DNA Replication Pathways Research Articles

A prognostic and therapeutic hallmark developed by the integrated profile of basement membrane and immune infiltrative landscape in lung adenocarcinoma.

Basement membranes (BMs) are specialised extracellular matrices that maintain cellular integrity and resist the breaching of carcinoma cells for metastases while regulating tumour immunity. The tumour immune microenvironment (TME) is essential for tumour growth and the response to and benefits from immunotherapy. In this study, the BM score and TME score were constructed based on the expression signatures of BM-related genes and the presence of immune cells in lung adenocarcinoma (LUAD), respectively. Subsequently, the BM-TME classifier was developed with the combination of BM score and TME score for accurate prognostic prediction. Further, Kaplan-Meier survival estimation, univariate Cox regression analysis and receiver operating characteristic curves were used to cross-validate and elucidate the prognostic prediction value of the BM-TME classifier in several cohorts. Findings from functional annotation analysis suggested that the potential molecular regulatory mechanisms of the BM-TME classifier were closely related to the cell cycle, mitosis and DNA replication pathways. Additionally, the guiding value of the treatment strategy of the BM-TME classifier for LUAD was determined. Future clinical disease management may benefit from the findings of our research.

Identification and analysis of C17orf53 as a prognostic signature for hepatocellular carcinoma

C17orf53 is a novel gene for DNA synthesis and homologous recombination. However, the exact role of C17orf53 in hepatocellular carcinoma (HCC) remains unclear. In this study, we analyzed it using a set of public datasets. UALCAN, Human Protein Atlas (HPA), Kaplan‒Meier Plotter, Tumor Immune Estimation Resource (TIMER), cBioPortal, GEPIA, GeneMANIA, and LinkedOmics were used. Functional analysis was conducted in SK-Hep-1 cells by using small interfering RNA (siRNA). C17orf53 was highly expressed and predicted unfavorable survival in HCC patients. Moreover, it showed positive correlations with the abundance of B cells, macrophages and dendritic cells. In addition, we identified 126 genes that were positively correlated with C17orf53 and its coeffector minichromosome maintenance 8 (MCM8). These genes were mainly enriched in the cell cycle, DNA replication and Fanconi anemia pathways. Knockdown of C17orf53 significantly inhibited the proliferation of SK-Hep-1 cells and decreased the expression of MCM8, cyclin D1 and proliferating cell nuclear antigen (PCNA). Overall, C17orf53 is a novel prognostic signature for HCC.

HMGA1 As a Potential Prognostic and Therapeutic Biomarker in Breast Cancer.

High-mobility group AT-hook1 (HMGA1) protein plays an important role in various diseases. However, the contribution of HMGA1 in breast cancer remains to be tapped. The expression of HMGA1 was analyzed in The Cancer Genome Atlas (TCGA) and TIMER database, and immunohistochemistry was performed in 39 breast cancer (BC) patients. The correlation between HMGA1 expression and prognosis was evaluated using Kaplan-Meier plotter (KM plotter) in patients with breast cancer. Then, cBioPortal and bc-GenExMiner were requisitioned to analyze the contribution of HMGA1 expression to clinical features. In order to reveal the function of HMGA1 in breast cancer cells, enrichment analysis was performed using the clusterProfiler R software package. Moreover, CCK8 assay, EdU assay, and Cell Cycle Assay were performed to assess the proliferation, and transwell assay was used to evaluate cell migration and invasion. Flow cytometry was used to explore the role of HMGA1 on cell apoptosis. After that, the effect of HMGA1 on signaling pathways in BC cells was detected by western blot. HMGA1 was highly expressed in a variety of tumors tissues, including BC. High HMGA1 expression was correlated with poor prognosis in BC patients. Meanwhile, HMGA1 expression was increased in molecular phenotypes with poor prognosis (ER-, PR-, and HER2+) and associated with high-grade group, lymph node metastasis, and NPI (Nottingham Prognostic Index). Further, function analysis revealed HMGA1 was enriched in DNA replication and cell cycle pathways in breast cancer. Moreover, knockdown of HMGA1 caused apoptosis, inhibited proliferation, migration, and invasion of MCF-7 and MDA-MB-231 cells, in which the oncogenic signaling pathway of PI3K/AKT/MMP9 played a critical role. HMGA1 was important for breast cancer progression and was a critical prognostic indicator, prompting a potential therapeutic target of breast cancer.

