Identification of lncRNA-based regulatory mechanisms of Takifugu rubripes growth traits in fast and slow-growing family lines.

Family selection is an important method in fish aquaculture because growth is the most important economic trait. Fast-and slow-growing families of tiger puffer fish (Takifugu rubripes) have been established through family selection. The development of teleost fish is primarily controlled by the growth hormone (GH)-insulin-like growth factor 1 (IGF-1) axis that includes the hypothalamus-pituitary-liver. In this study, the molecular mechanisms underlying T. rubripes growth were analyzed by comparing transcriptomes from fast- and slow-growing families. The expressions of 214 lncRNAs were upregulated, and those of 226 were downregulated in the brain tissues of the fast-growing T. rubripes family compared to those of the slow-growing family. Differentially expressed lncRNAs centrally regulate mitogen-activated protein kinase (MAPK) and forkhead box O (FoxO) signaling pathways. Based on the results of lncRNA-gene network construction, we found that lncRNA3133.13, lncRNA23169.1, lncRNA23145.1, and lncRNA23141.3 regulated all four genes (igf1, mdm2, flt3, and cwf19l1). In addition, lncRNA7184.10 may be a negative regulator of rasgrp2 and a positive regulator of gadd45ga, foxo3b, and dusp5. These target genes are associated with the growth and development of organisms through the PI3K/AKT and MAPK/ERK pathways. Overall, transcriptomic analyses of fast- and slow-growing families of T. rubripes provided insights into the molecular mechanisms of teleost fish growth rates. Further, these analyses provide evidence for key genes related to growth regulation and the lncRNA expression regulatory network that will provide a framework for improving puffer fish germplasm resources.

A pattern recognition receptor CgTLR3 involves in regulating the proliferation of haemocytes in oyster Crassostrea gigas.

Toll-like receptors (TLRs) are expressed on various immune cells as key elements of innate and adaptive immunity, and they also play significant roles in regulating cell proliferation and differentiation. In the present study, the binding activity of CgTLR3 to PAMPs and CgMyD88-2, and its role in mediating the proliferation of haemocytes was investigated. The recombinant proteins of the extracellular six LRR domains (rCgTLR3-LRR) and intracellular TIR domain (rCgTLR3-TIR) of CgTLR3 were obtained respectively. rCgTLR3-LRR exhibited binding activity to lipopolysaccharide (LPS), peptidoglycan (PGN), mannan (MAN) and Poly (I:C), with the highest affinity for LPS. While rCgTLR3-TIR displayed binding activity to the recombinant protein of rCgMyD88-2, with KD value of 7.22 × 10-7 M. The CgTLR3 mRNA and protein were detected in three subpopulations of oyster haemocytes, and they were mainly concentrated in granulocytes, which was 7.27-fold (p < 0.05) of that in semi-granulocytes and 8.51-fold (p < 0.01) of that in agranulocytes. The percentage of CgTLR3 positive cells (FITC+ haemocytes) in granulocytes was 4.45-fold (p < 0.01) and 2.57-fold (p < 0.05) of that in agranulocytes and semi-granulocytes, respectively. After Vibrio splendidus stimulation, the mRNA expression level of CgTLR3 in haemocytes significantly upregulated at 6 h and 12 h, which was 2.93-fold (p < 0.05) and 4.15-fold (p < 0.05) of that in the control group. After the expression of CgTLR3 was inhibited by the injection of si-CgTLR3, the expression levels of transcription factors associated with hematopoiesis (CgGATA, CgRunx), cell cycle-related genes (CgPCNA, CgCDC-45, CgCDK-2), the agranulocyte marker CgCD-9, the granulocyte marker CgAATase, and the inflammatory factor CgIL17-1 significantly decreased (p < 0.05) after the V. splendidus stimulation, which were 0.43-fold, 0.83-fold, 0.48-fold, 0.44-fold, 0.53-fold, 0.7-fold, 0.62-fold, and 0.47-fold of that in NC + V. s group in vivo, respectively. Meanwhile, the percentage of EdU+ haemocytes in si-CgTLR3+V. s group was significantly reduced by 0.54-fold (p < 0.05) compared to the control group (2.7%). These results collectively indicated that CgTLR3 was involved in modulating the proliferation of haemocytes by regulating the expression of proliferation-related genes and inflammatory factor in oyster C. gigas.

