Search

Xanthone-chromanone homo- or heterodimers are regarded as a novel class of topoisomerase (Topo) inhibitors; however, limited information about these compounds is currently available. Here, 14 new (1–14) and 6 known tetrahydroxanthone chromanone homo- and heterodimers (15–20) are reported as isolated from Penicillium chrysogenumC-7-2-1. Their structures and absolute configurations were unambiguously demonstrated by a combination of spectroscopic data, single-crystal X-ray diffraction, modified Mosher’s method, and electronic circular dichroism analyses. Plausible biosynthetic pathways are proposed. For the first time, it was discovered that tetrahydroxanthones can convert to chromanones in water, whereas chromone dimerization does not show this property. Among them, compounds 5, 7, 8, and 16exhibited significant cytotoxicity against H23 cell line with IC50values of 6.9, 6.4, 3.9, and 2.6 μM, respectively.

Patients with hepatic failure are often accompanied by hepatic retinopathy, but the cellular and molecular mechanisms underlying the hepatic retinopathy remain unclear. In this study, we investigated how liver failure leads to hepatic retinopathy using bile duct ligation (BDL) rats as a cholestasis animal model. Light-dark box test was used to assess sensitivity to light, indexed as visual acuity. On D28 post-BDL, rats were subjected to light-dark box test and blood samples were collected for biochemical analyses. The rats then were euthanized. Liver, spleen and both side of eye were quickly harvested. We showed that BDL impaired rat sensitivity to light, significantly decreased the thickness of inner nuclear layer (INL), outer nuclear layer (ONL) and total retina, as well as the retinal cell numbers in ONL and ganglion cell layer (GCL). The expression of rhodopsin (RHO), brn-3a and GPX4 was significantly decreased in retina of BDL rats, whereas the expression of cleaved caspase 3, 8, 9, bax/bcl-2, RIP1, GFAP, and iba-1, as well as TUNEL-positive cells were significantly increased. In cultured retinal explant, we found that NH4Cl (0.2, 1, 5 mM) concentration-dependently impaired activity of retinal explant, decreased thickness of INL and ONL, downregulated expression of brn-3a, RHO and GFAP, increased expression of cl-caspase 3 and TUNEL-positive cell numbers, with NH4Cl (5 mM) almost completely disrupting the structure of the cultured retina; bilirubin (1 μM) significantly upregulated GFAP expression, whereas high level (10 μM) of bilirubin downregulated expression of GFAP. We further demonstrated in vivo that hyperammonemia impaired rat sensitivity to light, decreased thickness of INL and ONL, downregulated expression of RHO, brn-3a, GFAP and increased expression of cl-caspase 3; hyperbilirubinemia impaired rat sensitivity to light, upregulated expression of GFAP and iba-1. In conclusion, BDL impaired rat visual acuity due to the elevated levels of ammonia and bilirubin. Ammonia induced loss of retinal ganglion cells and rod photoreceptor cells via apoptosis-mediated cell death. Bilirubin impaired retinal function via activating microglia and Müller cells.

The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacterand Alistipeswere causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter, and members of Proteobacteriawere influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate and selenium. Two-sample Mendelian randomization with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies.

Altered mitochondrial function is tightly linked to lifespan regulation, but underlying mechanisms remain unclear. Here, we report the chronological and replicative lifespan variation across 167 yeast knock-out strains, each lacking a single nuclear-coded mitochondrial gene, including 144 genes with human homologs, many associated with diseases. We dissected the signatures of observed lifespan differences by analyzing profiles of each strain’s proteome, lipidome, and metabolome under fermentative and respiratory culture conditions, which correspond to the metabolic states of replicative and chronologically aging cells, respectively. Examination of the relationships among extended longevity phenotypes, protein, and metabolite levels revealed that although many of these nuclear-encoded mitochondrial genes carry out different functions, their inhibition attenuates a common mechanism that controls cytosolic ribosomal protein abundance, actin dynamics, and proteasome function to regulate lifespan. The principles of lifespan control learned through this work may be applicable to the regulation of lifespan in more complex organisms, since many aspects of mitochondrial function are highly conserved among eukaryotes.

