A quantitative PCR method to detect blood microRNAs associated with tumorigenesis in transgenic mice

Are genetic drift and stem cell adherence in laboratory culture issues for cultivated meat production?

Mesenchymal stem cell-based cultivated meat is a promising solution to the ecological and ethical problems posed by traditional meat production, since it exhibits a protein content and composition that is more comparable to original meat proteins than any other source of cultivated meat products, including plants, bacteria, and fungi. Nonetheless, the nature and laboratory behavior of mesenchymal stem cells pose two significant challenges for large-scale production: genetic drift and adherent growth in culture. Culture conditions used in the laboratory expose the cells to a selective pressure that causes genetic drift, which may give rise to oncogene activation and the loss of "stemness." This is why genetic and functional analysis of the cells during culture is required to determine the maximum number of passages within the laboratory where no significant mutations or loss of function are detected. Moreover, the adherent growth of mesenchymal stem cells can be an obstacle for their large-scale production since volume to surface ratio is limited for high volume containers. Multi-tray systems, roller bottles, and microcarriers have been proposed as potential solutions to scale-up the production of adherent cells required for cultivated meat. The most promising solutions for the safety problems and large-scale obstacles for cultivated meat production are the determination of a limit number of passages based on a genetic analysis and the use of microcarriers from edible materials to maximize the volume to surface proportion and decrease the downstream operations needed for cultivated meat production.

Identification of CALU and PALLD as Potential Biomarkers Associated With Immune Infiltration in Heart Failure

Background: Inflammatory activation and immune infiltration play important roles in the pathologic process of heart failure (HF). The current study is designed to investigate the immune infiltration and identify related biomarkers in heart failure patients due to ischemic cardiomyopathy. Methods: Expression data of HF due to ischemic cardiomyopathy (CM) samples and non-heart failure (NF) samples were downloaded from gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) between CM and NF samples were identified. Single sample gene set enrichment analysis (ssGSEA) was performed to explore the landscape of immune infiltration. Weighted gene co-expression network analysis (WGCNA) was applied to screen the most relevant module associated with immune infiltration. The diagnostic values of candidate genes were evaluated by receiver operating curves (ROC) curves. The mRNA levels of potential biomarkers in the peripheral blood mononuclear cells (PBMCs) isolated from 10 CM patients and 10 NF patients were analyzed to further assess their diagnostic values. Results: A total of 224 DEGs were identified between CM and NF samples in GSE5406, which are mainly enriched in the protein processing and extracellular matrix related biological processes and pathways. The result of ssGSEA showed that the abundance of dendritic cells (DC), mast cells, natural killer (NK) CD56dim cells, T cells, T follicular helper cells (Tfh), gammadelta T cells (Tgd) and T helper 2 (Th2) cells were significantly higher, while the infiltration of eosinophils and central memory T cells (Tcm) were lower in CM samples compared to NF ones. Correlation analysis revealed that Calumenin (CALU) and palladin (PALLD) were negatively correlated with the abundance of DC, NK CD56dim cells, T cells, Tfh, Tgd and Th2 cells, but positively correlated with the level of Tcm. More importantly, CALU and PALLD were significantly lower in PBMCs from CM patients compared to NF ones. Conclusion: Our study revealed that CALU and PALLD are potential biomarkers associated with immune infiltration in heart failure due to ischemic cardiomyopathy.

MicroRNAs as a novel class of diagnostic biomarkers for the detection of osteosarcoma: a meta-analysis