CgWnt-1 regulates haemocyte proliferation during immune response of oyster Crassostrea gigas.

Recent findings regarding the immunomodulatory role of Wnt signaling suggest that it is significant in regulating the differentiation and proliferation of immune cells. In the present study, a Wnt-1 homolog (designated as CgWnt-1) with a conserved WNT1 domain was identified from oyster Crassostrea gigas. The transcripts of CgWnt-1 were barely expressed in egg to gastrula stage during early embryogenesis, and up-regulated significantly in the trochophore to juvenile stage. The mRNA transcripts of CgWnt-1 were detected in different tissues of adult oyster, with an extremely high expression level in the mantle, which was 77.38-fold (p < 0.05) of that in labial palp. After Vibrio splendidus stimulation, the mRNA expression levels of CgWnt-1 and Cgß-catenin in haemocytes up-regulated significantly at 3, 12, 24, and 48 h (p < 0.05). After injection of recombinant protein (rCgWnt-1) into oyster in vivo, the expressions of Cgß-catenin, cell proliferation related genes CgRunx-1 and CgCDK-2 in haemocytes significantly up-regulated, which were 4.86-fold (p < 0.05), 9.33-fold (p < 0.05), 6.09-fold (p < 0.05) of those in rTrx group, respectively. The percentage of EDU+ cells in haemocytes also significantly increased (2.88-fold of that in control group, p < 0.05) at 12 h after rCgWnt-1 treatment. When the Wnt signal inhibitor C59 was injected simultaneously with rCgWnt-1, the expressions of Cgß-catenin, CgRunx-1, and CgCDK-2 were significantly reduced, which were 0.32-fold (p < 0.05), 0.16-fold (p < 0.05), and 0.25-fold (p < 0.05) of that in rCgWnt-1 group, respectively, and the percentage of EDU+ cells in haemocytes was also significantly inhibited (0.15-fold compared with that in rCgWnt-1 group, p < 0.05). These results suggested that the conserved CgWnt-1 could modulate haemocytes proliferation via regulating cell cycle related genes and involved in the immune response of oysters.

Myofibroblast Ccn3 is regulated by Yap and Wwtr1 and contributes to adverse cardiac outcomes.

Introduction: While Yap and Wwtr1 regulate resident cardiac fibroblast to myofibroblast differentiation following cardiac injury, their role specifically in activated myofibroblasts remains unexplored. Methods: We assessed the pathophysiological and cellular consequence of genetic depletion of Yap alone (Yap fl/fl ;Postn MCM ) or Yap and Wwtr1 (Yap fl/fl ;Wwtr1 fl/+ ;Postn MCM ) in adult mouse myofibroblasts following myocardial infarction and identify and validate novel downstream factors specifically in cardiac myofibroblasts that mediate pathological remodeling. Results: Following myocardial infarction, depletion of Yap in myofibroblasts had minimal effect on heart function while depletion of Yap/Wwtr1 resulted in smaller scars, reduced interstitial fibrosis, and improved ejection fraction and fractional shortening. Single cell RNA sequencing of interstitial cardiac cells 7 days post infarction showed suppression of pro-fibrotic genes in fibroblasts derived from Yap fl/fl ,Wwtr1 fl/+ ;Postn MCM hearts. In vivo myofibroblast depletion of Yap/Wwtr1 as well in vitro knockdown of Yap/Wwtr1 dramatically decreased RNA and protein expression of the matricellular factor Ccn3. Administration of recombinant CCN3 to adult mice following myocardial infarction remarkably aggravated cardiac function and scarring. CCN3 administration drove myocardial gene expression of pro-fibrotic genes in infarcted left ventricles implicating CCN3 as a novel driver of cardiac fibrotic processes following myocardial infarction. Discussion: Yap/Wwtr1 depletion in myofibroblasts attenuates fibrosis and significantly improves cardiac outcomes after myocardial infarction and we identify Ccn3 as a factor downstream of Yap/Wwtr1 that contributes to adverse cardiac remodeling post MI. Myofibroblast expression of Yap, Wwtr1, and Ccn3 could be further explored as potential therapeutic targets for modulating adverse cardiac remodeling post injury.

tRNA-Derived RNA Fragments Are Novel Biomarkers for Diagnosis, Prognosis, and Tumor Subtypes in Prostate Cancer.