The physicochemical exchange dynamics between the solid and solution phases of per- and polyfluoroalkyl substances (PFAS) in soils needs to be better understood. This study employed an in situtool, diffusive gradients in thin films (DGT), to understand the distribution and exchange kinetics of five typical PFAS in four soils. Results show a nonlinear relationship between the PFAS masses in DGT and time, implying that PFAS were partially supplied by the solid phase in all of the soils. A dynamic model DGT-induced fluxes in soils/sediments (DIFS) was used to interpret the results and derive the distribution coefficients for the labile fraction (Kdl), response time (tc), and adsorption/desorption rates (k1and k–1). The larger labile pool size (indicated by Kdl) for the longer chain PFAS implies their higher potential availability. The shorter chain PFAS tend to have a larger tcand relatively smaller k–1, implying that the release of these PFAS in soils might be kinetically limited but not for more hydrophobic compounds, such as perfluorooctanesulfonic acid (PFOS), although soil properties might play an important role. Kdlultimately controls the PFAS availability in soils, while the PFAS release from soils might be kinetically constrained (which may also hold for biota uptake), particularly for more hydrophilic PFAS.

Peptide labeling by isobaric tags is a powerful approach for the relative quantitative analysis of proteomes in multiple groups. There has been a revolution in the innovation of new isobaric reagents; however, great effort is being made to expand simultaneous labeling groups to identify more labeled peptides and reduce reporter ion signal suppression. We redesigned the original chemical structure of the deuterium isobaric amine-reactive tag developed in our laboratory. We optimized the synthetic pathway to create a new set of 16-plex isobaric tags (IBT-16plex). The novel reagent enabled almost complete labeling of peptides within 90 min, with all labeling reporter ions exhibiting comparable MS/MS signals. Compared to a typical 16plex reagent, TMTpro-16plex, the peptides and proteins identified by IBT-16plex in trypsinized HeLa cells were significantly increased by 14.8 and 8.6%, respectively. Moreover, differences in peptide abundance within 10-fold among multiple groups were barely suppressed in IBT-16plex, whereas the dynamic range in TMTpro-16plex-labeled groups was smaller. After quantitative examination of MCF7 cell proteins, IBT-16plex was confirmed as feasible and useful for evaluating protein responses of glucose-starved MCF7 cells to a glucose-rich medium.

Allergic rhinitis (AR) is a chronic inflammatory reaction by immunoglobulin E (IgE) mediators after individual contact with allergens. It affects 10–40% of the world’s population and reduces the quality of life. Long-term symptoms of rhinitis can cause inflammation to spread and trigger asthma, which can harm human health. Herein, we develop a Smart PeptIde defeNse (SPIN) web technique, which in situ constructs a peptide web, trapping IgE against AR. Two candidate SPINs, SPIN-1 and SPIN-2, are designed with different IgE-binding sequences. The SPIN-1 or SPIN-2 is able to bind to IgE and transform from nanoparticles into entangled nanofibers. In turn, the web of SPIN-1 or SPIN-2 acts as a long-term trap of IgE to prevent the IgE from binding to mast cells. SPIN-1 or SPIN-2 (10 mg/kg) is able to treat AR model Balb/c mice with high efficiency and reduced symptoms of rhinitis and inflammatory factors, even better than a first-line clinical drug, cetirizine (10 mg/kg). For example, the amount of IL-4 released in the AR group (185.5 ± 6.8 pg/mL) is significantly reduced after the treatment with SPIN-1 (70.4 ± 14.1 pg/mL), SPIN-2 (86.0 ± 9.3 pg/mL), or cetirizine (112.8 ± 19.3 pg/mL). More importantly, compared with the cetirizine group (1 day), the SPIN-1 or SPIN-2 group shows long-term therapeutic effects (1 week). The SPIN web technique shows the great potential for blocking IgE binding to mast cells in vivo, attenuating AR or other allergic reactions.

Red blood cells (RBCs) naturally delivery oxygen and kill pathogens through reactive oxygen species (ROS) generated from Fe-protoporphyrin component in hemoglobin, which might be also promising for cancer treatment in terms of relieving tumor hypoxia and inducing oxidative damage against cancer cells. However, the therapy efficacy is far from satisfactory due to the limited oxygen transport and ROS generation rate in tumor tissue. Herein, artificial RBCs (designated as FTP@RBCM) with radical storm production ability is developed for oncotherapy through multi-dimensional reactivity pathways of Fe-protoporphyrin based hybrid metal-organic framework (FTP, as the core), including photodynamic/chemodynamic (PDT/CDT)-like, catalase-like and glutathione (GSH) peroxidase-like activity. Meanwhile, owing to the advantages of reticuloendothelial system (RES) evasion and long circulation abilities of RBCs governed by their cell membranes (RBCMs), FTP with surface further coated with RBCMs (FTP@RBCM) could enormously accumulate at tumor site to achieve remarkably enhanced therapy efficiency.

