Genome-wide differential expression profiling of long non-coding RNAs in FOXA2 knockout iPSC-derived pancreatic cells

BACKGROUND

Our recent studies have demonstrated the crucial involvement of FOXA2 in the development of human pancreas. Reduction of FOXA2 expression during the differentiation of induced pluripotent stem cells (iPSCs) into pancreatic islets has been found to reduce α-and β-cell masses. However, the extent to which such changes are linked to alterations in the expression profile of long non-coding RNAs (lncRNAs) remains unraveled.

METHODS

Here, we employed our recently established FOXA2-deficient iPSCs (FOXA2-/- iPSCs) to investigate changes in lncRNA profiles and their correlation with dysregulated mRNAs during the pancreatic progenitor (PP) and pancreatic islet stages. Furthermore, we constructed co-expression networks linking significantly downregulated lncRNAs with differentially expressed pancreatic mRNAs.

RESULTS

Our results showed that 442 lncRNAs were downregulated, and 114 lncRNAs were upregulated in PPs lacking FOXA2 compared to controls. Similarly, 177 lncRNAs were downregulated, and 59 lncRNAs were upregulated in islet cells lacking FOXA2 compared to controls. At both stages, we observed a strong correlation between lncRNAs and several crucial pancreatic genes and TFs during pancreatic differentiation. Correlation analysis revealed 12 DE-lncRNAs that strongly correlated with key downregulated pancreatic genes in both PPs and islet cell stages. Selected DE-lncRNAs were validated using RT-qPCR.

CONCLUSIONS

Our data indicate that the observed defects in pancreatic islet development due to the FOXA2 loss is associated with significant alterations in the expression profile of lncRNAs. Therefore, our findings provide novel insights into the role of lncRNA and mRNA networks in regulating pancreatic islet development, which warrants further investigations. Video Abstract.

Expression profiling of N6-methyladenosine-modified mRNA in PC12 cells in response to unconjugated bilirubin

BACKGROUND

Abnormal methylation of N6-methyladenosine (m6A) is reportedly associated with central nervous system disorders. However, the role of m6A mRNA methylation in unconjugated bilirubin (UCB) neurotoxicity requires further research.

METHODS

Rat pheochromocytoma PC12 cells treated with UCB were used as in vitro models. After the PC12 cells were treated with UCB (0, 12, 18, and 24 µM) for 24 h, the total RNA m6A levels were measured using an m6A RNA methylation quantification kit. The expression of m6A demethylases and methyltransferases was detected through western blotting. We determined the m6A mRNA methylation profile in PC12 cells exposed to UCB (0 and 18 µM) for 24 h using methylated RNA immunoprecipitation sequencing (MeRIP-seq).

RESULTS

Compared with the control group, UCB (18 and 24 µM) treatment decreased the expression of the m6A demethylase ALKBH5 and increased the expression of the methyltransferases METTL3 and METTL14, which resulted in an increase in the total m6A levels in PC12 cells. Furthermore, 1533 m6A peaks were significantly elevated and 1331 peaks were reduced in the UCB (18 µM)-treated groups compared with those in the control group. Genes with differential m6A peaks were mainly enriched in protein processing in the endoplasmic reticulum, ubiquitin-mediated proteolysis, cell cycle, and endocytosis. Through combined analysis of the MeRIP-seq and RNA sequencing data, 129 genes with differentially methylated m6A peaks and differentially expressed mRNA levels were identified.

CONCLUSION

Our study suggests that the modulation of m6A methylation modifications plays a significant role in UCB neurotoxicity.

Integrative Transcriptomic Profiling of the Wilms Tumor

Our study aimed to identify relevant transcriptomic biomarkers for the Wilms tumor, the most common pediatric kidney cancer, independent of the histological type and stage. Using next-generation sequencing, we analyzed the miRNA profiles of 74 kidney samples, which were divided into two independent groups: fresh frozen tissue and formalin-fixed paraffin-embedded tissue samples. Subsequent mRNA expression profiling and pathway analysis were performed to establish the interplay and potential involvement of miRNAs and mRNA in the Wilms tumor. Comparative analysis, irrespective of post-dissection tissue processing, revealed 41 differentially expressed miRNAs, with 27 miRNAs having decreased expression and 14 miRNAs having increased expression in the Wilms tumor tissue compared to healthy kidney tissue. Among global mRNA transcriptomic profile differences, cross-sectional analysis suggested a limited list of genes potentially regulated by differentially expressed miRNAs in the Wilms tumor. This study identified the comprehensive miRNA and mRNA profile of the Wilms tumor using next-generation sequencing and bioinformatics approach, providing better insights into the pathogenesis of the Wilms tumor. The identified Wilms tumor miRNAs have potential as biomarkers for the diagnosis and treatment of the Wilms tumor, regardless of histological subtype and disease stage.