Chenodeoxycholic Acid (CDCA) Promoted Intestinal Epithelial Cell Proliferation by Regulating Cell Cycle Progression and Mitochondrial Biogenesis in IPEC-J2 Cells.

Chenodeoxycholic acid (CDCA), a primary bile acid (BA), has been demonstrated to play an important role as a signaling molecule in various physiological functions. However, the role of CDCA in regulating intestinal epithelial cell (IEC) function remains largely unknown. Herein, porcine intestinal epithelial cells (IPEC-J2) were used as an in vitro model to investigate the effects of CDCA on IEC proliferation and explore the underlying mechanisms. IPEC-J2 cells were treated with CDCA, and flow cytometry and transcriptome analysis were adopted to investigate the effects and potential molecular mechanisms of CDCA on the proliferation of IECs. Our results indicated that adding 50 μmol/L of CDCA in the media significantly increased the proliferation of IPEC-J2 cells. In addition, CDCA treatment also hindered cell apoptosis, increased the proportion of G0/G1 phase cells in the cell cycle progression, reduced intracellular ROS, and MDA levels, and increased mitochondrial membrane potential, antioxidation enzyme activity (T-AOC and CAT), and intracellular ATP level (p < 0.05). RNA-seq results showed that CDCA significantly upregulated the expression of genes related to cell cycle progression (Cyclin-dependent kinase 1 (CDK1), cyclin G2 (CCNG2), cell-cycle progression gene 1 (CCPG1), Bcl-2 interacting protein 5 (BNIP5), etc.) and downregulated the expression of genes related to mitochondrial biogenesis (ND1, ND2, COX3, ATP6, etc.). Further KEGG pathway enrichment analysis showed that CDCA significantly enriched the signaling pathways of DNA replication, cell cycle, and p53. Collectively, this study demonstrated that CDCA could promote IPEC-J2 proliferation by regulating cell cycle progression and mitochondrial function. These findings provide a new strategy for promoting the intestinal health of pigs by regulating intestinal BA metabolism.

Causal AI in silico Patient Model Identifies Minichromosome Maintenance (MCM) Family Genes As Novel Predictors for Overall Survival in Multiple Myeloma

The minichromosome maintenance (MCM) complex is among the best-known protein families involved in eukaryotic replication initiation. The six conserved proteins of the MCM complex, namely MCM2-MCM7, have been well studied and form a DNA helicase. Dysregulation of members of the MCM complex has been demonstrated in multiple cancer types, including gastric cancer, liver cancer, cervical cancer, and prostate cancer, among others. However, comparatively little is currently known about the role of the MCM complex in hematological oncology. We show here the first evidence of a causal link between members of the MCM complex, specifically MCM2, MCM3, and MCM4, and overall survival of multiple myeloma patients. This result was further validated in a separate, externally collected cohort of patients. In this study, an in-silico patient model of Multiple Myeloma Research Foundation (MMRF) IA19 CoMMpass data was developed using GNS Healthcare's Causal AI technology, REFSTM. REFSTM has been previously used to analyze MMRF data to identify the epigenetic regulator PHF19 as a marker of aggressive disease. Simulated genetic perturbations performed on the in-silico model identified changes in the expression of DNA replication genes MCM2, MCM3, and MCM4 as strong causal drivers of overall survival (OS) in MM patients (MCM2 and MCM4 shown in figure 1). These targets were validated using a Cox proportional-hazards model on an out-of-cohort Dana-Farber Cancer Institute MM dataset (DFCI). We report Cox hazard ratios of 1.62 (1.41, 1.85), 1.72 (1.42, 2.10), and 1.75 (1.50, 2.05) respectively, for MCM2, MCM3 and MCM4 in the MMRF IA19 dataset. Among patients in the DFCI dataset, we report Cox hazard ratios of 1.40 (1.09, 1.79), 1.50 (1.14, 1.99), and 1.56 (1.17, 2.08), respectively for MCM2, MCM3 and MCM4. In addition, causal modeling indicated large negative prognostic median effect sizes for overall survival. In summary, this work demonstrates MCM2, MCM3, and MCM4 as candidate genes involved in MM pathology. These genes are known targets in other cancers due to their role in DNA replication and cell cycle pathways. We could not identify any existing Open Targets literature related to these genes as drug targets or predictive markers in MM. Our results, validated out-of-cohort, suggest that MCM2, MCM3, and MCM4 are newly discovered predictors of overall survival among multiple myeloma patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Interaction of Arsenic Exposure and Transcriptomic Profile in Basal Cell Carcinoma.