BACKGROUND: tRNA-derived RNA fragments (tRFs) are a novel class of small ncRNA that are derived from precursor or mature tRNAs. Recently, the general relevance of their roles and clinical values in tumorigenesis, metastasis, and recurrence have been increasingly highlighted. However, there has been no specific systematic study to elucidate any potential clinical significance for these tRFs in prostate adenocarcinoma (PRAD), one of the most common and malignant cancers that threatens male health worldwide. Here, we investigate the clinical value of 5'-tRFs in PRAD. METHODS: Small RNA sequencing data were analyzed to discover new 5'-tRFs biomarkers for PRAD. Machine learning algorithms were used to identify 5'-tRF classifiers to distinguish PRAD tumors from normal tissues. LASSO and Cox regression analyses were used to construct 5'-tRF prognostic predictive models. NMF and consensus clustering analyses were performed on 5'-tRF profiles to identify molecular subtypes of PRAD. RESULTS: The overall levels of 5'-tRFs were significantly upregulated in the PRAD tumor samples compared to their adjacent normal samples. tRF classifiers composed of 13 5'-tRFs achieved AUC values as high as 0.963, showing high sensitivity and specificity in distinguishing PRAD tumors from normal samples. Multiple 5'-tRFs were identified as being associated with the PRAD prognosis. The tRF score, defined by a set of eight 5'-tRFs, was highly predictive of survival in PRAD patients. The combination of tRF and Gleason scores showed a significantly better performance than the Gleason score alone, suggesting that 5'-tRFs can offer PRAD patients additional and improved prognostic information. Four molecular subtypes of the PRAD tumor were identified based on their 5'-tRF expression profiles. Genetically, these 5'-tRFs PRAD tumor subtypes exhibited distinct genomic landscapes in tumor cells. Clinically, they showed marked differences in survival and clinicopathological features. CONCLUSIONS: 5'-tRFs are potential clinical biomarkers for the diagnosis, prognosis, and classification of tumor subtypes on a molecular level. These can help clinicians formulate personalized treatment plans for PRAD patients and may have similar potential applications for other disease types.

Characterization of lncRNAs in mycorrhizal tomato and elucidation of the role of lncRNA69908 in disease resistance.

Long noncoding RNAs (lncRNAs) have attracted widespread attention because of their meaningful roles in various plant biological processes. However, the potential functions of lncRNAs in the plant-beneficial microorganism interactions have not been fully explored. Arbuscular mycorrhiza (AM) symbiosis is accompanied by the systemic induction of defense responses in the host leaves. In the present study, we globally profiled lncRNA expression and explored their potential regulatory roles in AM fungi-inoculated tomato leaves. Among 851 differentially expressed lncRNAs, a novel lncRNA (lncRNA69908) that was significantly downregulated in the leaves of AM fungi inoculated tomato, affected tomato resistance after pathogen infection. One of the competing endogenous RNA networks, lncRNA69908-sly-miR319c, was verified by using a coexpression system. Silencing of lncRNA69908 or overexpression of sly-miR319c enhanced tomato resistance to Phytophthora infestans, whereas overexpression of lncRNA69908 decreased the reactive oxygen species scavenging. As above, we speculated that lncRNA69908 may be involved in mycorrhiza-induced defense responses. Our findings can broaden the knowledge on the potential regulatory roles of ncRNAs in AM symbiosis.

Circulating S-Glutathionylated cMyBP-C as a Biomarker for Cardiac Diastolic Dysfunction.

Background cMyBP-C (Cardiac myosin binding protein-C) regulates cardiac contraction and relaxation. Previously, we demonstrated that elevated myocardial S-glutathionylation of cMyBP-C correlates with diastolic dysfunction (DD) in animal models. In this study, we tested whether circulating S-glutathionylated cMyBP-C would be a biomarker for DD. Methods and Results Humans, African Green monkeys, and mice had DD determined by echocardiography. Blood samples were acquired and analyzed for S-glutathionylated cMyBP-C by immunoprecipitation. Circulating S-glutathionylated cMyBP-C in human participants with DD (n=24) was elevated (1.46±0.13-fold, P=0.014) when compared with the non-DD controls (n=13). Similarly, circulating S-glutathionylated cMyBP-C was upregulated by 2.13±0.47-fold (P=0.047) in DD monkeys (n=6), and by 1.49 (1.22-2.06)-fold (P=0.031) in DD mice (n=5) compared with the respective non-DD controls. Circulating S-glutathionylated cMyBP-C was positively correlated with DD in humans. Conclusions Circulating S-glutathionylated cMyBP-C was elevated in humans, monkeys, and mice with DD. S-glutathionylated cMyBP-C may represent a novel biomarker for the presence of DD.