Prospective Evaluation of a Circulating Tumor Cell Sensitivity Profile to Predict Response to Cisplatin Chemotherapy in Metastatic Breast Cancer Patients

Background

Cisplatin (cDDP) has regained interest for metastatic breast cancer (MBC) patients, given the platinum sensitivity in subtypes and better manageable toxicity. Here, the primary aim was to determine whether molecular characteristics of circulating tumor cells (CTCs) could identify patients responding to cDDP and to describe the outcomes to cDDP monotherapy in a large group of MBC patients pretreated with anthracycline- and taxane-based treatments.

Methods

Based on cell line data, a CTC-cDDP-sensitivity profile was generated. Applying an A’Herns single-stage phase II design, further investigation was considered worthwhile if 5/10 patients with a favorable profile responded to cDDP. Patients received 70mg/m² cDDP every three weeks, CTCs were enumerated and the CTC-cDDP-sensitivity profile was determined. In total, 65 heavily pretreated MBC patients (77% received ≥2 lines of previous chemotherapy for MBC) were eligible for the per-protocol analysis. Primary endpoint was response rate, secondary endpoints included best observed response, progression-free survival (PFS) and overall survival (OS).

Results

The best observed response during cDDP therapy was a partial response in 7% and stable disease in 56% of the patients. None of the patients with a favorable CTC-cDDP-sensitivity profile had a response. The median baseline CTC count was 8 (range 0-3254). Patients with <5 CTCs had a better PFS and OS than patients with ≥5 CTCs (median PFS 4.5 months (95%CI 2.38-6.62) vs. 2.1 months [(95%CI 1.34-2.80)(p=0.009)] and median OS 13.1 months (95%CI 9.89-16.33) vs. 5.6 months [(95%CI 3.60-7.64)(p=0.003)]. No other factors than CTC count were associated with outcome to cDDP therapy, including triple-negative breast cancer versus ER-positive tumors.

Conclusions

The CTC-cDDP-sensitivity profile was unable to select patients responding to cDDP monotherapy. In an unselected group of heavily pretreated MBC patients, cDDP yields outcomes comparable to other chemotherapeutic regimens for heavily pretreated MBC patients. CTC count was the only factor associated with outcome in these patients.

Clinical Trial Registration

(https://www.trialregister.nl/trial/3885, identifier NTR4046)

Calculating LRs for presence of body fluids from mRNA assay data in mixtures

Messenger RNA (mRNA) profiling can identify body fluids present in a stain, yielding information on what activities could have taken place at a crime scene. To account for uncertainty in such identifications, recent work has focused on devising statistical models to allow for probabilistic statements on the presence of body fluids. A major hurdle for practical adoption is that evidentiary stains are likely to contain more than one body fluid and current models are ill-suited to analyse such mixtures. Here, we construct a likelihood ratio (LR) system that can handle mixtures, considering the hypotheses H₁: the sample contains at least one of the body fluids of interest (and possibly other body fluids); H₂: the sample contains none of the body fluids of interest (but possibly other body fluids). Thus, the LR-system outputs an LR-value for any combination of mRNA profile and set of body fluids of interest that are given as input. The calculation is based on an augmented dataset obtained by in silico mixing of real single body fluid mRNA profiles. These digital mixtures are used to construct a probabilistic classification method (a 'multi-label classifier'). The probabilities produced are subsequently used to calculate an LR, via calibration. We test a range of different classification methods from the field of machine learning, ways to preprocess the data and multi-label strategies for their performance on in silico mixed test data. Furthermore, we study their robustness to different assumptions on background levels of the body fluids. We find logistic regression works as well as more flexible classifiers, but shows higher robustness and better explainability. We test the system's performance on lab-generated mixture samples, and discuss practical usage in case work.

Protective effects of P2X7R antagonist in sepsis-induced acute lung injury in mice via regulation of circ_0001679 and circ_0001212 and downstream Pln, Cdh2, and Nprl3 expression

BACKGROUND

Sepsis induces pulmonary P2X₇ receptor (P2X₇ R) expression and P2X₇ R-knockout reduced lung inflammation in mice. The present study investigated the expression of circular RNA (circRNA) and mRNA in sepsis-induced acute lung injury (ALI) treated with a P2X₇ R antagonist.

