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Objective Transglutaminase (TGM)2 and peroxisome proliferator-activated receptor (PPAR)γ are thought to participate in the pathogenesis of nasal polyp formation in cystic fibrosis (CF). We herein investigated expressions of cystic fibrosis transmembrane conductance regulator (CFTR), TGM2, PPARγ and isopeptide bonds, a reaction product of TGM, in non-CF nasal polyps. Methods Nasal polyps and inferior turbinates were collected from chronic rhinosinusitis patients without CF during transnasal endoscopic sinonasal surgery. Expressions of CFTR, TGM2, isopeptide bonds and PPARγ were examined by fluorescence immunohistochemistry and quantitative RT-PCR. Expression of CFTR was also analyzed by Western blot. Results Immunohistochemical fluorescence of the nasal polyp was significantly lower for CFTR and PPARγ, and significantly higher for TGM2 and isopeptide bonds than that of the turbinate mucosa. Lower expression of CFTR in the nasal polyp than in the turbinate mucosa was also observed in Western blot. Expression of PPARG mRNA was significantly lower in the nasal polyp than in the turbinate mucosa, whereas expressions of CFTR mRNA or TGM2 mRNA did not differ between the two tissues. Immunohistochemical fluorescence for CFTR showed significant negative correlation with that for TGM2 and isopeptide bonds, and significant positive correlation with that for PPARγ. The fluorescence for TGM2 was positively correlated with that for isopeptide bonds and negatively correlated with that for PPARγ. The fluorescence for isopeptide bonds tended to be negatively correlated with that for PPARγ. Conclusions These results suggest a possible role of the CFTR-TGM2-PPARγ cascade in the pathogenesis of nasal polyp formation in non-CF patients as in CF patients.

Background Gene dosage imbalance caused by copy number variations (CNVs) is a prominent contributor to brain disorders. In particular, 15q11.2 CNV duplications and deletions have been associated with autism spectrum disorder and schizophrenia, respectively. The mechanism underlying these diametric contributions remains unclear. Methods We established both loss-of-function and gain-of-function mouse models of Cyfip1, one of four genes within 15q11.2 CNVs. To assess the functional consequences of altered CYFIP1 levels, we performed systematic investigations on behavioral, electrophysiological, and biochemical phenotypes in both mouse models. In addition, we utilized RNA immunoprecipitation sequencing (RIP-seq) analysis to reveal molecular targets of CYFIP1 in vivo. Results Cyfip1 loss-of-function and gain-of function mouse models exhibited distinct and shared behavioral abnormalities related to autism spectrum disorder and schizophrenia. RIP-seq analysis identified messenger RNA targets of CYFIP1 in vivo, including postsynaptic NMDA receptor (NMDAR) complex components. In addition, these mouse models showed diametric changes in levels of postsynaptic NMDAR complex components at synapses because of dysregulated protein translation, resulting in bidirectional alteration of NMDAR-mediated signaling. Importantly, pharmacological balancing of NMDAR signaling in these mouse models with diametric Cyfip1 dosages rescues behavioral abnormalities. Conclusions CYFIP1 regulates protein translation of NMDAR and associated complex components at synapses to maintain normal synaptic functions and behaviors. Our integrated analyses provide insight into how gene dosage imbalance caused by CNVs may contribute to divergent neuropsychiatric disorders.

Nonsense-mediated mRNA decay (NMD) serves as a quality control mechanism by degrading mRNAs with premature termination codons (PTCs), and it also regulates the abundance of physiological RNAs encoding functional proteins. Recent work showed that NMD can be triggered with a certain probability by each translation termination event. Readthrough of the PTC can render NMD-sensitive mRNA molecules immune to NMD, which can explain why a certain fraction of an otherwise NMD-sensitive mRNA population persists. Accurate prediction of NMD-sensitive transcripts based on sequence information is currently not possible; experimental testing is necessary. NMD modulates the severity of many genetic diseases and affects antigen presentation in cancer cells and the progression of developmental diseases. NMD targets many viral RNAs, but viruses circumvent this by expressing NMD-inhibiting proteins and harboring NMD-suppressing sequence elements in their RNAs.

Background: Epithelial splicing regulatory proteins (ESRPs) can regulate alternative splicing of RNA and play roles in tumorigenesis and development of various malignancies. In this study, bioinfor...

Purpose: N6-methyladenosine (m6A) methylation was the most abundant internal modification on messenger RNAs in eukaryotes. This study intended to explore the role of m6A methylation in endometrial cancer (EC). Materials and Methods: The m6A-sequencing data "GSE93911" of human EC were downloaded from Gene Expression Omnibus database. Hisat2 software and MACS2 were used to perform the alignment of reads and m6A methylation peak calling, and the peaks were annotated using Chipseeker. Then, differential m6A methylation peaks between normal and tumor samples were analyzed, followed by the functional enrichment analysis of the differentially methylated genes in promoter and 3' untranslated region (UTR) using Clusterprofiler. Based on the 450K methylated chip data, gene expression and clinical data in The Cancer Genome Atlas, the differentially methylated genes were verified, followed by Cox univariate/multivariate regression analysis and survival analysis. Finally, a risk prognosis model was constructed. Results: The m6A peak number was decreased in EC. The distribution of m6A peaks was highly enriched near transcriptional start site, in promoter, UTR, intron and exon, followed by distal intergenic. A total of 581 differentially methylated genes (361 hyper- and 220 hypomethylated genes) were identified in promoter and UTR regions that were enriched in insulin resistance (IR) and extracellular matrix (ECM). A total of 181 genes with significant differential expressions and differential methylation site in EC were selected. Of which, 31 genes were correlated with survival, and an 11-gene risk prognosis model was identified, including GDF7, BNC2, SLC8A1, B4GALNT3, DHCR24, ESRP1, HOXB9, IGSF9, KIAA1324, MSnX1, and PHGDH. Conclusion: The m6A methylation regulated EC progression by targeting the genes related to IR and ECM. A 11-gene risk prognosis model was identified to predict survival of patients with EC.

Small molecules designed to modulate protein function have been remarkably successful in advancing human health. As the frontiers of medicine and understanding of disease pathogenesis continue to expand, small molecule scientists must also pursue the development of novel therapeutic modalities beyond functional protein modulation to address diseases of unmet medical need. In this vein, this Perspective will highlight two emerging modalities, selective mRNA splice modulation and targeted protein degradation, as mechanisms that affect protein abundance, rather than protein function, to broaden the scope of low-molecular-weight treatable diseases. Key to the elucidation and development of these mechanisms was the interplay and contemporaneous efforts in medicinal chemistry and chemical biology. Continued research at the intersection of these two fields will be critical for the identification of novel targets and mechanisms toward the development of the next generation of small molecule therapeutics.

Background: This study intended to investigate the mechanisms underlying the epidermal growth factor receptor (EGFR) mutations in nonsmall cell lung cancer (NSCLC). Materials and Methods: Lung cancer tissue samples were collected from 20 patients with NSCLC (6 EGFR mutation types assigned into 2 categories and 14 EGFR wild types assigned to 4 categories). The samples were subjected to transcriptome sequencing, followed by identification of the differentially expressed mRNAs (DEMs), differentially expressed lncRNAs (DELs), and differentially expressed circRNAs (DECs) between the mutation and nonmutation groups. Function analysis and microRNA (miRNA) prediction for DEMs were performed. The correlations between long noncoding RNA (lncRNA)/circular RNA (circRNA) and messenger RNA (mRNA) were analyzed. In addition, the targeting lncRNA and circRNA of miRNA were predicted. Finally, competing endogenous RNA (ceRNA) network was constructed, and survival analysis for the mRNAs involved in the network was performed. Results: In total, 323 DEMs, 284 DELs, and 224 DECs were identified between EGFR mutation and nonmutation groups. The DEMs were significantly involved in gene ontology functions related to cilium morphogenesis and assembly. ceRNA networks were constructed based on the DEMs, DELs, DECs, and predicted miRNAs. Survival analysis showed that four genes in the ceRNA network, including ABCA3, ATL2, VAMP1, and APLN, were significantly associated with prognosis. The four genes were involved in several ceRNA pathways, including RP1-191J18/circ_000373/miR-520a-5p/ABCA3, RP5-1014D13/let-7i-5p/ATL2, circ_000373/miR-1293/VAMP1, and RP1-191J18/circ_000373/miR-378a-5p/APLN. Conclusion: EGFR mutations in NSCLC may be associated with cilium dysfunction and complex ceRNA regulatory mechanisms. The key RNAs in the ceRNA network may be used as promising biomarkers for predicting EGFR mutations in NSCLC.

Epithelial-to-mesenchymal transition (EMT) endows tumor cells with the ability to invade and migrate, and to suppress antitumor immunity. In this issue, Parajuli and colleagues report that EMT tumors often express the RNA-binding protein AT-rich interactive domain 5a (Arid5a), which they find stabilizes the mRNAs encoding indoleamine 2,3 dioxygenase (IDO1) and CCL2. As a new link between EMT and tumoral immune resistance, Arid5a represents a therapeutic target of interest. See related article by Parajuli et al., p. 862 (4).