Exposure to inorganic arsenic (As) is recognized as risk factor for basal cell carcinoma (BCC). We have followed-up 7000 adults for 6 years who were exposed to As and had manifest As skin toxicity. Of them, 1.7% developed BCC (males = 2.2%, females = 1.3%). In this study, we compared transcriptome-wide RNA sequencing data from the very first 26 BCC cases and healthy skin tissue from independent 16 individuals. Genes in " cell carcinoma pathway", "Hedgehog signaling pathway", and "Notch signaling pathway" were overexpressed in BCC, confirming the findings from earlier studies in BCC in other populations known to be exposed to As. However, we found that the overexpression of these known pathways was less pronounced in patients with high As exposure (urinary As creatinine ratio (UACR) > 192 µg/gm creatinine) than patients with low UACR. We also found that high UACR was associated with impaired DNA replication pathway, cellular response to different DNA damage repair mechanisms, and immune response. Transcriptomic data were not strongly suggestive of great potential for immune checkpoint inhibitors; however, it suggested lower chance of platinum drug resistance in BCC patients with high UACR compared high platinum drug resistance potential in patients with lower UACR.

BIOM-45. DETERMINANTS OF GBM VULNERABILITY TO INHIBITORS OF NEDD8 ACTIVATING ENZYME (NAE)

Abstract Advancing new therapeutics to FDA approval for GBM is hampered by intra- and inter-tumoral heterogeneity. Design of clinical trials to enroll patients likely to respond to a new treatment seems critical to build the arsenal of agents against this disease. Neddylation is a protein modification pathway aligned to protein degradation and cytological localization within the ubiquitin/proteasome system. Components of the neddylation pathway are frequently overexpressed or hyperactivated in GBM, and whose upregulation has been associated with glioma progression and worse survival. Among glioblastoma cell lines and patient-derived stem cells, subsets were found to be selectively susceptible to NAE inhibitors. We previously showed that PTEN signaling, DNA replication, and chromatin instability pathways are the most significant differentiators between MLN4924 sensitive vs. non-sensitive models. To test a candidate molecular “signature of vulnerability”, two subsets of PDX models (PTEN wildtype and PTEN del or mutated) were treated with a panel of 3 NAE inhibitors. 5 GBM PTENwt models were shown vulnerable to MLN4924 and TAS4464 with average EC50 values 5-10 folds lower than 6 PTENmt/del models. CDC activity was greater against PTENwt, but only 2-fold different vs PTENmt/del. Transcriptomic data mining uncovered additional determinants of response to NAE inhibitors. To disclose the relationship between constitutive expression of three gene sets: DNA Replication Fork Progressing, Replication Fork Protection, and Replication Fork Protection Complex, we found that the genes involved in these are significantly under expressed in PTENmt models when comparing to PTENwt models. The molecular determinants of drug response to NAE inhibitors will be further verified in the extended preclinical models and lead to a patient-enrollment “signature of vulnerability” to increase the likelihood of demonstrating therapeutic efficacy in the early stage of clinical trials.

SKA1/2/3 is a biomarker of poor prognosis in human hepatocellular carcinoma.