Potential Use of Serum Proteomics for Monitoring COVID-19 Progression to Complement RT-PCR Detection.

RT-PCR is the primary method to diagnose COVID-19 and is also used to monitor the disease course. This approach, however, suffers from false negatives due to RNA instability and poses a high risk to medical practitioners. Here, we investigated the potential of using serum proteomics to predict viral nucleic acid positivity during COVID-19. We analyzed the proteome of 275 inactivated serum samples from 54 out of 144 COVID-19 patients and shortlisted 42 regulated proteins in the severe group and 12 in the non-severe group. Using these regulated proteins and several key clinical indexes, including days after symptoms onset, platelet counts, and magnesium, we developed two machine learning models to predict nucleic acid positivity, with an AUC of 0.94 in severe cases and 0.89 in non-severe cases, respectively. Our data suggest the potential of using a serum protein-based machine learning model to monitor COVID-19 progression, thus complementing swab RT-PCR tests. More efforts are required to promote this approach into clinical practice since mass spectrometry-based protein measurement is not currently widely accessible in clinic.

Magnesium Deficiency Causes a Reversible, Metabolic, Diastolic Cardiomyopathy.

Background Dietary Mg intake is associated with a decreased risk of developing heart failure, whereas low circulating Mg level is associated with increased cardiovascular mortality. We investigated whether Mg deficiency alone could cause cardiomyopathy. Methods and Results C57BL/6J mice were fed with a low Mg (low-Mg, 15-30 mg/kg Mg) or a normal Mg (nl-Mg, 600 mg/kg Mg) diet for 6 weeks. To test reversibility, half of the low-Mg mice were fed then with nl-Mg diet for another 6 weeks. Low-Mg diet significantly decreased mouse serum Mg (0.38±0.03 versus 1.14±0.03 mmol/L for nl-Mg; P<0.0001) with a reciprocal increase in serum Ca, K, and Na. Low-Mg mice exhibited impaired cardiac relaxation (ratio between mitral peak early filling velocity E and longitudinal tissue velocity of the mitral anterior annulus e, 21.1±1.1 versus 15.4±0.4 for nl-Mg; P=0.011). Cellular ATP was decreased significantly in low-Mg hearts. The changes were accompanied by mitochondrial dysfunction with mitochondrial reactive oxygen species overproduction and membrane depolarization. cMyBPC (cardiac myosin-binding protein C) was S-glutathionylated in low-Mg mouse hearts. All these changes were normalized with Mg repletion. In vivo (2-(2,2,6,6-tetramethylpiperidin-1-oxyl-4-ylamino)-2-oxoethyl)triphenylphosphonium chloride treatment during low-Mg diet improved cardiac relaxation, increased ATP levels, and reduced S-glutathionylated cMyBPC. Conclusions Mg deficiency caused a reversible diastolic cardiomyopathy associated with mitochondrial dysfunction and oxidative modification of cMyBPC. In deficiency states, Mg supplementation may represent a novel treatment for diastolic heart failure.

ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets.

SUMMARY: The rapid progresses of high-throughput sequencing technology-based omics and mass spectrometry-based proteomics, such as data-independent acquisition and its penetration to clinical studies have generated increasing number of proteomic datasets containing hundreds to thousands of samples. To analyze these quantitative proteomic datasets and other omics (e.g. transcriptomics and metabolomics) datasets more efficiently and conveniently, we present a web server-based software tool ProteomeExpert implemented in Docker, which offers various analysis tools for experimental design, data mining, interpretation and visualization of quantitative proteomic datasets. ProteomeExpert can be deployed on an operating system with Docker installed or with R language environment. AVAILABILITY AND IMPLEMENTATION: The Docker image of ProteomeExpert is freely available from https://hub.docker.com/r/lifeinfo/proteomeexpert. The source code of ProteomeExpert is also openly accessible at http://www.github.com/guomics-lab/ProteomeExpert/. In addition, a demo server is provided at https://proteomic.shinyapps.io/peserver/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon.