Background: Recurrent Miscarriage (RM) affects 1% to 5% of couples, and the mechanisms still stay unclear. In this study, we explored the underlying molecular mechanism and potential molecular biomarkers of RM as well as constructed a miRNA-mRNA regulation network. Methods: The microarray datasets GSE73025 and GSE22490, which represent mRNA and miRNA profiles, respectively, were downloaded from the Gene Expression Omnibus (GEO) database. Differentially Expressed Genes (DEGs) with p-value < 0.05 and fold-change > 2 were identified while the miRNAs with p-value < 0.05 and fold-change > 1.3 were considered as significant differentially expressed miRNAs (DEMs). Results: A total of 373 DEGs, including 218 up-regulated genes and 155 down-regulated genes, were identified, while 138 up-regulated and 68 down-regulated DEMs were screened out. After functional enrichment analysis, we found GO Biological Process (BP) terms significantly enriched in the Fc-gamma receptor signaling pathway involved in phagocytosis. Moreover, signaling pathway analyses indicated that the neurotrophin signaling pathway (hsa04722) was the top KEGG enrichment. 6 hub genes (FPR1, C5AR1, CCR1, ADCY7, CXCR2, NPY) were screened out to construct a complex regulation network in RM because they had the highest degree of affecting the network. Besides, we constructed miRNA-mRNA network between DEMs target genes and DEGs in RM, including hsa-miR-1297- KLHL24 and hsa-miR-548a-5p-KLHL24 pairs. Conclusions: In conclusion, the novel differentially expressed molecules in the present study could provide a new sight to explore the pathogenesis of RM as well as potential biomarkers and therapeutic targets for RM diagnosis and treatment.

For most genes, mRNA transcript abundance scales with cell size to ensure a constant concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with regulation of the activity and abundance of RNA polymerase II (Pol II) now emerging as a key point of control. However, there is also considerable evidence for feedback mechanisms that kinetically couple the rates of mRNA synthesis, nuclear export, and degradation to allow cells to compensate for changes in one by adjusting the others. Researchers are beginning to integrate results from these different fields to reveal the mechanisms underlying transcript homeostasis. This will be crucial for moving beyond our current understanding of relative gene expression towards an appreciation of how absolute transcript levels are linked to other aspects of the cellular phenotype.

Three COVID-19 vaccines are licensed for emergency use in the USA: the Pfizer/BioNTech and Moderna/NIH mRNA-based vaccines, and the Johnson & Johnson (J&J)/Janssen human adenovirus (Ad26) vaccine. These vaccines have immunized [~]160 million people nationwide, comprising [~]53% Pfizer, 39% Moderna, and 8% J&J recipients [1]. Although at varying stages of clinical investigation for use in children, no COVID-19 vaccines are yet available for this population, posing a significant public health concern. One method to protect infants and young children may be passive immunization via antibodies (Abs) provided in the milk of a lactating vaccinated person. Our early work [2] and other recent reports [3-5] examining the milk Ab response to mRNA-based COVID-19 vaccination have demonstrated that unlike the post-SARS-CoV-2 infection milk Ab profile, which is rich in specific secretory (s)IgA, the vaccine response is highly IgG-dominant. In this report, we present a comparative assessment of the milk Ab response elicited by not only the Pfizer and Moderna vaccines, but importantly, the J&J vaccine as well. This analysis revealed that compared to mRNA vaccine recipients, 49% - 63% fewer J&J vaccine recipient milk samples were positive for Spike-specific IgG, with positive samples exhibiting significantly lower mean IgG titers. J&J recipient milk samples contained significantly less specific IgA than Moderna recipient milk samples, which exhibited significantly greater relative IgA increases compared to both Pfizer and J&J recipients. Absolute and relative vaccine-induced secretory Ab titers were similarly low for all groups, though [~]25% more Moderna recipients exhibited a relative increase compared to Pfizer and J&J recipients. These data indicate that J&J vaccine poorly elicits Spike-specific Ab in milk compared to mRNA-based vaccines and that this vaccine should be considered a last choice for immunizing those intending to elicit a strong Ab response in their milk. These data also suggest that Moderna vaccine elicits a superior, albeit moderate, milk (s)IgA response, and highlight the need to design vaccines with optimal protection of the breastfeeding infant in mind.

Background: The dynamic changes that bone undergoes during the ensemble of remodeling are administered by vital factors like Runx2 (a bone transcription factor) and matrix metalloproteinases (MMPs). Aims: Parathyroid hormone (PTH), an FDA approved drug for bone-related ailments, was seen to stimulate MMP-13 expression via Runx2 to ultimately aid in the bone remodeling process. MicroRNAs (miRNAs) have been shown to play a major role in controlling bone metabolism, and the use of miRNAs has recently become promising therapeutic avenues for the treatment of many diseases, including bone disorders. Thus, in this study, we attempted to investigate and evaluate the expression of MMP-13 via a miRNA profile targeting Runx2 under PTH-regulation in rat osteoblastic cells. Methods: PTH stimulated the expression of MMP-13 mRNA significantly at 4 h in rat osteoblastic cells (UMR106-01). Runx2 was required for PTH-stimulation of MMP-13 expression, in silico scrutiny generated 14 unique miRNAs targeting Runx2, and among these miRNAs, miR-290 was significantly downregulated by PTH-treatment in UMR106- 01 cells and in rat primary osteoblasts. Results: Overexpression of miR-290 decreased the expression of Runx2, the binding of Runx2 at the MMP-13 promoter, and the expression of MMP-13 mRNA in PTH-treated UMR106-01 cells. A dual luciferase reporter assay identified the direct targeting of Runx2 mRNA by miR-290 in these cells. Conclusion: Our findings indicate that the PTH-responsive miR-290 regulated Runx2- mediated MMP-13 expression in rat osteoblastic cells, suggesting miR-290 as a molecular marker or target in bone and bone-related diseases.

Infectious bursal disease virus (IBDV) can cause a highly contagious immunosuppressive disease in young chickens, resulting in considerable economic losses to the poultry industry. MicroRNAs (miRNAs) are crucial regulators of gene expression and are involved in the pathogenesis of IBDV infection. To investigate the roles of miRNA in chicken bursae of Fabricius in response to very virulent IBDV (vvIBDV) infection, RNA sequencing was performed. For this, we established an IBDV infection model as observed using histopathology, transmission electron microscopy (TEM), viral load detection, and cytokine expression levels. In total, 77 differentially expressed (DE) miRNAs were identified, of which 42 were upregulated and 35 were downregulated. A gene ontology analysis showed that genes associated with cellular processes, cells, and binding were enriched, and pathway analyses suggested that axon guidance, tight junctions, and endocytosis may be activated following vvIBDV infection. Moreover, we predicted the target genes of DE miRNAs and constructed an miRNA-mRNA regulatory network. In total, 189 pairs of miRNA-target genes were identified, comprising 67 DE miRNAs and 73 mRNAs. In this network, gga-miR-1684b-3p was identified with the highest fold change, and gga-miR-1788-3p and gga-miR-3530-5p showed a high degree of change, suggesting that they play vital roles in vvIBDV-host interactions. This study is the first to perform a comprehensive analysis of DE miRNAs in the bursa of Fabricius in response to vvIBDV infection, and it provides new insights into the molecular mechanisms underlying vvIBDV infection and pathogenesis.

Organismal growth and development rely on RNA Polymerase II (RNAPII) synthesizing the appropriate repertoire of messenger RNAs (mRNAs) from protein-coding genes. Productive elongation of full-length transcripts is essential for mRNA function, however what determines whether an engaged RNAPII molecule will terminate prematurely or transcribe processively remains poorly understood. Notably, despite a common process for transcription initiation across RNAPII-synthesized RNAs1, RNAPII is highly susceptible to termination when transcribing non-coding RNAs such as upstream antisense RNAs (uaRNAs) and enhancers RNAs (eRNAs)2, suggesting that differences arise during RNAPII elongation. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in uaRNAs and eRNAs, rather than specific sequence motifs, underlies the propensity for RNAPII termination on these transcripts. Further, we demonstrate that 5’ splice sites exert both splicing-dependent and autonomous, splicing-independent stimulation of transcription, even in the absence of polyadenylation signals. Together, our results reveal a potent role for transcribed sequence in dictating gene output at mRNA and non-coding RNA loci, and demonstrate the power of INSERT-seq towards illuminating these contributions.

