Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer.

BACKGROUND: RNA 5-methylcytosine (m5C) modification plays critical roles in the pathogenesis of various tumors. However, the function and molecular mechanism of RNA m5C modification in tumor drug resistance remain unclear. METHODS: The correlation between RNA m5C methylation, m5C writer NOP2/Sun RNA methyltransferase family member 2 (NSUN2) and EGFR-TKIs resistance was determined in non-small-cell lung cancer (NSCLC) cell lines and patient samples. The effects of NSUN2 on EGFR-TKIs resistance were investigated by gain- and loss-of-function assays in vitro and in vivo. RNA-sequencing (RNA-seq), RNA bisulfite sequencing (RNA-BisSeq) and m5C methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) were performed to identify the target gene of NSUN2 involved in EGFR-TKIs resistance. Furthermore, the regulatory mechanism of NSUN2 modulating the target gene expression was investigated by functional rescue and puromycin incorporation assays. RESULTS: RNA m5C hypermethylation and NSUN2 were significantly correlated with intrinsic resistance to EGFR-TKIs. Overexpression of NSUN2 resulted in gefitinib resistance and tumor recurrence, while genetic inhibition of NSUN2 led to tumor regression and overcame intrinsic resistance to gefitinib in vitro and in vivo. Integrated RNA-seq and m5C-BisSeq analyses identified quiescin sulfhydryl oxidase 1 (QSOX1) as a potential target of aberrant m5C modification. NSUN2 methylated QSOX1 coding sequence region, leading to enhanced QSOX1 translation through m5C reader Y-box binding protein 1 (YBX1). CONCLUSIONS: Our study reveals a critical function of aberrant RNA m5C modification via the NSUN2-YBX1-QSOX1 axis in mediating intrinsic resistance to gefitinib in EGFR-mutant NSCLC.

DNAH2 facilitates the homologous recombination repair of Fanconi anemia pathway through modulating FANCD2 ubiquitination.

Fanconi anemia (FA), an X-linked genetic or autosomal recessive disease, exhibits complicated pathogenesis. Previously, we detected the mutated Dynein Axonemal Heavy Chain 2 (DNAH2) gene in 2 FA cases. Herein, we further investigated the potential association between DNAH2 and the homologous recombination repair pathway of FA. The assays of homologous recombination repair, mitomycin C (MMC) sensitivity, immunofluorescence, and ubiquitination modification were performed in U2OS and DR-U2OS cell lines. In MMC-treated U2OS cells, the downregulation of the DNAH2 gene increased the sensitivity of cells to DNA inter-strand crosslinks. We also observed the reduced enrichment of FANCD2 protein to DNA damage sites. Furthermore, the ubiquitination modification level of FANCD2 was influenced by the deficiency of DNAH2. Thus, our results suggest that DNAH2 may modulate the cell homologous recombination repair partially by increasing the ubiquitination and the enrichment to DNA damage sites of FANCD2. DNAH2 may act as a novel co-pathogenic gene of FA patients.

m6A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2.

N6-methyladenosine (m6A), catalyzed by the methyltransferase complex consisting of Mettl3 and Mettl14, is the most abundant RNA modification in mRNAs and participates in diverse biological processes. However, the roles and precise mechanisms of m6A modification in regulating neuronal development and adult neurogenesis remain unclear. Here, we examined the function of Mettl3, the key component of the complex, in neuronal development and adult neurogenesis of mice. We found that the depletion of Mettl3 significantly reduced m6A levels in adult neural stem cells (aNSCs) and inhibited the proliferation of aNSCs. Mettl3 depletion not only inhibited neuronal development and skewed the differentiation of aNSCs more toward glial lineage, but also affected the morphological maturation of newborn neurons in the adult brain. m6A immunoprecipitation combined with deep sequencing (MeRIP-seq) revealed that m6A was predominantly enriched in transcripts related to neurogenesis and neuronal development. Mechanistically, m6A was present on the transcripts of histone methyltransferase Ezh2, and its reduction upon Mettl3 knockdown decreased both Ezh2 protein expression and consequent H3K27me3 levels. The defects of neurogenesis and neuronal development induced by Mettl3 depletion could be rescued by Ezh2 overexpression. Collectively, our results uncover a crosstalk between RNA and histone modifications and indicate that Mettl3-mediated m6A modification plays an important role in regulating neurogenesis and neuronal development through modulating Ezh2.

5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m5C reader.

5-methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory role in mRNA metabolism is still largely unknown. Here, we reveal that m5C modification is enriched in CG-rich regions and in regions immediately downstream of translation initiation sites and has conserved, tissue-specific and dynamic features across mammalian transcriptomes. Moreover, m5C formation in mRNAs is mainly catalyzed by the RNA methyltransferase NSUN2, and m5C is specifically recognized by the mRNA export adaptor ALYREF as shown by in vitro and in vivo studies. NSUN2 modulates ALYREF's nuclear-cytoplasmic shuttling, RNA-binding affinity and associated mRNA export. Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2. Our study provides comprehensive m5C profiles of mammalian transcriptomes and suggests an essential role for m5C modification in mRNA export and post-transcriptional regulation.

Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing.

The regulatory role of N(6)-methyladenosine (m(6)A) and its nuclear binding protein YTHDC1 in pre-mRNA splicing remains an enigma. Here we show that YTHDC1 promotes exon inclusion in targeted mRNAs through recruiting pre-mRNA splicing factor SRSF3 (SRp20) while blocking SRSF10 (SRp38) mRNA binding. Transcriptome assay with PAR-CLIP-seq analysis revealed that YTHDC1-regulated exon-inclusion patterns were similar to those of SRSF3 but opposite of SRSF10. In vitro pull-down assay illustrated a competitive binding of SRSF3 and SRSF10 to YTHDC1. Moreover, YTHDC1 facilitates SRSF3 but represses SRSF10 in their nuclear speckle localization, RNA-binding affinity, and associated splicing events, dysregulation of which, as the result of YTHDC1 depletion, can be restored by reconstitution with wild-type, but not m(6)A-binding-defective, YTHDC1. Our findings provide the direct evidence that m(6)A reader YTHDC1 regulates mRNA splicing through recruiting and modulating pre-mRNA splicing factors for their access to the binding regions of targeted mRNAs.

FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis.

The role of Fat Mass and Obesity-associated protein (FTO) and its substrate N6-methyladenosine (m6A) in mRNA processing and adipogenesis remains largely unknown. We show that FTO expression and m6A levels are inversely correlated during adipogenesis. FTO depletion blocks differentiation and only catalytically active FTO restores adipogenesis. Transcriptome analyses in combination with m6A-seq revealed that gene expression and mRNA splicing of grouped genes are regulated by FTO. M6A is enriched in exonic regions flanking 5'- and 3'-splice sites, spatially overlapping with mRNA splicing regulatory serine/arginine-rich (SR) protein exonic splicing enhancer binding regions. Enhanced levels of m6A in response to FTO depletion promotes the RNA binding ability of SRSF2 protein, leading to increased inclusion of target exons. FTO controls exonic splicing of adipogenic regulatory factor RUNX1T1 by regulating m6A levels around splice sites and thereby modulates differentiation. These findings provide compelling evidence that FTO-dependent m6A demethylation functions as a novel regulatory mechanism of RNA processing and plays a critical role in the regulation of adipogenesis.

Incremental analysis of the reengineering of an outpatient billing process: an empirical study in a public hospital.

BACKGROUND: A smartcard is an integrated circuit card that provides identification, authentication, data storage, and application processing. Among other functions, smartcards can serve as credit and ATM cards and can be used to pay various invoices using a 'reader'. This study looks at the unit cost and activity time of both a traditional cash billing service and a newly introduced smartcard billing service in an outpatient department in a hospital in Taipei, Taiwan. METHODS: The activity time required in using the cash billing service was determined via a time and motion study. A cost analysis was used to compare the unit costs of the two services. A sensitivity analysis was also performed to determine the effect of smartcard use and number of cashier windows on incremental cost and waiting time. RESULTS: Overall, the smartcard system had a higher unit cost because of the additional service fees and business tax, but it reduced patient waiting time by at least 8 minutes. Thus, it is a convenient service for patients. In addition, if half of all outpatients used smartcards to pay their invoices, along with four cashier windows for cash payments, then the waiting time of cash service users could be reduced by approximately 3 minutes and the incremental cost would be close to breaking even (even though it has a higher overall unit cost that the traditional service). CONCLUSIONS: Traditional cash billing services are time consuming and require patients to carry large sums of money. Smartcard services enable patients to pay their bill immediately in the outpatient clinic and offer greater security and convenience. The idle time of nurses could also be reduced as they help to process smartcard payments. A reduction in idle time reduces hospital costs. However, the cost of the smartcard service is higher than the cash service and, as such, hospital administrators must weigh the costs and benefits of introducing a smartcard service. In addition to the obvious benefits of the smartcard service, there is also scope to extend its use in a hospital setting to include the notification of patient arrival and use in other departments.

ALKBH4-dependent demethylation of actin regulates actomyosin dynamics.

Regulation of actomyosin dynamics by post-transcriptional modifications in cytoplasmic actin is still poorly understood. Here we demonstrate that dioxygenase ALKBH4-mediated demethylation of a monomethylated site in actin (K84me1) regulates actin-myosin interaction and actomyosin-dependent processes such as cytokinesis and cell migration. ALKBH4-deficient cells display elevated K84me1 levels. Non-muscle myosin II only interacts with unmethylated actin and its proper recruitment to and interaction with actin depend on ALKBH4. ALKBH4 co-localizes with the actomyosin-based contractile ring and midbody via association with methylated actin. ALKBH4-mediated regulation of actomyosin dynamics is completely dependent on its catalytic activity. Disorganization of cleavage furrow components and multinucleation associated with ALKBH4 deficiency can all be restored by reconstitution with wild-type but not catalytically inactive ALKBH4. Similar to actin and myosin knock-out mice, homozygous Alkbh4 mutant mice display early embryonic lethality. These findings imply that ALKBH4-dependent actin demethylation regulates actomyosin function by promoting actin-non-muscle myosin II interaction.

ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility.

N(6)-methyladenosine (m(6)A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as another mammalian demethylase that oxidatively reverses m(6)A in mRNA in vitro and in vivo. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice have increased m(6)A in mRNA and are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1,551 differentially expressed genes that cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. The discovery of this RNA demethylase strongly suggests that the reversible m(6)A modification has fundamental and broad functions in mammalian cells.

Energetic-assisted scanning thermal lithography for patterning silver nanoparticles in polymer films.

Energetic-assisted scanning thermal lithography (SThL) was demonstrated with the addition of benzoyl peroxide (BPO) for patterning silver nanoparticles. SThL samples were prepared by spin-coating poly(methyl methacrylate) (PMMA) thin films preloaded with BPO and silver nitrate precursors. Localized thermal analysis via probe heating demonstrated that the BPO decomposition in the polymer film took place at the temperature of 80 °C. Above this temperature, the thermal probe initiated the decomposition of the peroxide, which resulted in the in situ discharge of exothermal energy to compensate the joule shortage and the rapid cooling in the SThL thin film samples. The additional joule energy thermally enhanced the synthesis of silver nanoparticles, which were patterned and embedded in the PMMA thin film. Surface plasmon resonance scattering of these silver nanoparticles was observed by dark-field optical microscopy, whereas the nanoparticle distribution was examined by transmission electron microscopy. Variations in the scanning probe temperatures and peroxide concentrations were carefully investigated to optimize the thermal lithography efficiency upon the addition of energetics.

Enhancement of light scattering and photoluminescence in electrospun polymer nanofibers.

Poly(methyl methacrylate) nanofibers with desired fiber diameters that ranged from 336 to 896 nm were electrospun as light scattering and propagation materials. The light scattering behavior of these samples as a function of the fiber diameter and fiber deposition thickness was examined by UV-vis spectrophotometry, which revealed the scattering bands in the absorption spectra. The scattering bands of these nanofibers were linearly proportional to the fiber diameter, which shows good agreement with a scattering model based on the Mie theory. The light scattering and prolonged light path lengths in the nanofiber scaffolds were monitored and quantified by the photoluminescence of a fluorescent dye, Coumarin 6, which was preloaded into the polymer nanofibers. The photoluminescence after proper normalization showed a second-order dependence on the dye loading per unit area, which is significantly different from the spin-coated thin-film samples following a first-order relationship. Nonlinear photoluminescence enhancements indicated prolonged light path lengths and multiple light absorptions within the fiber scaffolds as a result of light scattering. Even with relatively broad scattering band widths, the light scattering and photoluminescence of the electrospun nanofibers exhibited considerable wavelength selectivity, especially as the scattering bands overlapped with the excitation wavelengths of the fluorescence reagent.

Accumulation of butyltin compounds in cobia Rachycentron canadum raised in offshore aquaculture sites.

Butyltin residues (monobutyltin, MBT; dibutyltin, DBT; tributyltin, TBT; tetrabutyltin, TeBT) in the sea water and in the cobia (Rachycentron canadum) from aquaculture sites located offshore of Penhu island, Taiwan, were collected and quantified. The average concentrations of MBT, DBT, TBT and TeBT in sea water were n.d.-28+/-3, 4.0+/-0.6-88+/-13, n.d.-43+/-4, and n.d.-7+/-1 ng l(-1), respectively. The total butyltin (sum of MBT, DBT, TBT, TeBT) residues in the skin, dorsal muscle, ventral muscle, dark muscle, and liver of the cobia were in the range of 72+/-12-2270+/-85, 79+/-11-688+/-33, 82+/-14-1715+/-104, 93+/-13-803+/-47, and n.d.-52,745+/-252 ng g(-1) (wet weight), respectively. Although in this study in most cases, the highest concentration of total butyltin residues was found in liver or skin, in some cases, the highest concentration was found in muscle tissue. The crude lipid content in the skin, dorsal muscle, ventral muscle, dark muscle, and liver of these cobia was in the range of 7.9+/-0.1-28+/-1%, 11.7+/-0.8-29+/-1%, 11.5+/-0.3-44+/-3%, 24.2+/-0.4-48.4+/-0.4%, and 55.7+/-0.1-87.7+/-0.4% (wet weight), respectively. The concentrations of crude lipid content, and the concentrations of total butyltin residues in these tissues were not correlated.