ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer types.

Human endogenous retroviruses (HERVs) comprise approximately 8% of the human genome, co-opted into the dynamic regulatory network of cellular potency in early embryonic development. In recent studies, resurgent HERVs' transcriptional activity has been frequently observed in many types of human cancers, suggesting their potential functions in the occurrence and progression of malignancy. However, a dedicated web resource for querying the relationship between activation of HERVs and cancer development is lacking. Here, we have constructed a database to explore the sequence information, expression profiles, survival prognosis, and genetic interactions of HERVs in diverse cancer types. Our database currently contains RNA sequencing data of 580 HERVs across 16246 samples, including that of 6478 tumoral and 634 normal tissues, 932 cancer cell lines, as well as 151 early embryonic and 8051 human adult tissues. The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics, pathology, pharmacology, and related areas, enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance. The ERVcancer database is available at http://kyuanlab.com/ervcancer/.

A Comprehensive Review: Versatile Imaging Probe Based on Chemical Materials for Biomedical Applications.

Imaging probe and contrast agents play significant role in combating cancer. Based on special chemical materials, imaging probe can convert cancer symptoms into information-rich images with high sensitivity and signal amplification, accompanying with detection, diagnosis, drug delivery and treatment. In the paper, some inorganic and organic chemical materials as imaging probe, including Ultrasound imaging (US), Optical imaging (OP), Photoacoustic imaging (PA), X-ray Computed Tomography (CT), Magnetic Resonance imaging (MRI), Radionuclide imaging (RNI) probe, as well as multi-modality imaging probe for diagnosis and therapy of tumour were introduced. The sophisticated and comprehensive chemical materials as imaging probe were highlighted in detail. Meanwhile, the advantages and disadvantages of the imaging probe were compared. In order to provide some reference and help researchers for construction imaging probe for tumour diagnosis and treatment, it attempts to exhaustively cover the whole field. Finally, the prospect and challenge for imaging probe were discussed.

ARID1A loss derepresses a group of human endogenous retrovirus-H loci to modulate BRD4-dependent transcription.

Transposable elements (TEs) through evolutionary exaptation have become an integral part of the human genome, offering ample regulatory sequences and shaping chromatin 3D architecture. While the functional impacts of TE-derived sequences on early embryogenesis have been recognized, their roles in malignancy are only starting to emerge. Here we show that many TEs, especially the pluripotency-related human endogenous retrovirus H (HERVH), are abnormally activated in colorectal cancer (CRC) samples. Transcriptional upregulation of HERVH is associated with mutations of several tumor suppressors, particularly ARID1A. Knockout of ARID1A in CRC cells leads to increased transcription at several HERVH loci, which involves compensatory contribution by ARID1B. Suppression of HERVH in CRC cells and patient-derived organoids impairs tumor growth. Mechanistically, HERVH transcripts colocalize with nuclear BRD4 foci, modulating their dynamics and co-regulating many target genes. Altogether, we uncover a critical role for ARID1A in restraining HERVH, whose abnormal activation can promote tumorigenesis by stimulating BRD4-dependent transcription.

In situ photoinitiated fabrication of phosphorylcholine-functionalized polyhedral oligomeric silsesquioxane hybrid monolithic column for mixed-mode capillary electrochromatography.

A monolithic-based mixed-mode stationary phase was prepared for capillary electrochromatography via the fast photoinitiated polymerization of 2-methacryloyloxyethyl phosphorylcholine and polyhedral oligomeric silsesquioxane methacrylate (POSS-MA) monomers in the presence of crosslinker pentaerythritol triacrylate (PETA). Several copolymerization parameters, including the composition of monomers or porogens, ratio of crosslinkers to monomers, and polymerization time, were systematically optimized to tune the permeability and efficiency of monolithic columns. The morphologies and structures of the as-prepared monoliths were characterized by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy, thermogravimetry and nitrogen adsorption/desorption analysis, indicating a typical POSS skeleton morphology with numerous mesopores on the monolith. Owing to the incorporation of zwitterionic functional groups and rigid POSS skeleton on the hybrid monolith, the resulting stationary phase exhibited both hydrophilic and electrostatic interactions, as well as good mechanical stability. Pressurized CEC separation of various kinds of polar compounds such as amides, nucleobases, nucleosides and benzoic acids, and polypeptide antibiotics was achieved by mixed-mode retention mechanisms including hydrophilic interaction chromatography (HILIC) and weak cation exchange chromatography (WCX) with a high column efficiency up to 93 500 plates per m (thiourea).

Preparation of a biomimetic ionic liquids hybrid polyphosphorylcholine monolithic column for the high efficient capillary microextraction of glycopeptide antibiotics.