How do age and normo- or oligoasthenozoospermia affect telomere length dynamics in spermatozoa and blood?Sperm and blood samples were collected from a cohort of 37 men aged 25 and under and 40 men aged 40 and over, with either normozoospermia (NZ) or oligoasthenozoospermia (OAZ). Telomere length was evaluated using quantitative fluorescence in-situ hybridization. Telomerase mRNA (TERC and TERT) and shelterin (TRF1) gene expression were analysed using quantitative real-time polymerase chain reaction. TRF1 protein immunoreactivity was also evaluated using immunofluorescence.Mean sperm telomere length (STL) increased with age in the NZ group; older NZ men accumulated the longest telomeres (P0.001). In peripheral blood mononuclear cells (PBMC), mean telomere length decreased with age in NZ groups, although not reaching statistical significance. Interestingly, the younger OAZ group had the shortest mean telomere length (versus young NZ, P = 0.0081; versus old NZ, P = 0.0116; versus old OAZ, P = 0.0009) and accumulated the highest percentage of short telomeres compared with the other groups (overall P = 0.0017). Analysis of TERC and TERT mRNA expression in spermatozoa and PBMC did not show significant differences among groups. Statistically significant positive correlations were found between STL and seminal parameters in younger NZ men (P = 0.009 for sperm count and P = 0.007 for total progressive motility). Protein immunoreactivity of TRF1 in blood was not significantly different in all groups analysed.The OAZ group did not show the increase of STL with age that is seen in NZ individuals, suggesting that telomere length elongation mechanisms fail in OAZ patients. In PBMC, younger OAZ individuals showed significantly shorter mean telomere length, suggesting that this parameter could be a good biomarker of OAZ in younger OAZ patients. Telomerase gene and TRF1 mRNA expression and TRF1 protein immunoreactivity did not differ significantly between groups, and so these factors cannot be used as OAZ biomarkers.

Cancer is a multifactorial disease that constitutes a serious public health problem worldwide. Prostate cancer advanced stages are associated with the development of androgen-independent tumors and an apoptosis-resistant phenotype that progresses to metastasis. By studying androgen-independent lymphoid nodule carcinoma of the prostate (LNCaP) cells induced to apoptosis by serum elimination, we identified the activation of a non-selective cationic channel of 23pS conductance that promotes incoming Ca2+ currents, as well as apoptosis final stages. arp2cDNA was isolated and identified to be of the same cell type, and mRNA was expressed in Xenopus laevis oocytes, which was found to be associated with the activation of incoming Ca2+ currents and induction to apoptosis. cDNA, which encodes the ARP2 protein, was overexpressed in LNCaP cells and Chinese hamster ovary cells, which induced apoptosis. Our evidence suggests that protein ARP2 overexpression and transit to the cell membrane allows an increased Ca2+ incoming current that initiates the apoptosis process in epithelial-type cells whose phenotype shows resistance to programmed cell death.

Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNA molecules across different life-cycle stages impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total cellular RNA, these intermediates are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications and differential expression analyses for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.

Research question : What is the expression pattern of inflammatory mRNA profiles of dehydroepiandrosterone (DHEA) plus high-fat diet (HFD)-induced polycystic ovary syndrome (PCOS) mouse model? Design : In this study, RNA sequencing was performed to investigate the mRNA expression profiles in the ovarian tissues of a DHEA plus HFD-induced PCOS mouse model. Six samples were divided into two groups (control and PCOS), with three biological replicates in each group. This was followed by hierarchical clustering, gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The relative expression levels of nine inflammatory genes were validated via quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results : A total of 436 genes were differentially expressed between the control and PCOS mice. Out of these, 137 genes were up-regulated while 299 genes were down-regulated. Gene ontology analysis indicated that differentially expressed mRNAs were associated with T cell-mediated cytotoxicity and homocysteine metabolic processes. Pathway analysis further showed that these abnormally expressed mRNAs were associated with signaling pathways, such as NF-kB signaling, tyrosine metabolism, and phenylalanine metabolism. All these pathways are involved in chronic inflammation and PCOS. Conclusion : The differentially expressed genes are potentially involved in the inflammation that is evident in PCOS, and so could serve as therapeutic options against the disease. Nevertheless, prospective studies are needed to test this hypothesis.

Cells of metazoans respond to internal and external stressors by activating stress response pathways that aim for re-establishing cellular homoeostasis or, if this cannot be achieved, triggering programmed cell death. Problems during translation, arising from defective mRNAs, tRNAs, ribosomes or protein misfolding, can activate stress response pathways as well as mRNA surveillance and ribosome quality control programs. Recently, ribosome collisions have emerged as a central signal for translational stress and shown to elicit different stress responses. Here, we review our current knowledge about the intricate mutual connections between ribosome collisions, stress response pathways and mRNA surveillance. A central factor connecting the sensing of collided ribosomes with degradation of the nascent polypeptides, dissociation of the stalled ribosomes and degradation of the mRNA by no-go or non-stop decay is the E3-ligase ZNF598. We tested whether ZNF598 also plays a role in nonsense-mediated mRNA decay (NMD) but found that it is dispensable for this translation termination-associated mRNA surveillance pathway, which in combination with other recent data argues against stable ribosome stalling at termination codons being the NMD-triggering signal.

Background: Bevacizumab (Bev) resistance is hypothesized to be overcome by combining inhibitors of other signalling pathways. Objective: We aimed to study the effect of combining Bev with knocked down β-catenin (Bev-β-cat-siRNA) on the expression of VEGF-A, Slug, NFкB, and its two target genes, c-Flip and FasR, in HepG2. Expression of VEGF-A and Slug was also studied in Caco-2 cells. Methods: Cultured cells were divided into six groups 1) cells treated with Bev, 2) cells treated with β-catenin-siRNA, 3) cells treated with Bev-β-cat-siRNA, 4) cells treated with negative control, 5) cells treated with Bev-negative control, and 6) untreated cells. Expressions were assessed using qPCR and western blotting. Results: Bev-β-cat-siRNA significantly reduced the mRNA level of VEGF-A, which was initially increased in response to Bev alone in HepG2 but not in Caco-2. Additionally, Bev-β-cat-siRNA significantly decreased Slug mRNA level compared to Bev treated HepG2 cells. In contrast, VEGF-A and Slug mRNA levels in Bev group were remarkably lower than Bev-β-cat-siRNA in Caco-2 cells. Distinct β-catenin and Slug protein expressions were noticed in HepG2 and Caco-2 cells. On the other hand, Bev-β-catsiRNA remarkably reduced the level of NFкB, FasR, and c-Flip compared to Bev treated HepG2 cells, although the difference was not statistically significant. Conclusion: We conclude that combining Bevacizumab with knocked down β-catenin reduces the expression of VEGF-A and Slug in HepG2 but not in Caco-2 cells.

BACKGROUND: Effective biomarkers for prediction of recurrence of lung adenocarcinoma cancer (LADC) patients are needed to determine treatment strategies post-surgery to improve outcome. OBJECTIVE: This study evaluates the efficacy of carboxypeptidase E (CPE) mRNA including its splice isoforms, CPE-ΔN, as a biomarker for predicting recurrence in adenocarcinoma patients. METHODS: RNA was extracted from resected tumors from 86 patients with different stages of non-small cell LADC. cDNA was synthesized and qRT-PCR carried out to determine the copy numbers of CPE/CPE-ΔN mRNA. Patients were followed for 7 years post-tumor resection to determine recurrence and death. RESULTS: ROC curve analysis showed the overall AUC for CPE/CPE-ΔN copy number was 0.563 in predicting recurrence and 0.562 in predicting death. Kaplan-Meier survival analysis showed statistical difference (p= 0.018), indicating that patients with high CPE/CPE-ΔN copy numbers had a shorter time of disease-free survival and also shorter time to death (p= 0.035). Subgroup analyses showed that association of disease-free survival time with CPE/CPE-ΔN copy number was stronger among stage I and II LADC patients (p= 0.047). CONCLUSIONS: CPE/CPE-ΔN mRNA is a potentially useful biomarker for predicting recurrence and death in LADC patients, especially in identifying patients at high risk of recurrence at early stages I and II.