The vagina contains at least a billion microbial cells, dominated by lactobacilli. Here we perform metagenomic shotgun sequencingon cervical and fecal samples from a cohort of 516 Chinese women of reproductive age, as well as cervical, fecal, and salivary samples from a second cohort of 632 women. Factors such as pregnancyhistory, delivery history, cesarean section, and breastfeedingwere all more important than menstrual cycle in shaping the microbiome, and such information would be necessary before trying to interpret differences between vagino-cervical microbiomedata. Greater proportion of Bifidobacterium brevewas seen with older age at sexual debut. The relative abundance of lactobacilli especially Lactobacillus crispatuswas negatively associated with pregnancy history. Potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, and contraceptives were also identified. Lactobacilli were rare during breastfeeding or post-menopause. Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome. Gut and salivary microbiomes, plasma vitamins, metals, amino acids, and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.

The vagina contains at least a billion microbial cells, dominated by lactobacilli. Here we perform metagenomic shotgun sequencingon cervical and fecal samples from a cohort of 516 Chinese women of reproductive age, as well as cervical, fecal, and salivary samples from a second cohort of 632 women. Factors such as pregnancyhistory, delivery history, cesarean section, and breastfeedingwere all more important than menstrual cycle in shaping the microbiome, and such information would be necessary before trying to interpret differences between vagino-cervical microbiomedata. Greater proportion of Bifidobacterium brevewas seen with older age at sexual debut. The relative abundance of lactobacilli especially Lactobacillus crispatuswas negatively associated with pregnancy history. Potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, and contraceptives were also identified. Lactobacilli were rare during breastfeeding or post-menopause. Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome. Gut and salivary microbiomes, plasma vitamins, metals, amino acids, and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.

Lung cancer is the world’s leading cause of cancer death and shows strong ancestry disparities. By sequencing and assembling a large genomic and transcriptomic dataset of lung adenocarcinoma (LUAD) in individuals of East Asian ancestry (EAS; n= 305), we found that East Asian LUADs had more stable genomes characterized by fewer mutations and fewer copy number alterations than LUADs from individuals of European ancestry. This difference is much stronger in smokers as compared to nonsmokers. Transcriptomic clustering identified a new EAS-specific LUAD subgroup with a less complex genomic profile and upregulated immune-related genes, allowing the possibility of immunotherapy-based approaches. Integrative analysis across clinical and molecular features showed the importance of molecular phenotypes in patient prognostic stratification. EAS LUADs had better prediction accuracy than those of European ancestry, potentially due to their less complex genomic architecture. This study elucidated a comprehensive genomic landscape of EAS LUADs and highlighted important ancestry differences between the two cohorts.

Peptides have shown great potential in cancer treatment due to their good biocompatibility and low toxicity. However, the bioavailability and adverse immune response of peptides limit their further translation from bench to bedside. Over the past few decades, various peptide-based nanomaterials have been developed for drug delivery and cancer treatment. Compared with therapeutic peptides alone, self-assembled peptide nanomaterials have obvious advantages, such as improved stability and biodistribution for high-performance cancer therapy. In this review, we have described the synthesis, self-assembly and the anti-cancer application of therapeutic peptides and their conjugates, particularly polymer–peptide conjugates (PPCs).

Due to their unique afterglow ability, long-wavelength-light rechargeable persistent luminescence (PersL) nanoparticles (PLNPs) have been emerging as an important category of imaging probes. Among them, ZnGa2O4:0.6% Cr3+(ZGC) PLNPs have gained widespread recognition due to the ease of synthesis and uniform morphology. Unfortunately, the limited absorption arising from the low molar extinction coefficient of Cr3+results in relatively low afterglow intensity and rapid decay after long-wavelength LED light irradiation. Herein, we discovered a strategy that boosting dye-sensitization performance was able to effectively amplify the PersL signal under white LED light. Specifically, Dil served as a highly efficient sensitizer for Cr3+, promoting the absorption of the excitation light. By adjusting the Pr dopant concentrations, ZGCP0.5PLNPs with optimal trap densities were obtained, which showed the highest PersL intensity and dye-sensitized performance. Strikingly, ZGCP0.5-Dil PLNPs exhibited a 24.3-fold enhancement in intensity and a 2-fold prolongation of decay time over bare ZGC PLNPs through the synergy effect of optimal electron traps and dye sensitization. Photostable ZGCP0.5-Dil PLNPs enabled imaging of the HepG2 tumor and effectively guided tumor surgical resection verified by the H&E staining analysis. This strategy could be a significant reference in other dye-sensitization PLNPs to enhance longer-wavelength rechargeable PersL.