A large amount of omics data and number of bioinformatics tools has been produced. However, the methods for further exploring omics data are simple, in particular, to mine key regulatory genes, which are a priority concern in biological systems, and most of the specific functions are still unknown. First, raw data of two genotypes of melon (susceptible and resistant) were obtained by transcriptome analysis. Second, 391 transcription factors (TFs) were identified from the plant transcription factor database and cucurbit genomics database. Then, functional enrichment analysis indicated that these genes were mainly annotated in the process of transcription regulation. Third, 243 and 230 module-specific TFs were screened by weighted gene coexpression network analysis and short time series expression miner, respectively. Several TF genes, such as WRKYs and bHLHs, were regarded as key regulatory genes according to the values of significantly different modules. The coexpression network showed that these TF genes were significant correlated with resistance (R) genes, such as DRP2, RGA3, DRP1 and NB-ARC. Fourth, cis-acting element analysis illustrated that these R genes may bind to WRKY and bHLH. Finally, the expression of WRKY genes was verified by quantitative reverse transcription PCR (RT-qPCR). Phylogenetic analysis was carried out to further confirm that these TFs may play a critical role in Curcurbitaceae disease resistance. This study provides a new optimized combination strategy to explore the functions of TFs in a wide spectrum of biological processes. This strategy may also effectively predict potential relationships in the interactions of essential genes.

Interactions and links among the noncoding RNAs in plants under stresses.

KEY MESSAGE: The complex interplay among sRNAs, lncRNAs and circRNAs has been implicated in plants under biotic and abiotic stresses. Here, we review current advances in our understanding of ncRNA interactions and links, which have considerable potential for improving the agronomic traits and the environmental adaptability of plants. Plants can respond to biotic or abiotic stresses. To cope with various conditions, numerous intricate molecular regulatory mechanisms have evolved in plants. Noncoding RNAs (ncRNAs) can be divided into small noncoding RNAs (sRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). Emerging evidence has demonstrated that interplay among the ncRNAs acts as a novel layer in the regulatory mechanisms, which has attracted substantial interest. Links between sRNAs can affect plant immune responses and development in synergistic or antagonistic manners. Additionally, multiple interactions between lncRNAs and sRNAs are involved in crop breeding, disease resistance and high tolerance to environmental stresses. Here, we summarize current knowledge of the interactions and links among the ncRNAs in plant responses to stresses and the methods for identifying ncRNA interactions. Furthermore, challenges and prospects for further progress in elucidating ncRNA interactions and links are highlighted.

Evidence for Inflammation as a Driver of Atrial Fibrillation.

Atrial fibrillation (AF) is one of the most common types of arrhythmias and increases cardiovascular morbidity and mortality. Current therapeutic approaches to AF that focus on rhythm control have high recurrence rates and no life prolongation value. While possible explanations include toxicity of current therapies, another likely explanation may be that current therapies do not address fundamental mechanisms of AF initiation and maintenance. Inflammation has been shown to affect signaling pathways that lead to the development of AF. This paper reviews the roles of inflammation in the occurrence, development, and mechanisms of AF and reviews the therapeutic implications of the correlation of inflammation and AF.

Development of fan-shaped tracker for single particle tracking.

With the development of super-resolution fluorescence microscopy, complex dynamic processes in living cells can be observed and recorded with unprecedented temporal and spatial resolution. Single particle tracking (SPT) is the most important step to explore the relationship between the spatio-temporal dynamics of subcellular molecules and their functions. Although previous studies have developed SPT algorithms to quantitatively analyze particle dynamics in cell, traditional tracking methods have poor performance when dealing with intersecting trajectories. This can be attributed to two main reasons: (a) they do not have point compensation process for overlapping objects; (b) they use inefficient motion prediction models. In this paper, we present a novel fan-shaped tracker (FsT) algorithm to reconstruct the trajectories of subcellular vesicles in living cells. We proposed a customized point compensation method for overlapping objects based on the fan-shaped motion trend of the particles. Furthermore, we validated the performance of the FsT in both simulated time-lapse movies with variable imaging quality and in real vesicle moving images. Meanwhile, we compared the performance of FsT with other five state-of-the-art tracking algorithms by using commonly defined measures. The results showed that our FsT achieves better performance in high signal-to-noise ratio conditions and in tracking of overlapping objects. We anticipate that our FsT method will have vast applications in tracking of moving objects in cell.