[EN] Objective Recently, we reported on a new MDD-like mouse model based on a regionally selective knockdown of astroglial glutamate transporters, GLAST/GLT-1, in infralimbic cortex (IL) which evokes widespread changes in mouse brain associated with the typical alterations found in MDD patients. To further characterize this new MDD-like mouse model, here we examine some transcriptional elements of glutamatergic/GABAergic neurotransmission and neuroplasticity in forebrain regions in the GLT-1 knockdown mice. Furthermore, we assess the acute ketamine effects on these transcriptional processes. Material and methods We used a small interfering RNA (siRNA) pool targeting GLT-1 mRNA to disrupt the GLT-1 transcription in mouse IL. Histological assays were performed to examine postsynaptic density protein-95 (PSD95), neuritin (NRN), glutamine acid descarboxilase-65 (GAD65), and GLT-1 mRNA expression in IL and hippocampus. Results Knockdown of GLT-1 in mouse IL leads to decreased expression of PSD95 and NRN neuroplasticity mRNAs in IL and hippocampus, which was reversed by an acute dose of ketamine antidepressant. Likewise, a single dose of ketamine also increased the mRNA levels of GAD65 and GLT-1 in IL of GLT-1 knockdown mice, reaching the basal values of control mice. Conclusions The glutamatergic neuronal hyperactivity and deficits in the GABA system resulting from siRNA-induced astroglial glutamate transporter knockdown in IL can compromise the integrity/plasticity of neurocircuits affected in MDD. Suitable depressive-like animal models to address the neurobiological changes in MDD are an unmet need and the development of the GLAST/GLT-1 knockdown mouse model may represent a better option to understand the rapid-acting antidepressant effects of ketamine., [ES] Objetivo Recientemente, informamos sobre un nuevo modelo de ratón de depresión basado en una reducción parcial de la transcripción de los transportadores de glutamato, GLAST/GLT-1, en los astrocitos de la corteza infralímbica (IL), que conduce a cambios generalizados de la función cerebral del ratón, que refleja alteraciones típicas encontradas en pacientes con depresión. Para caracterizar más detalladamente este nuevo modelo de ratón de depresión, aquí examinamos algunos elementos transcripcionales relacionados con la neurotransmisión glutamatérgica/GABAérgica y la neuroplasticidad en regiones corticales y subcorticales de los ratones con niveles reducidos de GLT-1. Además, evaluamos los efectos agudos de la ketamina, antidepresivo de acción rápida, en estos procesos transcripcionales. Material y métodos Utilizamos ARN de interferencia (siRNA) dirigido al mRNA de GLT-1 para interrumpir su transcripción en la IL de ratón. Se realizaron ensayos histológicos para examinar la expresión de los mRNA de las siguientes proteínas: proteína de densidad postsináptica-95 (PSD95), neuritina (NRN), descarboxilasa de ácido glutámico-65 (GAD65) y GLT-1 en la IL e hipocampo. Resultados La reducción de la expresión de GLT-1 en IL de ratón conduce a una disminución de la expresión de los mRNA de neuroplasticidad PSD95 y NRN en la IL y el hipocampo, efecto que se revirtió con una única administración del antidepresivo ketamina. Asimismo, una sola dosis de ketamina también aumentó los niveles de los mRNA de GAD65 y GLT-1 en la IL de ratones silenciados para GLT-1, que alcanzaron los valores basales de los ratones control. Conclusiones La hiperactividad neuronal glutamatérgica y los déficits en el sistema GABAérgico resultantes de la reducción de los niveles del transportador de glutamato astroglial inducida por siRNA en IL pueden comprometer la integridad/plasticidad de aquellos neurocircuitos afectados en la depresión. Sin embargo, no disponemos de modelos animales de depresión adecuados para abordar los cambios neurobiológicos que se suceden en esta enfermedad y su tratamiento. El desarrollo del modelo de ratón con reducción parcial de GLAST/GLT-1 puede representar una mejor opción para comprender los efectos antidepresivos de acción rápida de la ketamina., This study was supported by grants SAF2016-75797-R, PID2019-105136RB-100, Ministry of Economy and Competitiveness (MINECO) and European Regional Development Fund (ERDF), UE; and CB/07/09/0034 Center for Networked Biomedical Research on Mental Health (CIBERSAM).

Background: Cognitive impairment is a common neurocognitive disorder that affects millions of worldwide people’s health,related tofolate deficiency. Objective: The present study aimed to investigate the lncRNA-mRNA functional networks associated with cognitive impairment in folate-deficient mice and elucidate their possible molecular mechanisms. Methods: We downloaded the gene expression profile (GSE148126) of lncRNAs and mRNAs from NCBI Gene Expression Omnibus (GEO) database. Four groups of mouse hippocampi were analyzed, including 4 months (4mo) and 18 months (18mo) of folic acid (FA) deficiency/supplementation. The differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified using gplots and heatmap packages. The functions of the DEmRNAs were evaluated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The hub genes wereidentified by CytoHubba plugins of Cytoscape, and protein-protein interaction (PPI) network of deregulated mRNAs was performed using STRING database. Finally, lncRNA-mRNA co-expression and competitive endogenous RNA (ceRNA) network analyses were constructed. Results: In total, we screened 67 lncRNAs with 211 mRNAs, and 89 lncRNAs with 229 mRNAs were differentially expressed in 4mo_FAand 18mo_FA deficient mice, respectively. GO analyses indicated that DEmRNAs were highly related to terms involved in binding and biological regulation. KEGG pathway analyses demonstrated that these genes were significantly enriched for Renin secretion, Pancreatic secretion and AMPK signaling pathways in 18mo_FA deficiency group. Subsequently, the top 5 hub genes werescreened from the PPI network, which may be key genes with the progression of folate deficiency. Upon the lncRNA-mRNA co-expression network analysis, we identified the top 10 lncRNAs having the maximum number of connections with related mRNAs. Finally, a ceRNA network was constructed for DE lncRNAs and DEmRNAs, and several pivotal miRNAs were predicted. Conclusions: This study identified the lncRNA-mRNA expression profiles and functional networks associated with cognitive impairment in folate-deficient mice, which provided support for the possible mechanisms and therapy for this disease.

Aims: The aim of the study was to assess the effect of blocking TLR9 signaling on the proliferation of cervical cancer cells and its angiogenic property. Background: Toll-Like Receptors (TLRs) have been implicated for their crucial role in not only cervical cancer but also in other malignancies. TLR9 is expressed on an array of cells such as macrophages, dendritic cells, melanocytes, and keratinocytes and is reported to modulate oncogenesis along with tumorigenesis by augmenting NF-κB mediated inflammation within the tumor environment. TLR9 has also been reported to positively regulate oncogenesis within the cervix and as a marker to evaluate malignant remodeling of cervical squamous cells. Therefore, this study was designed to explore the functional relevance of blocking the TLR9signaling pathway in cervical cancer cells. Objective: The objective of the current study was to investigate the effect of human TLR9 antagonist, ODN INH-18, on apoptosis and cell cycle regulation, and angiogenic property of human cervical cancer Caski cells. Method: MTT assay was performed to measure cell viability and flow cytometry analysis was performed to assess cell cycle arrest. Quantitative Real-Time PCR (qRT-PCR) analysis was performed to measure fold change in the gene expression of various markers of apoptosis, cell cycle regulation, and angiogenesis. Result: The qRT-PCR results showed a higher expression level of TLR9 mRNA in Caski cervical cancer cells as compared to normal cervical keratinocytes. The apoptotic, angiogenic, and cell cycle regulatory factors were also deregulated in Caski cells in comparison to normal keratinocytes. The MTT assay demonstrated that treatment of TLR9 antagonist, ODN INH18, significantly reduced the proliferation of Caski cells in a dose-dependent manner. Treatment of ODN INH18 led to substantial cell cycle arrest in Caski cells at G0/G1 phase. Moreover, the qRT-PCR results demonstrated that ODN INH18 treatment led to suppressed mRNA expression of Bcl-2 and enhanced expression of Bax, signifying the induction of apoptosis in Caski cells. Moreover, the expression of cyclin D1, Cdk4, and Cdc25A was found to be reduced whereas expression of p27 was increased in ODN INH18-treated Caski cells; indicating G0/G1 phase arrest. Interestingly, expression of VEGF and VCAM-1 was found to be significantly inhibited in ODN INH18-treated Caski cells, substantiating alleviation of angiogenic property of cervical cancer cells. Conclusion: The results of our study suggest that inhibiting TLR9 signaling might be an interesting therapeutic intervention for the treatment of cervical cancer.