To enhance the bonding properties between ramie fiber and epoxy resin, the ramie fiber was modified using nano-silica grafting. Hydrophilic nano-silica treated with water-soluble sodium dodecyl sulfate (SDS) and organic silane coupling agents was grafted onto the surface of ramie fiber. The surface roughness of the fibers was considerably increased after grafting. The nano-silica particles on the fiber surface enhanced the mechanical and thermal properties of the fiber-epoxy composite plates. Based on an analysis of contact angle measurements and a water absorption study, it was determined that the hydrophilicity of the treated fiber was weakened.

Currently, the commercial reagents for isobaric peptides labeling (TMT and iTRAQ) have some drawbacks, such as high cost in experiments, especially in quantitation for the modified peptides, and inconvenient handling for variable sizes of samples. Herein, we developed a set of 10-plex isobaric tags (IBT) with high stability and low cost. The labeled peptides were sensitively detected on Orbitrap Q Exactive MS with an MS2 resolution of 35 000 at 30% NCE, while the peptides were efficiently labeled over 97% by IBT at a ratio of 10:1 of reagent/peptide (w/w) in 200 mM TEAB buffer for 2 h. The IBT labeling was demonstrated with a wide dynamic range of 50-fold without obvious matrix effects on quantification. Importantly, there was little quantification bias found among the individual IBT tags, indicating that the peptides labeled by different tags were quantitatively comparable. The IBT 10-plex reagents were applied for dynamically monitoring the quantitative responses of phosphoproteome stimulated by EGF treatment in HeLa cells. In total, 5 361 unique phosphopeptides were identified, which reached a similar conclusion as others reported. The IBT reagents were therefore experimentally proven as a new type of reagents for isobaric peptides labeling and useful in a large quantity peptides of quantitative proteomics.

Objective This study was performed to investigate the effects of age and sex on 10 salivary steroid hormones and analyze the correlations between salivary and plasma hormones.Methods The concentrations of 10 salivary steroid hormones in 1090 Chinese adult volunteers were examined using liquid chromatography–tandem mass spectrometry, and a related investigation was performed on the concentrations of salivary hormones in this population.Results The concentrations of androstenedione (A4), 17α-hydroxyprogesterone (17-OHP), aldosterone (ALD), cortisone (COR), corticosterone (CORT), cortisol (F), progesterone (P), and testosterone were significantly different between men and women (Student’s t-test). Differences in 17-OHP and ALD concentrations were highly significant between women in the follicular and luteal phases of their menstrual cycle (Student’s t-test). Five salivary steroid hormones (17-OHP, A4, CORT, COR, and F) significantly decreased with increasing age (Kruskal–Wallis test). A high linear correlation between salivary and plasma 17-OHP, P, A4, and F were observed with obvious sex-related differences (Pearson’s correlation, r > 0.7).Conclusions Our results provide important knowledge regarding the descriptive characteristics of salivary hormones in relation to age and sex and their correlations with plasma hormones.

Maturity-onset diabetes of the young (MODY) is an inherited monogenic type of diabetes. Genetic mutations in MODY often cause nonsynonymous changes that directly lead to the functional distortion of proteins and the pathological consequences. Herein, we proposed that the inherited mutations found in a MODY family could cause a disturbance of protein abundance, specifically in serum. The serum samples were collected from a Uyghur MODY family through three generations, and the serum proteins after depletion treatment were examined by quantitative proteomics to characterize the MODY-related serum proteins followed by verification using target quantification of proteomics. A total of 32 serum proteins were preliminarily identified as the MODY-related. Further verification test toward the individual samples demonstrated the 12 candidates with the significantly different abundance in the MODY patients. A comparison of the 12 proteins among the sera of type 1 diabetes, type 2 diabetes, MODY, and healthy subjects was conducted and revealed a protein signature related with MODY composed of the serum proteins such as SERPINA7, APOC4, LPA, C6, and F5.