Spindle and kinetochore-associated complex subunits 1-3 (SKA1-3) stabilize the kinetochore-attached spindle microtubules in metaphase. Due to the dysregulation in multiple cancers, SKA1-3 is considered a predictor for the prognosis of the patients. However, the potential clinical applications of SKA1-3, particularly in hepatocellular carcinoma (HCC) prognosis and progression, have completely unknown yet. For the analysis of SKA1-3 expression and applications in clinics in HCC patients, several databases, such as STRING, UALCAN, GEO, and TCGA, were searched. In addition, the underlying mechanisms of SKA for the regulation of HCC occurrence, development, and progression were also explored. Compared to the normal controls, HCC patients showed dramatically elevated SKA1-3 expression at the mRNA level, and the values of the area under the curve (AUC) were 0.982, 0.887, and 0.973, respectively. Increased SKA1-3 expression levels were associated with the clinical stage, age, body mass index, tumor grade, tissue subtype, and Tp53 mutation status in HCC patients. The analyses of Kyoto Encyclopedia of Genes and Genome (KEGG) and Gene ontology (GO) demonstrated that SKA1-3 are enriched mainly in the Fanconi anemia, homologous recombination, spliceosome, DNA replication, and cell cycle signaling pathways. The hub genes, such as CDK1, CCNB1, CCNA2, TOP2A, BUB1, AURKB, CCNB2, BUB1B, NCAPG, and KIF11, were identified in protein-protein interactions (PPIs). The expression levels of hub genes were increased in HCC patients and predictive of a poor prognosis. Finally, the expression levels of SKA1-3 were determined using the GEO database. SKA1-3 are potential prognostic biomarkers of and targets for HCC. In addition, SKA1-3 may affect HCC prognosis via the Fanconi anemia pathway, homologous recombination, spliceosome, DNA replication, and cell cycle signaling pathway.

Dose-related shifts in proteome and function of extracellular vesicles secreted by fetal neural stem cells following chronic alcohol exposure

Accumulating evidence indicates that extracellular vesicles (EVs) mediate endocrine functions and also pathogenic effects of neurodevelopmental perturbagens like ethanol. We performed mass-spectrometry on EVs secreted by fetal murine cerebral cortical neural stem cells (NSCs), cultured ex-vivo as sex-specific neurosphere cultures, to identify overrepresented proteins and signaling pathways in EVs relative to parental NSCs in controls, and following exposure of parental NSCs to a dose range of ethanol. EV proteomes differ substantially from parental NSCs, and though EVs sequester proteins across sub-cellular compartments, they are enriched for distinct morphogenetic signals including the planar cell polarity pathway. Ethanol exposure favored selective protein sequestration in EVs and depletion in parental NSCs, and also resulted in dose-independent overrepresentation of cell-cycle and DNA replication pathways in EVs as well as dose-dependent overrepresentation of rRNA processing and mTor stress pathways. Transfer of untreated EVs to naïve cells resulted in decreased oxidative metabolism and S-phase, while EVs derived from ethanol-treated NSCs exhibited diminished effect. Collectively, these data show that NSCs secrete EVs with a distinct proteome that may have a general growth-inhibitory effect on recipient cells. Moreover, while ethanol results in selective transfer of proteins from NSCs to EVs, the efficacy of these exposure-derived EVs is diminished.

The transcriptomic signature of responses to larval crowding in Drosophila melanogaster.

Intraspecific competition at the larval stage is an important ecological factor affecting life-history, adaptation and evolutionary trajectory in holometabolous insects. However, the molecular pathways underpinning these ecological processes are poorly characterized. We reared Drosophila melanogaster at three egg densities (5, 60, and 300 eggs/mL) and sequenced the transcriptomes of pooled third-instar larvae. We also examined emergence time, egg-to-adult viability, adult mass, and adult sex-ratio at each density. Medium crowding had minor detrimental effects on adult phenotypes compared to low density and yielded 24 differentially expressed genes (DEGs), including several chitinase enzymes. In contrast, high crowding had substantial detrimental effects on adult phenotypes and yielded 2107 DEGs. Among these, upregulated gene sets were enriched in sugar, steroid and amino acid metabolism as well as DNA replication pathways, whereas downregulated gene sets were enriched in ABC transporters, taurine, Toll/Imd signaling, and P450 xenobiotics metabolism pathways. Overall, our findings show that larval crowding has a large consistent effect on several molecular pathways (i.e., core responses) with few pathways displaying density-specific regulation (i.e., idiosyncratic responses). This provides important insights into how holometabolous insects respond to intraspecific competition during development.