MicroRNAs (miRNAs) have been considered as promising diagnostic biomarkers for many diseases, especially for cancers. Numerous studies have reported the value of miRNAs in the diagnosis of osteosarcoma (OS), but the results vary greatly across different studies. Therefore, we conducted this meta-analysis to assess the prospective diagnostic value of miRNAs in diagnosing OS. All relevant articles from prior to July 28, 2017 were selected from PubMed, EMBASE, Web of Science, Cochrane Library, Chinese National Knowledge Infrastructure, and Wan-fang databases. The Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was performed to assess the quality of each article. A random-effects model was used to pool the sensitivity and specificity of the positive likelihood ratio (PLR), negative likelihood ratio (NLR) and, diagnostic odds ratio (DOR) together with the area under the curve (AUC) to evaluate diagnostic values. Seventeen studies comprising 2,214 OS patients and 1,534 healthy humans were included in our meta-analysis. The pooled estimations indicated that the miRNAs had a high accuracy for diagnosing OS, with a sensitivity of 0.82, specificity of 0.88, PLR of 10.96, NLR of 0.20, DOR of 54.55, and AUC of 0.93. Twenty-five miRNAs were differentially expressed in OS, including 17 upregulated and 8 downregulated. These miRNAs were correlated with survival time, tumor size, cell differentiation, tumor node metastasis staging, metastasis, tumor/cell invasion, pathological type, and response to radiotherapy and chemotherapy. Several different miRNAs are expressed in OS, and some of them might be potential biomarkers for the early diagnosis of OS.

Detecting Tumor Metastases: The Road to Therapy Starts Here

Metastasis is the complex process by which primary tumor cells migrate and establish secondary tumors in an adjacent or distant location in the body. Early detection of metastatic disease and effective therapeutic options for targeting these detected metastases remain impediments to effectively treating patients with advanced cancers. If metastatic lesions are identified early, patients might maximally benefit from effective early therapeutic interventions. Further, monitoring patients whose primary tumors are effectively treated for potential metastatic disease onset is also highly valuable. Finally, patients with metastatic disease can be monitored for efficacy of specific therapeutic interventions through effective metastatic detection techniques. Thus, being able to detect and visualize metastatic lesions is key and provides potential to greatly improve overall patient outcomes. In order to achieve these objectives, researchers have endeavored to mechanistically define the steps involved in the metastatic process as well as ways to effectively detect metastatic progression. We presently overview various preclinical and clinical in vitro and in vivo assays developed to more efficiently detect tumor metastases, which provides the foundation for developing more effective therapies for this invariably fatal component of the cancerous process.

miRNA for diagnosis and clinical implications of human hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies, as a result of being asymptomatic at early stage, subsequent late clinical confirmation and poor prognosis. It is urgent to search more accurate biomarkers for diagnosing early HCC and predicting prognosis. Many factors participate in liver carcinogenesis, including dysregulation of miRNA. miRNA were endogenously expressed non-coding single-stranded small RNA with 19-25 nucleotides. Accumulating evidences have showed that miRNA from circulation and solitary tumors may be useful to classify the differentiation degree and stages of HCC, detect the hepatitis B/C virus-related HCC, and predict the survival rate after surgical resection or orthotopic liver transplantation. In this review, we summarize dysregulated miRNA, their roles in diagnosis and clinical implications of HCC.

Clinical significance of serum miR-223, miR-25 and miR-375 in patients with esophageal squamous cell carcinoma

Changes in the expression profiles of microRNAs (miRNAs) have been found in many cancers. The study was aimed to investigate the expression of miR-25, miR-223, and miR-375 in the serum of patients with esophageal squamous cell carcinoma (ESCC) and its effect on survival outcome. We examined the expression levels of miR-25, miR-223, and miR-375 in 20 pairs of ESCC cancer and matched paracancerous tissues, serum samples from 94 healthy volunteers and 194 patients with ESCC using quantitative reverse transcription polymerase chain reaction, and analyzed the relationship between expressions of serum miR-25, miR-223, and miR-375 and ESCC clinicopathological parameters as well as survival. Expressions of miR-25 and miR-223 were significantly increased in ESCC tissues compared with paracancerous tissues (P = 0.008 and 0.009, respectively), whereas the expression of miR-375 was significantly decreased in ESCC tissues compared with paracancerous tissues (P = 0.006). Expressions of serum miR-25 and miR-223 were significantly higher in ESCC patients than those in healthy controls, and, inversely, expression of serum miR-375 was significantly lower in ESCC patients than those in healthy controls (P = 0.007). High expression of serum miR-25 was significantly associated with lymph node metastasis (P = 0.01). Survival analysis showed that high expression of serum miR-223 and low expression of serum miR-375 were associated with poor survival in ESCC patients [hazard ratio (HR) = 1.717, 95% confidence intervals (CI) 1.139-2.588, P = 0.01; HR = 1.750, 95% CI 1.111-2.756, P = 0.016, respectively). Furthermore, Patients with high miR-223 and low miR-375 expression had higher risk of death than those with low miR-223 and high miR-375 expression (HR = 3.599, 95% CI 1.800-7.195, P = 2.92 × 10(-4)). In conclusion, miR-25, miR-223, and miR-375 were abnormally expressed in ESCC tissues and sera. Serum miR-223 and miR-375 are potential prognostic biomarkers for ESCC.

