The transforming growth factor-β (TGF-β) signalling pathway participates in various biological processes. Dysregulation of Smad4, a central cellular transducer of TGF-β signalling, is implicated in a wide range of human diseases and developmental disorders. However, the mechanisms underlying Smad4 dysregulation are not fully understood. Using a functional screening approach based on luciferase reporter assays, we identified 39 microRNAs (miRNAs) as potential regulators of Smad4 from an expression library of 388 human miRNAs. The screening was supported by bioinformatic analysis, as 24 of 39 identified miRNAs were also predicted to target Smad4. MiR-199a, one of the identified miRNAs, was inversely correlated with Smad4 expression in various human cancer cell lines and gastric cancer tissues, and repressed Smad4 expression and blocked canonical TGF-β transcriptional responses in cell lines. These effects were dependent on the presence of a conserved, but not perfect seed paired, miR-199a-binding site in the Smad4 3′-untranslated region (UTR). Overexpression of miR-199a significantly inhibited the ability of TGF-β to induce gastric cancer cell growth arrest and apoptosis in vitro, and promoted anchorage-independent growth in soft agar, suggesting that miR-199a plays an oncogenic role in human gastric tumourigenesis. In conclusion, our functional screening uncovers multiple miRNAs that regulate the cellular responsiveness to TGF-β signalling and reveals important roles of miR-199a in gastric cancer by directly targeting Smad4.

Non‐small–cell lung cancer (NSCLC) is one of the most prevalent type of lung cancers with an increased mortality rate in both developed and developing countries worldwide. Dieckol is one such polyphenolic drug extracted from brown algae which has proven antioxidant and anti‐inflammatory properties. In the present study, we evaluated the anticancer property of dieckol against NSCLC cell line A549. The LC50 value of dieckol was found to be 25 µg/mL by performing 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay and the antiapoptotic property of dieckol was analyzed by dual staining technique with acridine orange/propidium iodide (AO/PI) stains. It was further confirmed with flow cytometry analysis with Annexin FITC and JC‐1 staining and the anti‐invasive property was assessed by Transwell assay. The molecular mechanism of dieckol anticancer activity was confirmed by estimating the levels of caspases and by estimating the signaling proteins of Pi3K/AKT/mTOR signaling pathway using the immunoblotting technique. Our data suggest that dieckol is potent anticancer agent, it effectively inhibits the invasive and migratory property A549 cells and it also induces apoptosis via inhibiting Pi3K/AKT/mTOR signaling, activating the tumor suppressor protein E‐cadherin signifying that dieckol is potent natural anticancer drug to treat NSCLC.

The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5′-UTR and 3′-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

Motivation: Synonymous codon usage bias has been shown to be correlated with many genomic features among different organisms. However, the biological significance of codon bias with respect to gene function and genome organization remains unclear.Results: Guanine and cytosine content at the third codon position (GC3) could be used as a good indicator of codon bias. Here, we used relative GC3 bias values to compare the strength of GC3 bias of genes in human and mouse. We reported, for the first time, that GC3-rich and GC3-poor gene products might have distinct sub-cellular spatial distributions. Moreover, we extended the view of genomic gene domains and identified conserved GC3 biased gene domains along chromosomes. Our results indicated that similar GC3 biased genes might be co-translated in specific spatial regions to share local translational machineries, and that GC3 could be involved in the organization of genome architecture.Availability and implementation: Source code is available upon request from the authors.Contact: zhaozh@nic.bmi.ac.cn or zany1983@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.