Identification of lncRNAs and their regulatory relationships with target genes and corresponding miRNAs in melon response to powdery mildew fungi.

Melon (Cucumis melo L.), an economically beneficial crop widely cultivated around the world, is vulnerable to powdery mildew (PM). However, the studies on molecular mechanism of melon response to PM fungi is still limited. Long non coding RNAs (lncRNAs) have emerged as new regulators in plants response to biotic stresses. We predicted and identified the intricate regulatory roles of lncRNAs in melon response to PM fungi. A total of 539 lncRNAs were identified from PM-resistant (MR-1) and susceptible melon (Top Mark), in which 254 were significantly altered after PM fungi infection. Multiple target genes of lncRNAs were found to be involved in the hydrolysis of chitin, callose deposition and cell wall thickening, plant-pathogen interaction and plant hormone signal transduction pathway. Additionally, a total of 42 lncRNAs possess the various functions with microRNAs (miRNAs), including lncRNAs that are targeted by miRNAs and function as miRNA precursors or miRNA sponges. These findings provide a comprehensive view of potentially functional lncRNAs, corresponding target genes and related lncRNA-miRNA pairs, which will greatly increase our knowledge of the mechanism underlying susceptibility and resistance to PM in melon.

Genome-wide identification, characterization and expression analysis of the TLP gene family in melon (Cucumis melo L.).

Thaumatin-like proteins (TLPs), which belong to pathogenesis-related (PR) protein family 5 (PR5), are involved in plant host defense and various developmental processes. The functions of the TLP family have been extensively discussed in multiple organisms, whereas the detailed information of this family in melon has not been reported yet. In this study, we identified 28 TLP genes in the melon genome and a N-terminal signal peptide was found highly conserved within each member of this family. Phylogeny analysis indicated that TLPs from melon and other plant species were clustered into ten groups. Twelve segmental and seven tandem duplication gene pairs that underwent purifying selection were identified. TLP genes expressed differentially in different tissues/organs, and were significantly induced after Podosphaera xanthii infection. TLPs in breeding line MR-1 tend to express early after pathogen infection compared with cultivar Top Mark. Our study provides a comprehensive understanding of the melon TLP family and demonstrates their potential roles in disease resistance, therefore provides more reference for further research.

LncRNA39026 Enhances Tomato Resistance to Phytophthora infestans by Decoying miR168a and Inducing PR Gene Expression.

Our previous study has indicated that a long noncoding RNA (lncRNA), lncRNA39026, can be responsive to Phytophthora infestans infection. However, the function and regulation mechanism of lncRNA39026 during tomato resistance to P. infestans are unknown. In this study, an lncRNA39026 sequence was cloned from tomato Zaofen No. 2, and this sequence contained an endogenous target mimicry for miR168a, which might suppress the expression of miR168a. LncRNA39026 was strongly downregulated at 3 h in the tomato plants infected with P. infestans, and its expression level displayed a negative correlation with the expression level of miR168a and a positive correlation with the expression levels of SlAGO1 genes (target gene of miR168a) upon P. infestans infection. Tomato plants in which lncRNA39026 was overexpressed displayed enhanced resistance to P. infestans, decreased level of miR168a, and increased level of SlAGO1, whereas the resistance was impaired, level of miR168a was increased, and level of SlAGO1 was decreased after lncRNA39026 silencing. In addition, lncRNA39026 could also induce the expression of pathogenesis-related (PR) genes, as shown by increased and decreased expression levels of PR genes in tomato plants with overexpressed and silenced lncRNA39026, respectively. The result demonstrated that lncRNA39026 might function to decoy miR168a and affect the expression of PR genes in tomato plants, increasing resistance to disease.

Sec3 knockdown inhibits TGF-ß induced epithelial-mesenchymal transition through the down-regulation of Akt phosphorylation in A549 cells.

The exocyst, an evolutionarily conserved octomeric protein complex, has been demonstrated as an essential component for vesicle tethering during cell exocytosis, and participates in various physiological processes in the cell. Although subunits of the exocyst complex have been reported to be involved in the regulation of TGF-ß induced cancer cell migration and epithelial-mesenchymal transition (EMT), the potential function of Sec3 in these regulated processes remains unclear. Here, we show that Sec3 knockdown abolishes TGF-ß stimulated A549 lung cancer cell migration in vitro and causes defects in the regulated EMT process. In addition, we find that depletion of Sec3 significantly inhibits TGF-ß stimulated Akt phosphorylation in A549 cells, whereas the increase of Smad2 phosphorylation is unaffected. Furthermore, replenishment of an RNAi-resistant form of Sec3 is shown to restore the defects of TGF-ß induced cell migration, EMT and Akt signaling activation. In summary, our study provides evidence that Sec3 is involved in TGF-ß induced cell migration and EMT processes, presumably through the regulation of PI3K/Akt signaling activation in A549 cancer cells.