METHODS

Sepsis was induced by tracheal administration of lipopolysaccharide (LPS), and the mice were then divided into two groups: without [sepsis + dimethyl sulfoxide (DMSO)] or with P2X₇ R antagonist treatment (sepsis + P2X₇ A). Sham mice were administrated sterile normal saline. Serum levels of interleukin (IL)-1β and tumor necrosis factor (TNF)-α, pathological changes, cell apoptosis and P2X₇ R expression in lung were assessed, followed by RNA sequencing (RNA-seq) and bioinformatics analyses. A quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) was used to validate circRNAs and mRNAs.

RESULTS

Compared to the sham group, LPS-induced sepsis produced obvious pathological changes in lung tissue, as well as increased apoptotic lung cells, serum TNF-α and IL-1β levels, and P2X₇ R expression; P2X₇ R antagonism significantly ameliorated these changes. RNA-seq identified many dysregulated circRNAs and mRNAs during sepsis, whereas this changed with P2X₇ R antagonism. RT-qPCR confirmed that Mus musculus (mmu)_circ_0001679, mmu_circ_0001212, phospholamban (Pln), cadherin-2 (Cdh2) and nitrogen permease regulator 3-like (Nprl3) expression were significantly increased in the sepsis + DMSO group compared to that in the sham group but were decreased in the sepsis + P2X₇ A group compared to that in the sepsis + DMSO group. The circRNA-microRNA-mRNA coexpression network indicated that mmu_circ_0001679 may regulate Nprl3 and that mmu_circ_0001212 may similarly regulate Pln, Cdh2 and Nprl3 as a competing endogenous RNA.

CONCLUSIONS

P2X₇ R antagonism attenuates sepsis-induced ALI by inhibiting dysregulated expression of circRNA (circ_0001679, circ_0001212) and mRNA (Pln, Cdh2 and Nprl3).

Identification and verification of key genes in varicocele rats through high-throughput sequencing and bioinformatics analysis

Varicocele (VC) is the most common treatable cause of infertility, but it is difficult to distinguish fertile from infertile VC populations because the pathogenesis is unclear. In order to study the related mechanism of VC causing male sterility, we made VC rat model by surgery, analysed the rat epididymal spermatozoa and used the transcriptome sequencing to compare all the mRNA expression differences in testicular tissue between VC rats and control rats. The differentially expressed genes (DEGs) of testicular tissue were also screened by the limma package in R software (version 3.6.1). The 273 DEGs were identified from the four profile data sets including 124 up-regulated genes and 149 down-regulated genes in the VC group compared to control group. We found that Sod1, Casp9, Atg7, Casp3 and Sirt1 in module 1 had higher degrees of connectivity in the first 10 hub genes. Gene ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that Sod1, Casp9, Atg7, Casp3 and Sirt1 are enriched in regulation of oxidative stress-induced cell death (GO:1,903,201) and Amyotrophic lateral sclerosis (KEGG:05,014). From the above evidence, we speculate that hypoxia plays an important role in the occurrence and development of VC, and it induced the abnormal expression of autophagy and apoptosis-related proteins may involve in the development of VC-associated infertility. Sod1, Casp9, Atg7, Casp3 and Sirt1 as well as their module are hub genes for VC, which will have attractive applications to provide new treatment targets for VC.

Prediction of High-Grade Clear Cell Renal Cell Carcinoma Based on Plasma mRNA Profiles in Patients with Localized Pathologic T1N0M0 Stage Disease

A high nuclear grade is crucial to predicting tumor recurrence and metastasis in clear cell renal cell carcinomas (ccRCCs). We aimed to compare the mRNA profiles of tumor tissues and preoperative plasma in patients with localized T1 stage ccRCCs, and to evaluate the potential of the plasma mRNA profile for predicting high-grade ccRCCs. Data from a prospective cohort (n = 140) were collected between November 2018 and November 2019. Frozen tumor tissues and plasma were used to measure PBRM1, BAP1, SET domain-containing 2 (SETD2), KDM5C, FOXC2, CLIP4, AQP1, DDX11, BAIAP2L1, and TMEM38B mRNA levels, and correlation with the Fuhrman grade was investigated. Multivariate logistic regression analysis revealed significant association between high-grade ccRCC and SETD2 and DDX11 mRNA levels in tissues (odds ratio (b) = 0.021, 95% confidence interval (CI): 0.001-0.466, p = 0.014; b = 6.116, 95% CI: 1.729-21.631, p = 0.005, respectively) and plasma (b = 0.028, 95% CI 0.007-0.119, p < 0.001; b = 1.496, 95% CI: 1.187-1.885, p = 0.001, respectively). High-grade ccRCC prediction models revealed areas under the curve of 0.997 and 0.971 and diagnostic accuracies of 97.86% and 92.86% for the frozen tissue and plasma, respectively. SETD2 and DDX11 mRNA can serve as non-invasive plasma biomarkers for predicting high-grade ccRCCs. Studies with long follow-ups are needed to validate the prognostic value of these biomarkers in ccRCCs.