Cathepsin D is reportedly to be closely associated with tumor development, migration, and invasion, but its pathological mechanism is not fully elucidated. We aimed to evaluate phenotypic changes and molecular events in response to cathepsin D knockdown. Lowering endogenous cathepsin D abundance (CR) induced senescence in HeLa cells, leading to reduced rate of cell proliferation and impaired tumorigenesis in a mouse model. Quantitative proteomics revealed that compared with control cells (EV), the abundances of several typical lysosomal proteases were decreased in the lysosomal fraction in CR cells. We further showed that cathepsin D knockdown caused increased permeability of lysosomal membrane and reactive oxygen species accumulation in CR cells, and the scavenging of reactive oxygen species by antioxidant was able to rescue cell senescence. Despite the increased reactive oxygen species, the proteomic data suggested a global reduction of redox-related proteins in CR cells. Subsequent analysis indicated that the transcriptional activity of nuclear factor erythroid-related factor 2 (Nrf2), which regulates the expression of groups of antioxidant enzymes, was down-regulated by cathepsin D knockdown. Importantly, Nrf2 overexpression significantly reduced cell senescence. Although transient oxidative stress promoted the accumulation of Nrf2 in the nucleus, we showed that the Nrf2 protein exited nucleus if oxidative stress persisted. In addition, when cathepsin D was transiently knocked down, the cathepsin-related events followed a sequential order, including lysosomal leakage during the early stage, followed by oxidative stress augmentation, and ultimately Nrf2 down-regulation and senescence. Our results suggest the roles of cathepsin D in cancer cells in maintaining lysosomal integrity, redox balance, and Nrf2 activity, thus promoting tumorigenesis. The MS Data are available via ProteomeXchange with identifier PXD002844.

In the era of single-cell biology, spatial proteomics has emerged as an important frontier. However, it still faces several challenges in technology. Formalin-fixed paraffin-embedded (FFPE) tissues are an important material in spatial proteomics, in which fixed tissues are excised using laser capture microdissection (LCM), followed by protein identification with mass spectrometry. For a satisfied spatial proteomics upon FFPE tissues, the excision area is expected to be as small as possible, and the identified proteins are countered upon as much as possible. For a general laboratory for spatial proteomics, a routine workflow is required, not relying on any special device, and is easily operating. In view of these challenges in technology, we initiated a technology evaluation throughout the entire procedure of proteomic analysis with micro-FFPE tissues. In contrast to the protocols reported previously, several innovations in technology were proposed and conducted, such as removal of destaining, decross-linking with “hang-down”, solution simplification for peptide generation and balancing to excision area, and capture rate of micro-FFPE tissues. After optimization of all the necessary steps, a routine workflow was established, in which the minimized area for protein identification was 0.002 mm2, while the excision area for a consistent proteomic analysis was 0.05 mm2. Using the developed workflow and collecting the micro-FFPE tissues continuously, for the first time, a spatial proteomic atlas of mouse brain was preliminarily constructed, which exhibited the typical characteristics of spatial-dependent protein abundance and functional enrichment.

Noble metal compositing is a promising method to enhance radiance intensity of persistent luminescent (PersL) nanoparticles (NPs) via surface plasmon resonance (SPR) for better tumor imaging, but it rarely unites with the pH-response strategy due to the challenge of realizing rigorous pH-responsive spatial distance control as a “button switch” of SPR. Here, ZnGa2O4:Cr3+(ZGC) NPs as “pomegranate seeds” are cladded with sodium alginate to form nanoclusters (ZGC-SA), subsequently coated with carboxyl-rich polymers to acquire “pomegranate rind” (ZSPB) and finally decorated with 10 nm gold NPs (AuNPs) on the surface to obtain nanopomegranate structure (ZSPB@AuNPs). Though without deliberate distance control, there are plenty of “seeds” inside ZSPB@AuNPs fortunately at appropriate positions, which could be plasmon-enhanced by AuNPs. Furthermore, triggered by carboxyl protonation in subacid tumor, ZSPB@AuNPs aggregate and subsequently facilitate such plasmon enhancement effect, resulting in 4.4-fold PersL promotion at pH 5.5 (tumor microenvironment, TME) over pH 7.4 and in a maximum “tumor to normal tissue ratio” of PersL imaging signals of 125.9. Under surgical navigation of ZSPB@AuNPs, intramuscular tumors of mice could be resected without residue signals left. This nanopomegranate achieves TME pH-responsive plasmon-enhanced PersL for the first time and broadens the way for designing plasmon-enhanced PersL nanosystems.