Systemically circulating viral and tumor-derived microRNAs in KSHV-associated malignancies

MicroRNAs (miRNAs) are stable, small non-coding RNAs that modulate many downstream target genes. Recently, circulating miRNAs have been detected in various body fluids and within exosomes, prompting their evaluation as candidate biomarkers of diseases, especially cancer. Kaposi's sarcoma (KS) is the most common AIDS-associated cancer and remains prevalent despite Highly Active Anti-Retroviral Therapy (HAART). KS is caused by KS-associated herpesvirus (KSHV), a gamma herpesvirus also associated with Primary Effusion Lymphoma (PEL). We sought to determine the host and viral circulating miRNAs in plasma, pleural fluid or serum from patients with the KSHV-associated malignancies KS and PEL and from two mouse models of KS. Both KSHV-encoded miRNAs and host miRNAs, including members of the miR-17–92 cluster, were detectable within patient exosomes and circulating miRNA profiles from KSHV mouse models. Further characterization revealed a subset of miRNAs that seemed to be preferentially incorporated into exosomes. Gene ontology analysis of signature exosomal miRNA targets revealed several signaling pathways that are known to be important in KSHV pathogenesis. Functional analysis of endothelial cells exposed to patient-derived exosomes demonstrated enhanced cell migration and IL-6 secretion. This suggests that exosomes derived from KSHV-associated malignancies are functional and contain a distinct subset of miRNAs. These could represent candidate biomarkers of disease and may contribute to the paracrine phenotypes that are a characteristic of KS.

Circulating microRNAs (miRNAs), such as those found in exosomes, have emerged as diagnostic tools and hold promise as minimally invasive, stable biomarkers. Transfer of tumor-derived exosomal miRNAs to surrounding cells may be an important form of cellular communication. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), the most common AIDS-defining cancer worldwide. Here, we survey systemically circulating miRNAs and reveal potential biomarkers for KS and Primary Effusion Lymphoma (PEL). This expands previous tissue culture studies by profiling clinical samples and by using two new mouse models of KSHV tumorigenesis. Profiling of circulating miRNAs revealed that oncogenic and viral miRNAs were present in exosomes from KS patient plasma, pleural effusions and mouse models of KS. Analysis of human oncogenic miRNAs, including the well-known miR-17-92 cluster, revealed that several miRNAs were preferentially incorporated into exosomes in our KS mouse model. Gene ontology analysis of upregulated miRNAs showed that the majority of pathways affected were known targets of KSHV signaling pathways. Transfer of these oncogenic exosomes to immortalized hTERT-HUVEC cells enhanced cell migration and IL-6 secretion. These circulating miRNAs and KS derived exosomes may therefore be part of the paracrine signaling mechanism that mediates KSHV pathogenesis.

