreased in feline AD-MSC-derived exosomes. This was the first demonstration that feline AD-MSC-derived exosomes enhance the inflammatory suppressive effects and have potential for the treatment of immune diseases or as an inflammation-inhibition therapy.

Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

Dogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

Circulating microRNA as biomarkers of canine mammary carcinoma in dogs

Background

Differentiating benign from canine malignant mammary tumors requires invasive surgical biopsy. Circulating microRNAs (miRNA) may represent promising minimally invasive cancer biomarkers in people and animals.

Objectives

To evaluate the serum mRNA profile between dogs with and without mammary carcinoma, and to determine if any of these markers have prognostic significance.

Animals

Ten healthy client‐owned female dogs (5 intact, 5 spayed) and 10 dogs with histologically confirmed mammary carcinoma were included; 9 were client‐owned, whereas 1 was a research colony dog.

Methods

Retrospective study. Serum miRNA was evaluated by RNA deep‐sequencing (RNAseq) and digital droplet PCR (dPCR).Expression of candidate biomarkers miR‐18a, miR‐19b, miR‐29b, miR‐34c, miR‐122, miR‐125a, and miR‐181a was compared with clinical characteristics, including grade, metastasis, and survival.

Results

452 unique serum miRNAs were detected by RNAseq. Sixty‐five individual miRNAs were differentially expressed (>±1.5‐fold) and statistically significant between groups. Serum miR‐19b (P = .003) and miR‐125a (P < .001) were significantly higher in the mammary carcinoma group by dPCR. Both had high accuracy based on receiver operator characteristic area under the curve (0.930 for miR‐125a; 0.880 for miR‐19b). Circulating miR‐18a by RNAseq was significantly higher in mammary carcinoma dogs with histologic evidence of lymphatic invasion (P = 0.03). There was no significant association with any miRNA and survival or inflammatory status.

Conclusions and Clinical Importance

Circulating miRNAs are differentially expressed in dogs with mammary carcinoma. Serum miR‐19b and miR‐18a represent candidate biomarkers for diagnosis and prognosis, respectively.