Blocking the histone lysine 79 methyltransferase DOT1L alleviates renal fibrosis through inhibition of renal fibroblast activation and epithelial-mesenchymal transition.

Disruptor of telomeric silencing-1 like (DOT1L) protein specifically catalyzes the methylation of histone H3 on Lys79 (H3K79) and is implicated in tumors. But its role in tissue fibrosis remains unclear. Here we demonstrated that injury to the kidney increased DOT1L expression and H3K79 dimethylation in renal tubular epithelial cells and myofibroblasts in a murine model of unilateral ureteral obstruction. Administration of EPZ5676, a highly selective inhibitor of DOT1L, attenuated renal fibrosis. Treatment with EPZ5676 or DOT1L small interfering RNA also inhibited TGF-ß1 and serum-induced activation of renal interstitial fibroblasts and epithelial-mesenchymal transition (EMT) in vitro. Moreover, blocking DOT1L abrogated injury-induced epithelial G2/M arrest; reduced expression of Snail, Twist, and Notch1; and inactivated several profibrotic signaling molecules in the injured kidney, including Smad3, epidermal growth factor receptor, platelet-derived growth factor receptor, signal transducer and activator of transcription 3, protein kinase B, and NF-κB. Conversely, DOT1L inhibition increased expression of phosphatase and tensin homolog, a protein associated with dephosphorylation of tyrosine kinase receptors, and prevented decline in levels of Klotho and Smad7, 2 renoprotective factors. Thus, our data indicate that targeting DOT1L attenuates renal fibrosis through inhibition of renal fibroblasts and EMT by suppressing activation of multiple profibrotic signaling pathways while retaining expression of renoprotective factors.-Liu, L., Zou, J., Guan, Y., Zhang, Y., Zhang, W., Zhou, X., Xiong, C., Tolbert, E., Zhao, T. C., Bayliss, G., Zhuang, S. Blocking the histone lysine 79 methyltransferase DOT1L alleviates renal fibrosis through inhibition of renal fibroblast activation and epithelial-mesenchymal transition.

Selective inhibition of class IIa histone deacetylases alleviates renal fibrosis.

In this study, we examined the effect of MC1568, a selective class IIa histone deacetylase (HDAC) inhibitor, on the development and progression of renal fibrosis in a murine model of renal fibrosis induced by unilateral ureteral obstruction (UUO). All 4 class IIa HDAC isoforms, in particular HDAC4, were up-regulated in renal epithelial cells of the injured kidney. Administration of MC1568 immediately after UUO injury reduced expression of α-smooth muscle actin (α-SMA), fibronectin, and collagen 1. MC1568 treatment or small interfering RNA-mediated silencing of HDAC4 also suppressed expression of those proteins in cultured renal epithelial cells. Mechanistically, MC1568 abrogated UUO-induced phosphorylation of Smad3, NF-κB, and up-regulation of integrin ɑVß6 in the kidney and inhibited TGF-ß1-induced responses in cultured renal epithelial cells. MC1568 also increased renal expression of klotho, bone morphogenetic protein 7, and Smad7. Moreover, delayed administration of MC1568 at 3 d after ureteral obstruction reversed the expression of α-SMA, fibronectin, and collagen 1 and increased expression of matrix metalloproteinase (MMP)-2 and -9. Collectively, these results suggest that selectively targeting class IIa HDAC isoforms (in particular HDAC4) may inhibit development and progression of renal fibrosis by suppressing activation and expression of multiple profibrotic molecules and increasing expression of antifibrotic proteins and MMPs.-Xiong, C., Guan, Y., Zhou, X., Liu, L., Zhuang, M. A., Zhang, W., Zhang, Y., Masucci, M. V., Bayliss, G., Zhao, T. C., Zhuang, S. Selective inhibition of class IIa histone deacetylases alleviates renal fibrosis.