Identification of gonadal associated genes in black tiger shrimp ( Penaeus monodon ) using transcriptome analysis and high‐throughput sequencing

Black tiger shrimp (Penaeus monodon) is a commercially important species. It is reported to have low reproductive maturation rates in captivity. To improve the production of this species via sustainable aquaculture, genetic techniques are required to improve its maturation rates. However, to date, reports on P. monodon reproduction at a transcriptional level are limited. To address this, we conducted transcriptome sequencing of the ovaries and testes of P. monodon using high-throughput sequencing to identify sex-related pathways and genes. A total of 75.74 Gb of clean data were generated from nine gonadal tissue libraries. We obtained 62,276 unigenes with a mean length of 1452 bp and N50 of 2423 bp. A total of 11,411 significantly differentially expressed genes (DEGs) were identified between the testis and developed ovaries. Enrichment analysis of the DEGs identified 415 significantly enriched GO terms and 106 enriched KEGG pathways. Genes related to the P. monodon ovaries were enriched in the steroid biosynthesis, mRNA surveillance, nucleocytoplasmic transport, oxidative phosphorylation and DNA replication pathways. Five upregulated and five downregulated ovarian genes were confirmed using RT-PCR. This investigation has thus identified important sex-related functional genes, GO terms and pathways in P. monodon. In particular, we identified several important genes and pathways related to gonadal development, such as GnRH/GnRHR-like, Hsp90, PCNA, cathepsin L, Wnt signalling pathway and ovarian steroidogenesis pathway, which provide important insights into the mechanism analysis and sex regulation of shrimp gonadal development. The results will provide reference data for future research into the reproductive biology of shrimp, which will aid in improved black tiger shrimp breeding in captivity.

Serum-derived extracellular vesicles promote the growth and metastasis of non-small cell lung cancer by delivering the m6A methylation regulator HNRNPC through the regulation of DLGAP5.

Serum-derived extracellular vesicles (EVs) have been reported to play an important role in non-small cell lung cancer (NSCLC). The current study sought to explore the effect of serum-EVs delivering m6A methylation regulator heterogeneous nuclear ribonucleoprotein C (HNRNPC) on the development of NSCLC through the regulation of discs large-associated protein 5 (DLGAP5). NSCLC-related RNA-Seq and clinical data were first obtained from the TCGA database to screen differentially expressed m6A-related regulators, which were intersected with the differential genes in NSCLC-related microarray GSE43458 obtained from the GEO database for survival analysis and clinical correlation analysis. Correlation between HNRNPC and DLGAP5 expression was evaluated. Serum-EVs were isolated and identified, and the uptake of EVs by A549 cells was visualized using fluorescence microscopy. In vivo xenograft tumor models and tumor metastasis models were constructed in nude mice to observe growth and metastasis of NSCLC cells. HNRNPC was associated with poor prognosis and metastasis of NSCLC, and further implicated in the regulation of DNA replication and cell cycle-related pathways. HNRNPC might promote the growth and metastasis of NSCLC by identifying m6A modification of DLGAP5 mRNA. Serum-EVs delivered HNRNPC to NSCLC cells in vitro. In vivo experimentation further confirmed that serum-EVs could deliver HNRNPC to promote the growth and metastasis of NSCLC cells in nude mice. Our findings highlight that serum-EVs can deliver HNRNPC to NSCLC cells, wherein HNRNPC recognizes the m6A modification of DLGAP5 mRNA, thus ultimately promoting NSCLC growth and metastasis.