AIMS: Atherosclerotic plaque hypoxia is detrimental for macrophage function. Prolyl hydroxylases (PHDs) initiate cellular hypoxic responses, possibly influencing macrophage function in plaque hypoxia. Thus, we aimed to elucidate the role of myeloid PHDs in atherosclerosis.METHODS & RESULTS: Myeloid specific PHD knockout (PHDko) mice were obtained via bone marrow transplantation (PHD1ko, PHD3ko) or conditional knockdown through lysozyme M-driven Cre recombinase (PHD2cko). Mice were fed high cholesterol diet for 6-12 weeks to induce atherosclerosis. Aortic root plaque size was significantly augmented 2.6-fold in PHD2cko, and 1.4-fold in PHD3ko compared to controls, but was unchanged in PHD1ko mice. Macrophage apoptosis was promoted in PHD2cko and PHD3ko mice in vitro and in vivo, via the HIF1α/BNIP3 axis. Bulk and single cell RNA data of PHD2cko bone-marrow-derived macrophages (BMDM) and plaque macrophages, respectively, showed enhanced HIF1α/BNIP3 signaling, which was validated in vitro by siRNA silencing. Human plaque BNIP3 mRNA was positively associated with plaque necrotic core size, suggesting similar pro-apoptotic effects in human. Further, PHD2cko plaques displayed enhanced fibrosis, while macrophage collagen breakdown by matrix metalloproteinases, collagen production and proliferation were unaltered. Instead, PHD2cko BMDMs enhanced fibroblast collagen secretion in a paracrine manner. In silico analysis of macrophage-fibroblast communication predicted SPP1 (osteopontin) signaling as regulator, which was corroborated by enhanced plaque SPP1 protein in vivo. Increased SPP1 mRNA expression upon PHD2cko was preferentially observed in foamy plaque macrophages expressing "triggering receptor expressed on myeloid cells-2" (TREM2hi) evidenced by single-cell RNA, but not in neutrophils. This confirmed enhanced fibrotic signaling by PHD2cko macrophages to fibroblasts, in vitro as well as in vivo.CONCLUSION: Myeloid PHD2cko and PHD3ko enhanced atherosclerotic plaque growth and macrophage apoptosis, while PHD2cko macrophages further activated collagen secretion by fibroblasts in vitro, likely via paracrine SPP1 signaling through TREM2hi macrophages.TRANSLATIONAL OUTLOOK: This study shows that myeloid PHD isoforms PHD2 and PHD3 worsen plaque characteristics and phenotype, such as plaque size, macrophage accumulation, apoptosis, and collagen accumulation in mice. We show both direct effects on macrophages and paracrine effects of macrophage PHD2 loss on vessel wall fibroblast populations. Broad spectrum-PHD inhibitors, e.g. Roxadustat, are currently being prescribed to chronic kidney disease patients, who are already at risk for cardiovascular disease. When considering this study and the pro-fibrotic and pro-apoptotic effects we report, broad PHD inhibition may therefore be sub-optimal and more targeted PHD inhibition of PHD1 should be considered.

Studies are urgently needed to characterize immunogenicity, efficacy, and safety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccines in kidney transplant (KT) recipients, excluded from major clinical trials. Complex ELISPOT and other cellular response techniques have been applied, but simpler tools are needed. An easy-to-use real-world monitoring of SARS-CoV-2 IgG antibodies against the Spike protein and QuantiFERON® SARS-CoV-2 IFNI³ release assay (IGRA) were performed at baseline and 28 days after the second dose in KT recipients and controls (dialysis patients and healthy ones). All healthy controls and >95% dialysis controls became positive for anti-S IgG antibodies, while only 63.3% of KT patients seroconverted with a very low antibody level. A positive IGRA was documented in 96.9% of controls, 89.3% peritoneal dialysis, 77.6% hemodialysis, 61.3% of KT patients transplanted more than 1 year ago and only 36% of those transplanted within the previous 12 months. Overall, 100% of healthy controls, 95.4% of dialysis patients and 78.8% KT recipients developed any immune response (humoral and/or cellular) against SARS-CoV-2. KT patients showed low rates of immune responses to mRNA Coronavirus infectious disease 2019 vaccines, especially those with recent transplantations. Simple humoral and cellular monitoring is advisable, so that repeated doses may be scheduled according to the results.

Background: The aim of the study was to evaluate the variances in the expression pattern of mRNAs and miRNAs related to the EMT in the Ishikawa (histological grade 1; G1), EC-1A (histological grade 2; G2), and KLE (histological grade 3; G3) cell cultures under cisplatin treatment. Methods: Endometrial cancer cell lines were exposed to 75.22 mg (an average concentration of the drug used in patients with endometrial cancer) for 12.24 and 48 hours in comparison to the untreated cells (control). The molecular analysis included: extraction of total RNA, microarray analysis (mRNA and miRNA), RTqPCR, and the ELISA assay. Results: Out of 226 mRNAs associated with the EMT, the number of mRNAs differentially expressed in endometrial cancer cell cultures treated with cisplatin compared to a control culture was as follows: Ishikawa line - 87 mRNAs; EC-1A - 84 mRNAs; KLE - 71 mRNAs (p Conclusion: Cisplatin changes the expression profile of genes associated with EMT in endometrial cancer cell lines. It seems that the expression pattern of TGFβ1 might be a promising, supplementary molecular marker of the effectiveness of cisplatin therapy. The analysis showed that miR-30d, miR-300, and miR-106a are involved in the regulation of the expression of EMT-related genes.

Orexin and its receptors are involved in the mechanisms of pathological craving for alcohol and psychoactive drugs. The orexin system is also involved in the mechanisms of non-chemical forms of addiction: binge eating and gambling. The aim of this work was to study the level of orexin receptor mRNA in the hypothalamus, hippocampus, and prefrontal cortex of rats prone to impulsivity in behavior in a model for studying the elements of gambling addiction (a variant of the Iowa Gambling Task test). Brain structures were isolated on the 22nd day of the experiment. The expression of the OX1R gene was higher in the hypothalamus by 122% and in the hippocampus by 149% in rats that preferred to receive a high reward, but with a low probability as compared with a group of animals that preferred a low level of reinforcement, but with a 100% probability. In the prefrontal cortex, on the contrary, no significant changes were observed in the level of OX1R mRNA. The level of OX2R mRNA insignificantly changed in the hypothalamus, hippocampus, and prefrontal cortex of rats prone to impulsivity in behavior. The data indicate involvement of OX1R in the hypothalamus and hippocampus in mechanisms mediating impulsive behavior and the choice of the significance of positive reinforcement in terms of its varying strength and probability.Oreksin i ego retseptory vovlecheny v mekhanizmy patologicheskogo vlecheniia k alkogoliu i psikhoaktivnym veshchestvam. Sistema oreksina takzhe uchastvuet v mekhanizmakh nekhimicheskikh form zavisimosti — pishchevoĭ i igrovoĭ. Tsel'iu nastoiashchego issledovaniia bylo izuchenie urovnia mRNK retseptorov oreksina v gipotalamuse, gippokampe i prefrontal'noĭ kore mozga krys, sklonnykh k povyshennoĭ impul'sivnosti v povedenii, v modeli dlia izucheniia élementov igrovoĭ zavisimosti. Dlia étogo ispol'zovali variant metoda Iowa Gambling Task v trekhluchevom labirinte. Struktury mozga vydeliali na 22 den' éksperimenta. Ékspressiia gena oreksinovogo retseptora pervogo tipa (OX1R) byla vyshe v gipotalamuse na 122% i gippokampe — na 149% u krys, predpochitavshikh poluchat' vysokoe voznagrazhdenie, no s nizkoĭ doleĭ veroiatnosti po sravneniiu s gruppoĭ zhivotnykh, predpochitavshikh nizkiĭ uroven' podkrepleniia, no so 100% stepen'iu veroiatnosti. V prefrontal'noĭ kore, naprotiv, ne nabliudalos' dostovernykh izmeneniĭ v urovne mRNK OX1R. Pri issledovanii urovnia mRNK oreksinovogo retseptora vtorogo tipa (OX2R) dostovernykh izmeneniĭ u krys, sklonnykh k povyshennoĭ impul'sivnosti v povedenii, v gipotalamuse, gippokampe i prefrontal'noĭ kore otmecheno ne bylo. Dannye ukazyvaiut na vovlechennost' OX1R v gipotalamuse i gippokampe v mekhanizmy, oposreduiushchie impul'sivnoe povedenie i vybor zhivotnymi znachimosti polozhitel'nogo podkrepleniia v usloviiakh ego razlichnoĭ sily i veroiatnosti.

RNA sequencing is a powerful tool to analyze gene expression transcriptome wide. However, RNA sequencing in general and especially the recently developed methods of long read RNA sequencing are still low-throughput and cost-intensive. Here, one important design choice is to concentrate the sequencing capacity on specific parts of the transcriptome. Especially, abundant transcripts as ribosomal RNAs may dominate the available sequencing space, if not removed prior to sequencing. Several methods exist to reduce ribosomal RNA read numbers: either based on enrichment of the relevant fraction (polyA+ RNA) or depletion, respectively degradation of ribosomal RNAs. Furthermore, commercial kits are available to deplete globin transcripts from blood samples. However, so far, no solution exists to deal with other tissue-specific highly abundant transcripts. This is especially of interest in the heart and other muscle derived samples, where reads originating from mitochondrial RNAs make up to 30% of reads in polyA+ selected libraries and around 70% in single cell sequencing experiments. We present a simple method to diminish sequencing of mitochondrial RNAs in Oxford Nanopore direct RNA sequencing libraries by RNase H based clipping of the polyA tail. We show that mt-clipping enables enhanced detection of cytoplasmic mRNAs, among them genes involved in heart development and pathogenesis. Mt-clipping may be applied as well to other sequencing protocols that are based on oligo(dT) priming and can be easily adapted to other tissue-specific high-abundant transcripts.