Flax (Linum usitatissimumL.) as one of the versatile crops is a major source of unsaturated fatty acids in seeds. Stearoyl-acyl carrier protein desaturase (SAD) is a dehydrogenase enzyme that plays a key role in oleic acid biosynthesis as well as responses to biotic and abiotic stresses. However, the function of SADorthologs from L. usitatissimumhas not been assessed. Here, we found that two LuSADgenes, LuSAD1and LuSAD2, are present in the genome of L. usitatissimumcultivar ‘Longya 10’. Heterogeneous expression of either LuSAD1or LuSAD2in Arabidopsis thalianaresulted in the higher contents of total fatty acids and oleic acid in seeds. Interestingly, ectopic expression of LuSAD2in A. thalianacaused altered plant architecture. Consistently, the overexpression of either LuSAD1or LuSAD2in Brassica napusalso resulted in increased contents of total fatty acids and oleic acid in seeds. Furthermore, we demonstrated that either LuSAD1or LuSAD2enhances seedling resistance to cold and drought stresses viaimproving antioxidant enzyme activity and nonenzymatic antioxidant levels, as well as reducing membrane damage. These findings not only broaden our knowledge regarding the LuSADfunctions in plants, but also offer promising targets for improving oil quantity and quality, and abiotic stress tolerance of oil-producing crops through molecular manipulation.

A priority in solving the problem of drug resistance is to understand the molecular mechanism of how a drug induces the resistance response within cells. Because many cancer cells exhibit chromosome aneuploidy, we explored whether changes of aneuploidy status result in drug resistance. Two typical colorectal cancer cells, HCT116 and LoVo, were cultured with the chemotherapeutic drugs irinotecan (SN38) or oxaliplatin (QxPt), and the non- and drug-resistant cell lines were selected. Whole exome sequencing (WES) was employed to evaluate the aneuploidy status of these cells, and RNAseq and LC-MS/MS were implemented to examine gene expression at both mRNA and protein level. The data of gene expression was well-matched with the genomic conclusion that HCT116 was a near diploid cell, whereas LoVo was an aneuploid cell with the increased abundance of mRNA and protein for these genes located at chromosomes 5, 7, 12, and 15. By comparing the genomic, transcriptomic, and proteomic data, the LoVo cells with SN38 tolerance showed an increased genome copy in chromosome 14, and the expression levels of the genes on this chromosome were also significantly increased. Thus, we first observed that SN38 could impact the aneuploidy status in cancer cells, which was partially associated with the acquired drug resistance.

Because of its specificity and sensitivity, targeted proteomics using mass spectrometry for multiple reaction monitoring is a powerful tool to detect and quantify pre-selected peptides from a complex background and facilitates the absolute quantification of peptides using isotope-labeled forms as internal standards. How to generate isotope-labeled peptides remains an urgent challenge for accurately quantitative targeted proteomics on a large scale. Herein, we propose that isotope-labeled peptides fused with a quantitative tag could be synthesized through an expression system in vitro, and the homemade peptides could be enriched by magnetic beads with tag-affinity and globally quantified based on the corresponding multiple reaction monitoring signals provided by the fused tag. An Escherichia colicell-free protein expression system, protein synthesis using recombinant elements, was adopted for the synthesis of isotope-labeled peptides fused with Strep-tag. Through a series of optimizations, we enabled efficient expression of the labeled peptides such that, after Strep-Tactin affinity enrichment, the peptide yield was acceptable in scale for quantification, and the peptides could be completely digested by trypsin to release the Strep-tag for quantification. Moreover, these recombinant peptides could be employed in the same way as synthetic peptides for multiple reaction monitoring applications and are likely more economical and useful in a laboratory for the scale of targeted proteomics. As an application, we synthesized four isotope-labeled glutathione S-transferase (GST) peptides and added them to mouse sera pre-treated with GST affinity resin as internal standards. A quantitative assay of the synthesized GST peptides confirmed the absolute GST quantification in mouse sera to be measurable and reproducible.

Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, screening the biomarker candidates in the secreted proteins derived from the bladder cancer cell lines and verifying them in patient urines, defining the differential proteins through two-dimensional electrophoresis (2DE) and isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC–MS/MS, and implementing quantitative proteomics of profiling and targeting analysis. With proteomic survey, a total of 700 proteins were found with their abundance of secreted proteins in cancer cell lines different from normal, while 87 proteins were identified in the urine samples. The multiple reaction monitoring (MRM)-based quantification was adapted in verifying the bladder cancer related proteins in individual urine samples, resulting in 10 differential urine proteins linked with the cancer. Of these candidates, receiver operating characteristic analysis revealed that the combination of CO3 and LDHB was more sensitive as the cancer indicator than other groups. The discovery of the bladder cancer indicators through our strategy has paved an avenue to further biomarker validation.

A metallic glass coating with the composition of Fe51.33Cr14.9Mo25.67Y3.4C3.44B1.26(mole fraction, %) on the Q235 stainless steel was developed by the detonation gun (D-gun) spraying process. The microstructure and the phase aggregate were analyzed by scanning electron microscopy and X-ray diffractometry, respectively. Microhardness, wear resistance and corrosion behavior were assessed using a Vickers microhardness tester, a ball-on-disk wear testing machine and the electrochemical measurement method, respectively. Microstructural studies show that the coatings possess a densely layered structure with the porosity less than 2.1%. The tribological behavior of the coatings examined under dry conditions shows that their relative wear resistance is five times higher than that of the substrate material. Both adhesive wear and abrasive wear contribute to the friction, but the former is the dominant wear mechanism of the metallic glass coatings. The coatings exhibit low passive current density and extremely wide passive region in 3.5% NaCl solution, thus indicating excellent corrosion resistance.

The Ti–36Nb–2Ta–3Zr–0.35O (mass fraction, %) (TNTZO) alloy was produced by cold isostatic pressing and sintering from elemental powders, followed by hot and cold deformation. The effects of deformation process on microstructures and mechanical properties were investigated using the SEM, TEM, OM and the universal material testing machine. Results show that the alloy can be easily hot forged and cold swaged due to the fine-grained microstructure. Only after cold swaging by 85%, the alloy shows the typical “marble-like” structure. And the cold deformation is accompanied by stress-induced α”phase transformations. Moreover, both the strength and the ductility of the alloy are significantly improved by hot and cold working.

Considering the technical limitations of mass spectrometry in protein identification, the mRNAs bound to ribosomes (RNC-mRNA) are assumed to reflect the mRNAs participating in the translational process. The RNC-mRNA data are reasoned to be useful for appraising the missing proteins. A set of the multiomics data including free-mRNAs, RNC-mRNAs, and proteomes was acquired from three liver cancer cell lines. On the basis of the missing proteins in neXtProt (release 2014-09-19), the bioinformatics analysis was carried out in three phases: (1) finding how many neXtProt missing proteins have or do not have RNA-seq and/or MS/MS evidence, (2) analyzing specific physicochemical and biological properties of the missing proteins that lack both RNA-seq and MS/MS evidence, and (3) analyzing the combined properties of these missing proteins. Total of 1501 missing proteins were found by neither RNC-mRNA nor MS/MS in the three liver cancer cell lines. For these missing proteins, some are expected higher hydrophobicity, unsuitable detection, or sensory functions as properties at the protein level, while some are predicted to have nonexpressing chromatin structures on the corresponding gene level. With further integrated analysis, we could attribute 93% of them (1391/1501) to these causal factors, which result in the expression products scarcely detected by RNA-seq or MS/MS.

During an investigation of missing proteins with the RNA-seq data acquired from three liver cancer cell lines, the majority of the missing protein coding genes (MPGs) located at chromosome 11 (chr11) had no corresponding mRNAs, while a high percentage of the MPGs on chr19 were detected at the mRNA level. The phenomenon, which was also observed in more than 40 cell lines, led to an inquiry of causation of the different transcriptional statuses of the MPGs in the two chromosomes. We hypothesized that the special chromatin structure was a key element to regulate MPG transcription. Upon a systematical comparison of the effects of DNase I hypersensitive sites (DHSs), transcription factors (TFs), and histone modifications toward these genes or MPGs with/without mRNA evidence in chr11 and 19, we attributed the poor transcription of the MPGs to the weak capacity of these transcription regulatory elements, regardless of which chromosome the MPGs were located. We further analyzed the gene contents in chr11 and found a number of genes related to sensory functions in the presence of chr11. We postulate that a high number of sensory-related genes, which are located within special chromatin structure, could bring a low detection rate of MPGs in chr11.