Multi-Omics Analysis Reveals the Unexpected Immune Regulatory Effects of Arsenene Nanosheets in Tumor Microenvironment.

Arsenene, a two-dimensional (2D) monoelemental layered nanosheet composed of arsenic, was recently reported to feature outstanding anticancer activities. However, the specific biological mechanism of action remains unknown. In this work, we extensively analyzed the mechanism of arsenene in vivo and in vitro and discovered the unexpected immune regulatory capability of arsenene for the first time. Analysis of cell phenotypes in tumor microenvironment by single-cell RNA sequencing revealed that arsenene remodeled the tumor microenvironment by recruiting a high proportion of anticancer immune cells to eliminate the tumor. Mechanistically, arsenene significantly activated T cell receptor signaling pathways to produce antitumor immune cells while inhibiting DNA replication and TCA cycle pathways of tumor cells in vivo. Further proteomic analysis on tumor cells revealed that arsenene induced reactive oxygen species production and oxidative stress damage by targeting thioredoxin TXNL1. The overloaded reactive oxygen species (ROS) further triggered endoplasmic reticulum stress responses to release damage-associated molecular patterns (DAMPs) and "eat-me" signals from dying tumor cells, leading to the activation of antigen-presenting processes to induce the subsequent effector tumor-specific CD8+ T cell immune responses. This unexpected discovery indicated for the first time that 2D inorganic nanomaterials could effectively activate direct anticancer immune responses, suggesting arsenene as a promising candidate nanomedicine for future cancer immunotherapy.

Safeguarding DNA Replication: A Golden Touch of MiDAS and Other Mechanisms.

DNA replication is a tightly regulated fundamental process allowing the correct duplication and transfer of the genetic information from the parental cell to the progeny. It involves the coordinated assembly of several proteins and protein complexes resulting in replication fork licensing, firing and progression. However, the DNA replication pathway is strewn with hurdles that affect replication fork progression during S phase. As a result, cells have adapted several mechanisms ensuring replication completion before entry into mitosis and segregating chromosomes with minimal, if any, abnormalities. In this review, we describe the possible obstacles that a replication fork might encounter and how the cell manages to protect DNA replication from S to the next G1.

Mechanisms underlying the inhibitory effects of linalool on Aspergillus flavus spore germination.

Biogenic volatile organic compounds hold remarkable potential for controlling fungal decay in agro- and food products. Recently, we reported that linalool, the major volatile component of the Zanthoxylum schinifolium pericarp, showed great potential as a biofumigant to control Aspergillus flavus growth in postharvest grains. In this study, the inhibitory effects of linalool on A. flavus growth in stored grains and its underlying mechanism were investigated through transcriptomic and biochemical analyses. Linalool vapor at 800 μL/L can effectively prevent A. flavus growth in 22% moisture wheat grains. Linalool at 2 μL/mL completely inhibited the germination of A. flavus spores, and 10 μL/mL caused spore death. Scanning electron microscopy revealed that linalool treatment caused wrinkling and spore breakage. Transcriptomics showed that 3806 genes were significantly differentially expressed in A. flavus spores exposed to 2 μL/mL linalool, predominantly showing enrichment regarding the ribosome, DNA replication, glutathione metabolism, peroxisome, and MAPK signaling pathways. Flow cytometry showed that linalool treatment caused hyperpolarization of mitochondrial membrane potential. 4,6-Diamidino-2-phenylindole staining indicated that linalool caused DNA fragmentation in A. flavus spores, and monodansylcadaverine staining confirmed that linalool induced autophagy in A. flavus spores. We thus propose that linalool can damage the plasma membrane, cause mitochondrial dysfunction and DNA damage, and induce autophagy in A. flavus spores. These findings considerably improve our understanding of the mechanisms underlying the inhibitory effects of linalool on A. flavus, which is crucial regarding the development of applications to prevent postharvest grain spoilage due to A. flavus infestations. KEY POINTS: • The inhibitory potency of linalool on A. flavus spore germination was determined. • Transcriptomic analyses were performed to identify differentially expressed genes of A. flavus exposed to linalool. • A functional mechanism underlying the inhibitory effects of linalool on A. flavus spore germination is proposed.