3’-end processing of most human mRNAs is carried out by the cleavage and polyadenylation specificity factor (CPSF; CPF in yeast). Endonucleolytic cleavage of the nascent pre-mRNA defines the 3’-end of the mature transcript, which is important for mRNA localization, translation and stability. Cleavage must therefore be tightly regulated. Here, we reconstitute specific and efficient 3’-endonuclease activity of human CPSF with purified proteins. This requires the sevensubunit CPSF as well as three additional protein factors: cleavage stimulatory factor (CStF), cleavage factor IIm (CFIIm) and, importantly, the multi-domain protein RBBP6. Unlike its yeast homologue Mpe1, which is a stable subunit of CPF, RBBP6 does not copurify with CPSF and is recruited in an RNA-dependent manner. Sequence and mutational analyses suggest that RBBP6 interacts with the WDR33 and CPSF73 subunits of CPSF. Thus, it is likely that the role of RBBP6 is conserved from yeast to human. Overall, our data are consistent with CPSF endonuclease activation and site-specific pre-mRNA cleavage being highly controlled to maintain fidelity in RNA processing.

Background: Late-onset Alzheimer’s disease (LOAD) is associated with many environmental and genetic factors. The effect of systemic inflammation on the pathogenesis of neurodegenerative diseases such as AD has been strongly suggested. T helper cells (Th) are one of the important components of the immune system and can easily infiltrate the brain in pathological conditions. The development of each Th-subset depends on the production of unique cytokines and their main regulator. Objective: This study aimed to compare the mRNA levels of Th-related genes derived from peripheral blood mononuclear cells of LOAD patients with control. Also, the identification of the most important Th1/Th2 genes and downstream pathways that may be involved in the pathogenesis of AD was followed by computational approaches. Methods: This study involved 30 patients with LOAD and 30 non-demented controls. The relative expression of T-cell cytokines (IFN-γ, TNF-α, IL-4, and IL-5) and transcription factors (T-bet and GATA-3) were assessed using Real-time PCR. Additionally, protein-protein interaction (PPI) was investigated by gene network construction. Results: A significant decrease at T-bet, IFN-γ, TNF-α, and GATA-3 mRNA levels was detected in the LOAD group, compared to the controls. However, there was no significant difference in IL-4 or IL-5 mRNA levels. Network analysis revealed a list of the highly connected protein (hubs) related to mitogen-activated protein kinase (MAPK) signaling and Th17 cell differentiation pathways. Conclusion: The findings point to a molecular dysregulation in Th-related genes, which can promising in the early diagnosis or targeted interventions of AD. Furthermore, the PPI analysis showed that upstream off-target stimulation may involve MAPK cascade activation and Th17 axis induction.

1. MicroRNAs (miRNAs) play key roles in regulating lipid metabolism, adipogenesis and fat deposition in chicken. To date, there are only a few miRNAs that had been confirmed to be involved in chicken adipogenesis. The detailed mechanisms by which miRNAs regulate chicken adipogenesis remain largely unknown. 2. To identify candidate miRNAs involved in chicken preadipocyte differentiation and explore potential mechanisms behind their functions, the following study analysed and identified miRNA and mRNA expression levels in undifferentiated and differentiated preadipocytes. Hub miRNA-mRNA interactions were identified, and the degree of connectivity of DE miRNAs in the network was established. 3. A total of 145 DE miRNAs and 660 DE mRNAs were identified between undifferentiated and differentiated preadipocytes. An miRNA-mRNA network was constructed, including 29 DE miRNAs and 155 DE mRNAs, forming 470 miRNA-mRNA interactions. Functional enrichment analysis showed that DE mRNAs in the network were significantly enriched in 712 biological processes and 13 KEGG pathways. Based on the connectivity degree, five DE miRNAs with higher degrees miR-195-x, gga-miR-200a-3p, gga-miR-135a-5p, novel-m0067-5p and novel-m0270-5p were identified as hub miRNAs. Fifty-eight DE mRNAs interacted with these five hub miRNAs and formed 70 miRNA-mRNA interactions. 4. This study constructed a miRNA-mRNA network associated with chicken preadipocyte differentiation and identified five hub miRNAs in the network. The findings identified the number of chicken adipogenic miRNAs and laid the foundation for elucidating the miRNA-mediated regulatory mechanism in chicken adipogenesis.

FBXO31, a member of F-box protein family, has been shown to play an important role in preventing tumorigenesis by preserving genomic stability during cell proliferations as well as upon genotoxic stresses. Inactivation of FBXO31 due to loss of heterozygosity is associated with various cancers, including ovarian cancer, one of the deadliest forms of gynecological cancers. However, the role and regulation of FBXO31 in ovarian cancer remained elusive. Here, using biochemical and molecular biology techniques, we show that c-Myc suppresses the mRNA levels of FBXO31 in ovarian cancer cell lines and mouse model. Chromatin immunoprecipitation experiment showed that c-Myc is recruited to the promoter region of FBXO31 and prevents FBXO31 mRNA synthesis. In contrast, FBXO31 maintains the c-Myc expression at an optimum through proteasome pathway. FBXO31 interacts with and facilitates the polyubiquitination of c-Myc through the SCF complex and thereby inhibits ovarian cancer growth both in vitro and in vivo. Moreover, FBXO31-mediated proteasomal degradation of c-Myc is unique. Unlike other negative regulators, FBXO31 recognizes c-Myc in phosphorylation independent manner to direct its degradation. Further, expression levels analysis revealed that c-Myc and FBXO31 share a converse correlation of expression in ovarian cancer cell lines and patient samples. We observed an increase in the expression levels of c-Myc with a concomitant decrease in the levels of FBXO31 in higher grades of ovarian cancer patient samples. In conclusion, our study demonstrated that oncogene c-Myc impairs the tumor-suppressive functions of FBXO31 to promote ovarian cancer progression, and therefore c-Myc-FBXO31 axis can be explored to develop better cancer therapy. This article is protected by copyright. All rights reserved.

Obesity impairs host defense against Klebsiella pneumoniae, but responsible mechanisms are incompletely understood. To determine the impact of diet-induced obesity on pulmonary host defense against K. pneumoniae, we fed 6-wk-old male C57BL/6j mice a normal diet (ND) or high-fat diet (HFD) (13% vs. 60% fat, respectively) for 16 wk. Mice were intratracheally infected with Klebsiella, assayed at 24 or 48 h for bacterial colony-forming units, lung cytokines, and leukocytes from alveolar spaces, lung parenchyma, and gonadal adipose tissue were assessed using flow cytometry. Neutrophils from uninfected mice were cultured with and without 2-deoxy-d-glucose (2-DG) and assessed for phagocytosis, killing, reactive oxygen intermediates (ROI), transport of 2-DG, and glucose transporter (GLUT1–4) transcripts, and protein expression of GLUT1 and GLUT3. HFD mice had higher lung and splenic bacterial burdens. In HFD mice, baseline lung homogenate concentrations of IL-1β, IL-6, IL-17, IFN-γ, CXCL2, and TNF-α were reduced relative to ND mice, but following infection were greater for IL-6, CCL2, CXCL2, and IL-1β (24 h only). Despite equivalent lung homogenate leukocytes, HFD mice had fewer intraalveolar neutrophils. HFD neutrophils exhibited decreased Klebsiella phagocytosis and killing and reduced ROI to heat-killed Klebsiella in vitro. 2-DG transport was lower in HFD neutrophils, with reduced GLUT1 and GLUT3 transcripts and protein (GLUT3 only). Blocking glycolysis with 2-DG impaired bacterial killing and ROI production in neutrophils from mice fed ND but not HFD. Diet-induced obesity impairs pulmonary Klebsiella clearance and augments blood dissemination by reducing neutrophil killing and ROI due to impaired glucose transport.

We present a retrospective study of 65 cases of solitary fibrous tumors (SFTs) of several localizations including the most common site of origin in the pleura and lungs. SFTs are mesenchymal fibroblastic tumors with an unpredictable biological potential ranging from benign to malignant. We investigated morphologic characteristics, proliferation activity evaluated by immunohistochemical expression of Ki-67 antigen, and the existence of NAB2-STAT6 fusion gene together with Ki-67, TPX2, and TERT mRNA expression levels. The aim was to define relationships between proliferation activity and biological potential and progression of the disease. We measured Ki-67, TPX2, and TERT mRNA levels using quantitative real-time reverse transcription PCR (RQ-RT-PCR). We observed a significant association between increased Ki-67 and TERT mRNA levels and the SFTs with malignant potential. Also, we investigated the effect of TERT promoter mutation on telomerase activation and patient outcome in our SFT cohort. We verified that TERT promoter mutation was frequent (36.6%) and present in a majority of malignant SFTs and SFTs with uncertain biological behavior. TERT promoter mutation alone predicted the disease recurrence.

Cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates the translation of numerous mRNAs. We previously showed that AU‐rich binding factor 1 (AUF1) regulates Cpeb1 expression through the 3’ untranslated region (3’UTR). To investigate the molecular basis of the regulatory potential of the Cpeb1 3’UTR, here we performed reporter analyses that examined expression levels of Gfp reporter mRNA containing the Cpeb1 3’UTR. Our findings indicate that CPEB1 represses the translation of Cpeb1 mRNA and that miR‐145a‐5p and let‐7b‐5p are involved in the reduction in Cpeb1 expression in the absence of AUF1. These results suggest that Cpeb1 expression is post‐transcriptionally regulated by AUF1, CPEB1, and microRNAs., We have previously shown that loss of interaction between AREs in the Cpeb1 3’UTR and AUF1, an mRNA decay factor, increased Cpeb1 mRNA levels but reduced the protein levels (Oe S. et al. 2021, Biochem Biophys Res Commun 534, 491‐497). In this study, we revealed that Cpeb1 expression is post‐transcriptionally regulated by multiple inhibitory machineries that are regulated by AUF1, CPEB1, and microRNAs.

It has been reported that N6-methyladenosine (m6A) methyltransferase-like 3 (METTL3) plays an important role in zygote genome activation during embryonic development, but the effects of METTL3 under oxidative stress in the early development of goat embryos remain largely unknown. In this study, zygotes were monitored at 72 and 168 h after fertilization, and they developed to the 8-cell stage and blastocyst stage under hypoxic conditions and normoxic conditions. Single-cell transcriptome sequencing was performed at the 8-cell stage and the blastocyst stage in the goat embryos, the differentially expressed METTL3 was screened from the sequencing results. We found that microinjection of small interfering RNA (siRNA) against METTL3 caused developmental arrest, both 8-cell rates (37.45 ± 2.21% vs. 47.09 ± 1.38%; P < 0.01) and blastocyst rates of Si-METTL3 (12.17% ± 2.84 vs. 20.83 ± 3.61%; P < 0.01) in Si-METTL3 group were significantly decreased compared with that of control under hypoxic conditions, significant changes were found in the m6A-related genes and the expression levels of critical transcription factors, such as, NANOG, GATA3, CDX2 and SOX17, were decreased. This study revealed the key role of METTL3 in the regulation of embryonic development under oxidative stress, and laid the foundation for further study of the crucial mechanism of oxidative stress during the early embryonic development of goats.

Aminoacyl tRNA synthetases (ARSs) are a group of proteins, acting as transporters to transfer and attach the appropriate amino acids onto their cognate tRNAs for translation. So far, 18 out of 20 cytoplasmic ARSs are reported to be connected to different neuropathy disorders with multi-organ defects that are often accompanied with developmental delays. Thus, it is important to understand functions and impacts of ARSs at the whole organism level. Here, we systematically analyzed the spatiotemporal expression of 14 ars and 2 aimp genes during development in zebrafish that have not be previously reported. Not only in the brain, their dynamic expression patterns in several tissues such as in the muscles, liver and intestine suggest diverse roles in a wide range of development processes in addition to neuronal function, which is consistent with potential involvement in multiple syndrome diseases associated with ARS mutations. In particular, hinted by its robust expression pattern in the brain, we confirmed that aimp1 is required for the formation of cerebrovasculature by a loss-of-function approach. Overall, our systematic profiling data provides a useful basis for studying roles of ARSs during development and understanding their potential functions in the etiology of related diseases.

Fibrillin-1 (FBN1) functions as a structural protein in the ovary, while the role of its protein product asprosin remains unknown. Both proteins are encoded by the FBN1 gene and when it is cleaved at the C-terminal end, asprosin is produced. Asprosin is associated with various metabolic parameters and sex-related hormones in women. One goal of this research was to quantify FBN1 and the presumed asprosin receptor, olfactory receptor family 4 subfamily M member 1 (OR4M1) mRNA in water buffalo granulosa cells and correlate them to aromatase (CYP19A1) gene expression. A second goal was to determine the effect of asprosin on follicular growth in vivo. In Exp. 1, ovaries were collected from a local slaughterhouse, follicular fluid and granulosa cells from small (6 mm) and large (6-13 mm) follicles were aspirated, cellular RNA extracted for gene expression analysis, data analyzed using ANOVA, and Pearson correlation coefficients were calculated among FBN1, OR4M1, and CYP19A1 gene expression. In Exp. 2, an intra-follicular injection of asprosin (600 ng of asprosin/194 μL of PBS) or vehicle (200 μL of PBS; Controls) was given via the theca layer of the dominant follicle of synchronized cows (n = 5/group) 1 day after injection of PGF2α, follicle sizes were measured daily via transrectal ultrasonography for 3 days, a two-way repeated measures ANOVA was used to determine the effect of asprosin on growth rate of follicles from day 0-2, and Chi-square analysis for the percentage of cows ovulated 2 days following asprosin injections. In Exp. 1, FBN1 mRNA abundance was 1.9-fold greater in cells of follicular aspirates from small than large follicles (P 0.05), but abundance of OR4M1 and CYP19A1 mRNA did not differ (P 0.10) between the two sizes of follicles. Abundance of FBN1 mRNA was positively correlated with CYP19A1 (r = 0.55, P 0.05) and OR4M1 mRNA (r = 0.50, P 0.06) across follicle sizes. In Exp. 2, cows treated with asprosin revealed a greater follicle growth rate from day 0-2 (63.4% increase in diameter) than placebo cows (36.8% increase in diameter) post-injection, and more follicles from asprosin treatment vs. control group (100% vs. 20%; P 0.05) ovulated within 2 days. These findings suggest that FBN1 may be developmentally regulated in follicular cells, and that asprosin may induce follicular growth in buffaloes, but further studies will be required to determine if asprosin directly regulates estradiol production during follicle development.

As a common phenomenon existing in almost all genomes, codon usage bias has been studied for a long time. Codon optimization is a frequently used strategy to accelerate protein synthesis rate. Besides regulating protein translation speed, codon usage bias has also be reported to affect co-translation folding and transcription. P. pastoris is a well-developed expression system, whose efficiency is tightly correlated with commercial value. However, few studies focus on the role of codon usage bias in affecting protein expression in P. pastoris. Besides, many genes in P. pastoris genome show significant negative correlation between codon usage bias and protein structural disorder tendency. It’s not known whether this feature is important for their expression. In order to answer these questions, we picked 4 P. pastoris gene candidates with strong negative correlation between codon usage bias and protein structural disorder. We then performed full-length codon optimization which completely eliminated the correlation. Protein and RNA assays were then used to compare protein and mRNA levels before and after codon optimization. As a result, codon optimization failed to elevate their protein expression levels, and even resulted in a decrease. As represented by the trypsin sensitivity assays, codon optimization also altered the protein structure of 0616 and 0788. Besides protein, codon optimization also affected mRNA levels. Shown by in vitro and in vivo RNA degradation assays, the mRNA stability of 0616, 0788 and 0135 were also altered by codon optimization. For each gene, the detailed effect may be related with its specific sequence and protein structure. Our results suggest that codon usage bias is an important factor to regulate gene expression level, as well as mRNA and protein stabilities in P. pastoris. “Extreme” codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored. Compromised strategies should be tried if expression is not successful. Besides, codon optimization may affect protein structural conformation more severely in structural disordered proteins.

The conceptual origins of ribosome specialization can be traced back to the earliest days of molecular biology. Yet, this field has only recently begun to gather momentum, with numerous studies identifying distinct heterogeneous ribosome populations across multiple species and model systems. It is proposed that some of these compositionally distinct ribosomes may be functionally specialized and able to regulate the translation of specific mRNAs. Identification and functional characterization of specialized ribosomes has the potential to elucidate a novel layer of gene expression control, at the level of translation, where the ribosome itself is a key regulatory player. In this review, we discuss different sources of ribosome heterogeneity, evidence for ribosome specialization, and also the future directions of this exciting field.

Background: Allergic rhinitis (AR) is caused by allergic reaction to allergens such as pollen. Galanin (GAL), a neuropeptide that regulates inflammatory processes, is widely expressed in the central and peripheral nervous systems. Although neuropeptides are implicated in arthritis and chemically induced ileitis, their roles in AR remain unclear. Methods: We developed a murine model of AR and generated control, systemic sensitization, mild AR, and severe AR groups. We examined GAL and GAL receptor (GALR) mRNA and protein levels and localization patterns in each group using reverse transcription PCR, western blotting, and immunohistochemical analyses. Additionally, we evaluated the effects of M871, a GALR2 antagonist, on mice with severe AR. Results: Gal and Galr2 are expressed in nasal mucosa and brain (control) samples from control and AR mice. GAL and GALR2 were expressed at similar levels and localized to ciliated epithelial and submucosal gland cells of the nasal mucosa in all four groups. Intranasal M871 administration significantly reduced the incidence of nose rubbing behaviors and sneezing (p

Background It is hypothesized that demographic variables and mRNA expression levels in the N-methyl-D-aspartate receptor (NMDAR) genes can be employed as potential biomarkers to predict bipolar disorder using artificial intelligence and machine learning approaches. Methods To determine bipolar status, we established a logistic ridge regression model resulting from the analysis of age, gender, and mRNA expression levels in 7 NMDAR genes in the blood of 51 bipolar patients and 139 unrelated healthy individuals in the Taiwanese population. The NMDAR genes encompasses COMT, GCAT, NRG1, PSAT1, SHMT2, SLC1A4, and SRR. We also compared our approach with various state-of-the-art algorithms such as support vector machine and C4.5 decision tree. Results The analysis revealed that the mRNA expression levels of COMT, GCAT, NRG1, PSAT1, SHMT2, SLC1A4, and SRR were associated with bipolar disorder. Moreover, the logistic ridge regression model (area under the receiver operating characteristic curve = 0.922) performed maximally among predictive models to infer the complicated relationship between bipolar disorder and biomarkers. Additionally, the results for the age- and gender-matched cohort were similar to those of the unmatched cohort. Limitations The cross-sectional study design limited the predictive value. Conclusion This is the first study demonstrating that the mRNA expression levels in the NMDAR genes may be altered in patients with bipolar disorder, thereby supporting the NMDAR hypothesis of bipolar disorder. The study also indicates that the mRNA expression levels in the NMDAR genes could serve as potential biomarkers to distinguish bipolar patients from healthy controls using artificial intelligence and machine learning approaches.