Distinct microRNA profiles are associated with the severity of hepatitis C virus recurrence and acute cellular rejection after liver transplantation

Recurrent hepatitis C virus (HCV) infection is associated with accelerated fibrosis rates after liver transplantation (LT) and is the leading cause of graft failure. Furthermore, distinguishing recurrent HCV from acute cellular rejection (ACR) can be problematic, and this can lead to inappropriate treatments and adverse outcomes. We hypothesized that intragraft microRNA (miRNA) expression profiles could distinguish the severity of recurrent HCV and differentiate recurrent HCV from ACR. We established meticulously matched post-LT patient cohorts in order to derive robust global miRNA expression profiles and minimize the impact of variables known to influence HCV recurrence. These cohorts consisted of patients with slow HCV fibrosis progression (Ishak stage < F2), fast HCV fibrosis progression (Ishak stage ≥ F2), ACR, and nonviral etiologies. We found increased intragraft expression of miRNA-146a, miRNA-19a, miRNA-20a, and miRNA-let7e in slow progressors versus fast progressors, and we validated these findings with quantitative PCR. This miRNA network regulates the expression of cardinal genes implicated in promoting antifibrogenic, antiangiogenic, and anti-inflammatory pathways. miRNA-19a and miRNA-20a were also specifically detected in the serum of slow progressors. Furthermore, intragraft miRNA expression distinguished fast HCV progression from ACR. Here, changes in the expression of key miRNAs regulating fibrogenic and angiogenic pathways were associated with fast HCV progression. We demonstrate specific miRNA expression signatures that discriminate the rates of fibrosis progression in patients with recurrent HCV, and we distinguish recurrent HCV from ACR after LT. A pathway analysis indicates that specific miRNAs may play a regulatory role in these processes. Selected miRNAs may serve as intragraft and serum biomarkers for recurrent HCV after LT and help to distinguish between ACR and recurrent HCV.

MicroRNAs and liver disease

Posttranscriptional regulation of gene expression is now recognized as an important contributor to disease pathogenesis, whose mechanisms include alterations in the function of stability and translational elements within both coding and noncoding regions of messenger RNA. A major component in this regulatory paradigm is the binding both to RNA stability as well as to translational control elements by microRNAs (miRNAs). miRNAs are noncoding endogenously transcribed RNAs that undergo a well-characterized series of processing steps that generate short single-stranded (∼20-22) RNA fragments that bind to complementary regions within a range of targets and in turn lead to mRNA degradation or attenuated translation as a result of trafficking to processing bodies. This article will highlight selected advances in the role of miRNAs in liver disease including nonalcoholic fatty liver disease, viral hepatitis, and hepatocellular carcinoma and will briefly discuss the utility of miRNAs as biomarkers of liver injury and neoplasia.

dbDEMC: a database of differentially expressed miRNAs in human cancers

Background

MicroRNAs (miRNAs) are small noncoding RNAs about 22 nt long that negatively regulate gene expression at the post-transcriptional level. Their key effects on various biological processes, e.g., embryonic development, cell division, differentiation and apoptosis, are widely recognized. Evidence suggests that aberrant expression of miRNAs may contribute to many types of human diseases, including cancer. Here we present a database of differentially expressed miRNAs in human cancers (dbDEMC), to explore aberrantly expressed miRNAs among different cancers.

Results

We collected the miRNA expression profiles of 14 cancer types, curated from 48 microarray data sets in peer-reviewed publications. The Significance Analysis of Microarrays method was used to retrieve the miRNAs that have dramatically different expression levels in cancers when compared to normal tissues. This database provides statistical results for differentially expressed miRNAs in each data set. A total of 607 differentially expressed miRNAs (590 mature miRNAs and 17 precursor miRNAs) were obtained in the current version of dbDEMC. Furthermore, low-throughput data from the same literature were also included in the database for validation. An easy-to-use web interface was designed for users. Annotations about each miRNA can be queried through miRNA ID or miRBase accession numbers, or can be browsed by different cancer types.

Conclusions

This database is expected to be a valuable source for identification of cancer-related miRNAs, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. All the information is freely available through http://159.226.118.44/dbDEMC/index.html.