An ionic liquid hybrid zwitterionic polymer capillary microextraction (CME) column was prepared for the biomimetic enrichment of glycopeptides by one-step copolymerization of 2-methacryloyloxyethyl phosphorylcholine (MPC) and 1-butyl-3-vinylimidazolium bromide, in the presence of crosslinker trimethylolpropane trimethacrylate (TMA). The resultant monolith was characterized by scanning electron microscopy (SEM), fourier transform infrared (FT-IR) spectroscopy and pore size distribution measurement. Due to the incorporation of zwitterionic MPC owning a unique biomimic structure (i.e. hydrophilic cation/anion and hydrophobic long-alkyl chain), the monolithic column has large pore size and good biocompatibility, exhibiting high extraction efficiency, permeability and fast mass transfer to targets. Besides, the use of ionic liquids (ILs) as co-monomer in the polymerization endows the monolith with enhanced mechanical stability, uniformity and multiple interactions. The prepared column was successfully applied in CME coupled to capillary electrochromatography (CEC) for the efficient enrichment and separation of glycopeptide antibiotics in foodstuff. The method demonstrated a wide linear range (50.0-18000.0 µg L-1), low detection limits (5.0-10.0 µg L-1, S/N = 3) and satisfied recoveries (76.0-109.7%). This work shows the advantage of fine-tuning biomimetic monoliths in application-specific CME-CEC.

Task-specific solid-phase microextraction based on ionic liquid/polyhedral oligomeric silsesquioxane hybrid coating for sensitive analysis of polycyclic aromatic hydrocarbons by gas chromatography-mass spectrometry.

A direct immersion solid-phase microextraction (DI-SPME) approach for gas chromatography-mass spectrometry (GC-MS) based on hybrid fiber coating of ionic liquid and polyhedral oligomeric silsesquioxane (POSS) is presented. To fabricate the task-specific coating for the enrichment of polycyclic aromatic hydrocarbons (PAHs), 1-butyl-3-vinylimidazolium bis[(trifluoromethyl)sulfonyl]imide (IL) and POSS were rapidly photoinitiated copolymerized within 5 min on a stainless steel fiber. The high efficient extraction of target analytes can be attributed to a combined result of multiple interactions including the strong CF⋯HC pseudohydrogen bonding, π-π stacking, hydrophobic force, and molecular sieve effect. A wide linear range (0.04-400 ng L-1) with low detection limits in the range of 0.004 and 0.5 ng L-1 were obtained for PAHs by GC-MS. The applicability of this coupling method was successfully demonstrated by the analysis of trace PAHs in real river water and soil samples, with satisfied recoveries (84.2-108.6%) and relative standard deviations (<8.1%). Compared to the other commercial fiber-based SPME methods, the IL/POSS hybrid coating-based SPME is much cheaper, thermally stable and capable of eliminating possible deleterious effects as well.

[Determination of peptide antibiotics in animal food by capillary electrochromatography coupled with laser induced fluorescence].

A rapid and sensitive method was established for the analysis of peptide antibiotics (bacitracin, polymyxin B and colistin) in animal food by capillary electrochromatography (CEC) coupled with laser induced fluorescence (LIF) using 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F) as fluorogenic reagent. Peptide antibiotics were derivatized by NBD-F in 50 mmol/L borate buffer (pH 7.5) for 45 min at 60℃. The fluorescence derivatives of peptide antibiotics were separated on a packed phenyl capillary column with a mobile phase consisting of acetonitrile-potassium phosphate (pH 5.0, 10 mmol/L) (55:45, v/v) at the flow rate of 0.02 mL/min. A supplementary pressure of 3.8 MPa and a separation voltage of -10 kV were applied. The limits of detection (LODs, S/N=3) were 5.0-10.0 ng/mL, which fulfilled the requirement of maximum residue limits for examined peptide antibiotics. The method was applied to detect peptide antibiotics in milk and feed stuffs. The spiked recoveries of the three peptide antibiotics were 72.9%-112.4%. The method shows some advantages on the simpler pretreatment and higher sensitivity, which can be of great benefit to the residual analysis of the veterinary drugs.

Collective effects of common SNPs and risk prediction in lung cancer.

Lung cancer is the leading cause of cancer deaths in both men and women in the US. While most sporadic lung cancer cases are related to environmental factors such as smoking, genetic susceptibility may also play an important role and a number of lung cancer associated single-nucleotide polymorphisms (SNPs) have been identified although many remain to be found. The collective effects of genome-wide minor alleles of common SNPs, or the minor allele content (MAC) in an individual, have been linked with quantitative variations of complex traits and diseases. Here we studied MAC in lung cancer using previously published SNPs data sets (US and Finland samples) and found higher MAC in cases relative to matched controls. A set of 5400 SNPs with MA (MAF < 0.5) more common in cases (P < 0.08) and linkage disequilibrium (LD) r2 = 0.3 was found to have the best predictive accuracy. These results identify higher MAC in lung cancer susceptibility and provide a meaningful genetic method to identify those at risk of lung cancer.