ZNF143 is a ubiquitously expressed transcription factor conserved in vertebrates and might regulate the expression of numerous genes. But its function in mediating chromatin interactions remains elusive. By integrated analysis of public datasets, we provided evidence that a majority of ZNF143 binding sites (BSs) were involved in CTCF-mediated chromatin interaction networks (CTCF-CINs) by overlapping with cohesin-BSs and CTCF-BSs. We further showed that only a very few CTCF-CINs were associated with ZNF143 alone, whereas those associated with ZNF143 and cohesin simultaneously were highly overlapped with constitutive, conserved CTCF-BSs and enriched at boundaries of chromatin topologically associating domains. These observations implicate that as an important partner of CTCF, ZNF143 helps it establish the conserved chromatin structure by cooperating with cohesin. Abbreviations: BS, binding site; CIN, chromatin interaction network; TAD, topologically associating domain. 1 The article is published in the original. UDC 577.0.16.4:577.218 MOLECULAR CELL BIOLOGY 432 MOLECULAR BIOLOGY Vol. 50 No. 3 2016 YE et al.highly colocalized with cohesin. We also found that CTCF-CINs associated with ZNF143 and cohesin simultaneously were highly enriched at chromatin topologically associating domains (TADs) boundaries involved chromatin interactions. Our results strongly implicated that by cooperating with cohesin, ZNF143 helped CTCF establish the conserved chromatin structure. MATERIALS AND METHODSEnrichment of transcription factor binding at looping sites. All ChIA-PET, ChIP and Hi-C data of K562 cells were downloaded from NCBI GEO datasets (Assecssion No: GSM970216; GSE39495; GSE18199) and ENCODE Transcription Factor ChIP-seq Uniform Peaks track [13]. We assigned all possible CTCF-CINs based on the CTCF-BSs occupancy status, i.e. only those ChIA-PET interactions on each side with at least one CTCF-BS were denoted as direct CTCF-CINs strictly. Transcription factors (TFs) were considered as associating with CTCF-CINs only if the TF was present at both CTCF interaction sites. To tell if a transcription factor was enriched in CTCF-CINs, we calculated the odds ratio between the proportions of the overlap between the transcription factor binding sites and the CTCF interaction sites over non-interaction sites (one-sided Fisher's exact test).Transcription factor binding sites across chromatin states. Chromatin states were derived from the ENCODE ChromHMM track. The intersection between genomic annotations and the summit of the binding sites for transcription factors were determined using a custom Perl script. Three classes of partners associated with CTCF-mediated interactions include:

Chen (2020) miR-25-3p inhibition impairs tumorigenesis and invasion in gastric cancer cells invitro

Cetuximab improves the survival of patients with metastatic colorectal cancer. The main limitation is primary and secondary resistance, the underlying mechanism of which requires extensive investigation. We proved that PRSS expression levels are significantly negatively associated with the sensitivity of cancer cells to cetuximab. Detailed mechanistic analysis indicated that PRSS can cleave cetuximab, leading to resistance. Cetuximab or bevacizumab combined with SPINK1, a PRSS inhibitor, inhibited cell growth more efficiently than cetuximab or bevacizumab alone in xenograft models. PRSS levels in the serum of 156 patients with mCRC were analyzed, and poor efficacy of cetuximab therapy was observed in patients with aberrant PRSS expression. PRSS expression in monoclonal antibody (mAb)-treated patients with cancer from The Cancer Genome Atlas database was also evaluated to determine whether patients with higher PRSS expression have significantly reduced progression-free survival. Our work provides a strong scientific rationale for targeting PRSS in combination with cetuximab therapy.

Cisplatin is a first-line chemotherapy drug against ovarian cancer. However, its strong toxic side effects and the development of cisplatin resistance in human cancer cells seriously influence the effects of chemotherapy and quality of life in patients. Noscapine (Nos), a non-toxic benzylisoquinoline alkaloid extracted from opium, has been recently reported to have anti-cancer activity, but the mechanism of that effect has not been clearly established. In the present study, we investigated cytotoxicity of Nos in combination with cisplatin (DDP) in drug-resistant human ovarian cancer cell line SKOV3/DDP in vitro and in vivo null mice xenograft model. Cell proliferation was measured by MTT assay, flow cytometry was used to analyze cell cycle and apoptosis, protein expression of several apoptotic factors was investigated by flow cytometry and immunohistochemical method, and their mRNA expression levels were determined by real-time PCR. In vitro experiments showed that Nos significantly inhibited proliferation of SKOV3/DDP cells. DDP/Nos-combined treatment notably enhanced DDP-induced inhibition of cell proliferation and increased the pro-apoptotic effect of DDP in SKOV3/DDP cells. DDP/Nos administration increased the proportion of G2/M cells, reduced both protein and mRNA expression of anti-apoptotic factors XIAP, surviving and NF-kB, and augmented protein and mRNA levels of pro-apoptotic caspase-3. In vivo experiments revealed that Nos/DDP treatment increased the apoptotic rate of xenograft tumors in null mice. Tumor volume decreased from 1.733 ± 0.155 g in mice treated with DDP alone to 1.191 ± 0.106 g in animals treated with Nos/DDP. These observations suggest that Nos increases the anti-cancer activity of DDP against the drug-resistant ovarian cancer cell line SKOV3/DDP by modulating the cell cycle and activating apoptotic pathways. The study provides a new chemotherapy strategy for the treatment of DDP-resistant human ovarian cancer.