Arbidol inhibits human esophageal squamous cell carcinoma growth in vitro and in vivo through suppressing ataxia telangiectasia and Rad3-related protein kinase.

Human esophageal cancer has a global impact on human health due to its high incidence and mortality. Therefore, there is an urgent need to develop new drugs to treat or prevent the prominent pathological subtype of esophageal cancer, esophageal squamous cell carcinoma (ESCC). Based upon the screening of drugs approved by the Food and Drug Administration, we discovered that Arbidol could effectively inhibit the proliferation of human ESCC in vitro. Next, we conducted a series of cell-based assays and found that Arbidol treatment inhibited the proliferation and colony formation ability of ESCC cells and promoted G1-phase cell cycle arrest. Phosphoproteomics experiments, in vitro kinase assays and pull-down assays were subsequently performed in order to identify the underlying growth inhibitory mechanism. We verified that Arbidol is a potential ataxia telangiectasia and Rad3-related (ATR) inhibitor via binding to ATR kinase to reduce the phosphorylation and activation of minichromosome maintenance protein 2 at Ser108. Finally, we demonstrated Arbidol had the inhibitory effect of ESCC in vivo by a patient-derived xenograft model. All together, Arbidol inhibits the proliferation of ESCC in vitro and in vivo through the DNA replication pathway and is associated with the cell cycle.

Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation.

Plants play a primary role for the global sulfur cycle in the earth ecosystems by reduction of inorganic sulfate from the soil to organic sulfur-containing compounds. How plants sense and transduce the sulfate availability to mediate their growth remains largely unclear. The target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator of nutrient sensing and metabolic signaling to control cell proliferation and growth in all eukaryotes. By tissue-specific Western blotting and RNA-sequencing analysis, we investigated sulfate-TOR signal pathway in regulating shoot apex development. Here, we report that inorganic sulfate exhibits high potency activating TOR and cell proliferation to promote true leaf development in Arabidopsis in a glucose-energy parallel pathway. Genetic and metabolite analyses suggest that this sulfate activation of TOR is independent from the sulfate-assimilation process and glucose-energy signaling. Significantly, tissue specific transcriptome analyses uncover previously unknown sulfate-orchestrating genes involved in DNA replication, cell proliferation and various secondary metabolism pathways, which largely depends on TOR signaling. Systematic comparison between the sulfate- and glucose-TOR controlled transcriptome further reveals that TOR kinase, as the central growth integrator, responds to different nutrient signals to control both shared and unique transcriptome networks, therefore, precisely modulates plant proliferation, growth and stress responses.

MiR-342-3p Inhibits Acute Myeloid Leukemia Progression by Targeting SOX12.

Background It is well known that microRNAs (miRNAs) interfere with the progression of various human malignancies. This article is aimed at exploring the regulating role of miR-342-3p in acute myeloid leukemia (AML) and its mechanism. Methods We used the Gene Expression Omnibus (GEO) database to determine miR-342-3p differential expression patterns in AML patients' plasma and cells as well as healthy individuals' plasma and T cells. Quantitative real-time PCR and Western blotting were performed for plasma and cell miR-342-3p and SRY-related high-mobility-group box (SOX12) expression quantification, and cell counting kit-8 assay and flow cytometry were used for the determination of AML cell growth, cycle, and apoptosis. A dual-luciferase reporter gene assay was further carried out to identify the targeted association between miR-342-3p and SOX12 mRNA 3′UTR after prediction by a bioinformatics website. Pearson's correlation analysis was performed to analyze the connection between miR-342-3p and SOX12 expressions. The LinkedOmics database was utilized to explore the downstream pathways in which SOX12 was enriched. Results Evidently downregulated plasma miR-342-3p and markedly elevated SOX12 were observed in AML patients versus healthy individuals. miR-342-3p mimics suppressed AML cell growth, enhanced apoptosis, and induced G0/G1 phase arrest; conversely, enhanced capacity of AML cells to proliferate, suppressed apoptosis, and accelerated cell cycle were observed after treatment with miR-342-3p inhibitors. SOX12 was confirmed as miR-342-3p's target gene. Overexpressing or knocking down SOX12 reversed miR-342-3p's impacts on AML cell growth, apoptosis, and cycle. Upregulated SOX12 was positively related to DNA replication and RNA polymerase signaling pathways. Conclusion miR-342-3p affects apoptosis of AML cells and their ability to proliferate via targeted regulation of SOX12.