Background In many cancers, microRNAs (miRs) contribute to metastatic progression by modulating phenotypic reprogramming processes such as epithelial-mesenchymal plasticity. This can be driven by miRs targeting multiple mRNA transcripts, inducing regulated changes across large sets of genes. The miR-target databases TargetScan and DIANA-microT predict putative relationships by examining sequence complementarity between miRs and mRNAs. However, it remains a challenge to identify which miR-mRNA interactions are active at endogenous expression levels, and of biological consequence. Methods We developed a workflow to integrate TargetScan and DIANA-microT predictions into the analysis of data-driven associations calculated from transcript abundance (RNASeq) data, specifically the mutual information and Pearson’s correlation metrics. We use this workflow to identify putative relationships of miR-mediated mRNA repression with strong support from both lines of evidence. Applying this approach systematically to a large, published collection of unique melanoma cell lines – the Ludwig Melbourne melanoma (LM-MEL) cell line panel – we identified putative miR-mRNA interactions that may contribute to invasiveness. This guided the selection of interactions of interest for further in vitro validation studies. Results Several miR-mRNA regulatory relationships supported by TargetScan and DIANA-microT demonstrated differential activity across cell lines of varying matrigel invasiveness. Strong negative statistical associations for these putative regulatory relationships were consistent with target mRNA inhibition by the miR, and suggest that differential activity of such miR-mRNA relationships contribute to differences in melanoma invasiveness. Many of these relationships were reflected across the skin cutaneous melanoma TCGA dataset, indicating that these observations also show graded activity across clinical samples. Several of these miRs are implicated in cancer progression (miR-211, -340, -125b, −221, and -29b). The specific role for miR-29b-3p in melanoma has not been well studied. We experimentally validated the predicted miR-29b-3p regulation of LAMC1 and PPIC and LASP1, and show that dysregulation of miR-29b-3p or these mRNA targets can influence cellular invasiveness in vitro. Conclusions This analytic strategy provides a comprehensive, systems-level approach to identify miR-mRNA regulation in high-throughput cancer data, identifies novel putative interactions with functional phenotypic relevance, and can be used to direct experimental resources for subsequent experimental validation. Computational scripts are available: http://github.com/uomsystemsbiology/LMMEL-miR-miner Electronic supplementary material The online version of this article (doi:10.1186/s12943-016-0554-y) contains supplementary material, which is available to authorized users.

To examine the effect of acute and chronic exercise on adipose tissue GLUT4 expression, a total of 20 healthy, male subjects performed one of two studies. Ten subjects performed cycle ergometer exercise for 60 min at 73 ± 2% VO 2 peak and abdominal adipose tissue samples were obtained immediately before and after exercise and after 3 h of recovery. Another 10 subjects completed 10 days of exercise training, comprising a combination of six sessions of 60 min at 75% VO 2 peak and four sessions of 6 × 5 min at 90% VO 2 peak, separated by 3 min at 40% VO 2 peak. Abdominal adipose tissue and vastus lateralis muscle samples were obtained before training and 24 h after the last training session. A single bout of exercise did not change adipose tissue GLUT4 mRNA; however, there was a small, but significant, reduction in adipose tissue GLUT4 protein expression 3 h after exercise. There were no changes in adipose tissue GLUT4 or COX‐IV expression following exercise training. In contrast, skeletal muscle GLUT4 and COX‐IV were increased by 47% and 44%, respectively following exercise training. The exercise training‐induced increase in GLUT4 expression was similar in both type I and type IIa single muscle fibers. Our results indicate that neither a single exercise bout, nor 10 days of exercise training, increased adipose tissue GLUT4, in contrast with the increases observed in skeletal muscle GLUT4 expression.

Protein synthesis is a central process in gene expression and the development of efficient in vitro translation systems has been the focus of scientific efforts for decades. The production of translation-competent lysates originating from human cells or tissues remains challenging, mainly due to the variability of cell lysis conditions. Here we present a robust and fast method based on dual centrifugation that allows for detergent-free cell lysis under controlled mechanical forces. We optimized the lysate preparation to yield cytoplasm-enriched extracts from human cells that efficiently translate mRNAs in a cap-dependent as well as in an IRES-mediated way. Reduction of the phosphorylation state of eIF2α using recombinant GADD34 and 2-aminopurine considerably boosts the protein output, reinforcing the potential of this method to produce recombinant proteins from human lysates.

A tool to probe SARS-CoV-2 biology To develop therapies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emerging variants, it is important to understand the viral biology and the effect of mutations. However, this is challenging because live virus can only be studied in a few laboratories that meet stringent safety standards. Syed et al . describe a virus-like particle (VLP) that comprises the four SARS-CoV-2 structural proteins, but instead of packaging viral RNA, it packages messenger RNA (mRNA) that expresses a reporter protein (see the Perspective by Johnson and Menachery). The amount of reporter expressed in receiver cells depends on the efficiency of packaging and assembly in the producer cells and the efficiency of entry into receiver cells. Mutations in the nucleocapsid protein that are found in more transmissible variants increase mRNA packaging and expression. The VLPs provide a platform for studying the effect of mutations in the structural proteins and for screening therapeutics. —VV

MicroRNA (miRNA) expression is dysregulated in human tumors, thereby contributing to tumorigenesis through altered expression of mRNA. Thus, identification of the relationships between miRNAs and mRNAs is important for evaluating the molecular mechanisms of tumors. Additionally, elucidation of the molecular features of serrated lesions is essential in colorectal tumorigenesis. Here, we examined the relationships of miRNA and mRNA expressed in serrated lesions, including 26 sessile serrated lesions (SSLs), 12 traditional serrated adenomas (TSAs), and 11 colorectal cancers (CRCs) with a microsatellite instability (MSI) phenotype using crypt isolation. We divided the samples into the first and second cohorts for validation. Array-based expression analyses were used to evaluate miRNAs and mRNAs with opposite expression patterns in isolated tumor glands. In addition, we validated the relationships of miRNA/mRNA pairs in the second cohort using real-time polymerase chain reaction. We found that the expression of miRNA-5787 was correlated with reciprocal expression of 2 mRNAs, i.e., SRRM2 and POLR2J3, in SSL samples. In TSA samples, 2 pairs of miRNAs/mRNAs showing opposite expression patterns, i.e., miRNA-182-5p/ETF1 and miRNA-200b-3p/MYB, were identified. Ultimately, three pairs of miRNAs/mRNAs with opposite expression patterns, including miRNA-222-3p/SLC26A3, miRNA-6753-3p/FABP1, and miRNA-222-3p/OLFM4, were retained in CRC with an MSI phenotype. Finally, we performed transfection with an miR-222-3p mimic to confirm the expression of SLC26A3 and OLFM4; the results showed that ectopic expression of miR-222-3p moderately suppressed OLFM4 and downregulated SLC26A3 to some extent. Overall, our results provided basic insights into the evaluation of colorectal tumorigenesis of serrated lesions and CRC with an MSI phenotype. This article is protected by copyright. All rights reserved.

The BNT162b2 messenger RNA (mRNA) vaccine against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been shown to be safe and effective in immunocompetent patients. The safety and efficacy of this vaccine in liver transplantation (LT) recipients is still under evaluation. The objective of this study was to assess the safety and efficacy of the BNT162b2 vaccine among transplant recipients. The immune responses of 76 LT recipients receiving 2 doses of the vaccine were compared with those of 174 age‐matched immunocompetent controls. Postvaccination immunoglobulin G (IgG) antibodies against the receptor‐binding domain (RBD) of SARS‐CoV‐2 and neutralizing antibodies (NA) to the BNT162b2 mRNA vaccine were determined at least 14 days after the second dose of the vaccine. IgG antibody titers ≥1.1 were defined as positive antibodies. Adverse effects were monitored during the study period. Following administration of the second dose, transplant recipients showed reduced immune responses compared with controls (72% versus 94.2%; P