Cell cycle and histone modification genes were decreased in placenta tissue from unexplained early miscarriage

Genetic defect is a major cause of early miscarriage, but still in many cases the etiology are not fully understood. Recent studies have shown that dysregulation of genes in placenta tissue are participated in the pathogenesis of unexplained early miscarriage. The aim of our study is to explore mRNA expression profile in placental chorionic villi and to reveal the underlying mechanism of unexplained early miscarriage. Chorionic villous were isolated and extracted from early miscarriage (n=3) and control pregnancy (n=3) placenta with normal chromosome karyotype using MLPA assay, and then mRNA expression profiles were determined by microarray. For verification the reproducibility of the microarray, three up-regulated genes and six down-regulated genes were chosen and examined by real-time PCR (n=30). A total of 81 genes were up-regulated and 231 genes were down-regulated when compared to the control group, and the differences were reached statistically significances (P<0.05). After Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we found that almost down-regulation genes are associated with cell cycle and histone modification, and these genes are participated in several important physiological processes, such as cell proliferation, nuclear division, chromatic assembly, DNA packing and modification. These results indicated that cell cycle and histone modification genes, and related signaling pathway maybe contribute to the genesis and development of unexplained early miscarriage. Further studies and validations are necessary to elucidate the exact roles of these genes in miscarriage pathogenesis, which can develop tools for early detection and management.

Microcystin-LR induces dysfunction of insulin secretion in rat insulinoma (INS-1) cells: Implications for diabetes mellitus

Microcystins (MCs) are the most frequent cyanobacterial toxins observed in freshwater systems. Accumulating evidence suggests that MCs pose a serious threat to public health. However, the contributions of the exposure of MCs to the occurrence of human diseases remain largely unknown. This study provides the evidence of the effects of MC-LR on pancreatic β-cell function through the exposure of rat insulinoma (INS-1) cells to 0, 10, 20, or 40μM MC-LR for 72h and explores the underlying molecular mechanisms. Our results demonstrate that exposure to MC-LR for 72h suppresses cell viability, disturbs glucose-stimulated insulin secretion (GSIS), and decreases the expression of insulin protein. Moreover, MC-LR disrupts the cell cycle distribution and increases cell apoptosis at 20 or 40μM for 72h, respectively, indicating that the β-cell mass would be decreased by MC-LR exposure. A transcriptomic analysis revealed several key genes (e.g., Pdx-1, Neurod1, and Abcc8) involved in insulin secretion are significantly differentially expressed in INS-1 cells in response to MC-LR exposure. In addition, several signal transduction pathways associated with diabetes (e.g., type 1 and 2 diabetes) were also identified compared with the control cells. We recommend that MC be considered as a new environmental factor that promotes diabetes development. The identified key genes or pathways may potentially contribute to the future therapies in the environmental contaminants induced β-cell damage.

mRNA expression characteristics are different in irreversibly atrophic intrinsic muscles of the forepaw compared with reversibly atrophic biceps in a rat model of obstetric brachial plexus palsy (OBPP)

In obstetric brachial plexus palsy (OBPP), irreversible muscle atrophy occurs much faster in intrinsic muscles of the hand than in the biceps. To elucidate the mechanisms involved, mRNA expression profiles of denervated intrinsic muscles of the forepaw (IMF) and denervated biceps were determined by microarray using the rat model of OBPP where atrophy of IMF is irreversible while atrophy of biceps is reversible. Relative to contralateral control, 446 dysregulated mRNAs were detected in denervated IMF and mapped to 51 KEGG pathways, and 830 dysregulated mRNAs were detected in denervated biceps and mapped to 52 KEGG pathways. In denervated IMF, 10 of the pathways were related to muscle regulation; six with down-regulated and one with up-regulated mRNAs. The remaining three pathways had both up- and down-regulated mRNAs. In denervated biceps, 13 of the pathways were related to muscle regulation, six with up-regulated and seven with down-regulated mRNAs. Five of the pathways with up-regulated mRNAs were related to regrowth and differentiation of muscle cells. Among the 23 pathways with dysregulated mRNAs, 13 were involved in regulation of neuromuscular junctions. Our results demonstrated that mRNAs expression characteristics in irreversibly atrophic denervated IMF were different from those in reversibly atrophic denervated biceps; dysregulated mRNAs in IMF were associated with inactive pathways of muscle regulation, and in biceps they were associated with active pathways of regrowth and differentiation. Lack of self-repair potential in IMF may be a major reason why atrophy of IMF becomes irreversible much faster than atrophy of biceps after denervation.