Integrative analysis of synovial sarcoma transcriptome reveals different types of transcriptomic changes.

Background: Synovial sarcoma (SS) is a rare and aggressive cancer that can come from distinct soft tissue types including muscle and ligaments. However, the transcriptomic landscape of SS is still poorly understood. This study aimed to systematically dissect the changes in SS transcriptome from different perspectives. Methods: We performed deep total RNA sequencing on ten paired Synovial sarcoma and tumor-adjacent tissues to systematically dissect the transcriptomic profile of SS in terms of gene expression, alternative splicing, gene fusion, and circular RNAs. Results: A total of 2,309 upregulated and 1,977 downregulated genes were identified between SS and tumor-adjacent tissues. Those upregulated genes could lead to the upregulation of the cell cycle, ribosome, and DNA replication pathways, while the downregulated genes may result in the downregulation of a set of metabolic biological processes and signaling pathways. Moreover, 2,511 genes (including 21 splicing factors) were differentially alternative spliced, indicating that the deregulation of alternative splicing could be one important factor that contributes to tumorigenesis. Additionally, we identified the known gene fusions of SS18-SSX1/SSX2 as well as 11 potentially novel gene fusions. Interestingly, 49 circular RNAs were differentially expressed and their parental genes could function in muscle contraction and muscle system processes. Conclusions: Collectively, our comprehensive dissection of the transcriptomic changes of SS from both transcriptional and post-transcriptional levels provides novel insights into the biology and underlying molecular mechanism of SS.

Characterization of Transcriptional Responses to Genomovirus Infection of the White Mold Fungus, Sclerotinia sclerotiorum.

Soybean leaf-associated gemygorvirus-1 (SlaGemV−1) is a CRESS-DNA virus classified in the family Genomoviridae, which causes hypovirulence and abolishes sclerotia formation in infected fungal pathogens under the family Sclerotiniaceae. To investigate the mechanisms involved in the induction of hypovirulence, RNA-Seq was compared between virus-free and SlaGemV−1-infected Sclerotinia sclerotiorum strain DK3. Overall, 4639 genes were differentially expressed, with 50.5% up regulated and 49.5% down regulated genes. GO enrichments suggest changes in integral membrane components and transmission electron microscopy images reveal virus-like particles localized near the inner cell membrane. Differential gene expression analysis focused on genes responsible for cell cycle and DNA replication and repair pathways, ubiquitin proteolysis, gene silencing, methylation, pathogenesis-related, sclerotial development, carbohydrate metabolism, and oxalic acid biosynthesis. Carbohydrate metabolism showed the most changes, with two glycoside hydrolase genes being the most down regulated by −2396.1- and −648.6-fold. Genes relating to pathogenesis showed consistent down regulation with the greatest being SsNep1, SsSSVP1, and Endo2 showing, −4555-, −14.7-, and −12.3-fold changes. The cell cycle and DNA replication/repair pathways were almost entirely up regulated including a putative cyclin and separase being up regulated 8.3- and 5.2-fold. The oxalate decarboxylase genes necessary for oxalic acid catabolism and oxalic acid precursor biosynthesis genes and its metabolism show down regulations of −17.2- and −12.1-fold changes. Sclerotial formation genes also appear differentially regulated including a melanin biosynthesis gene Pks1 and a sclerotia formation gene Sl2 with fold changes of 3.8 and −2.9.