LINC00493-encoded microprotein SMIM26 exerts anti-metastatic activity in renal cell carcinoma.

Human microproteins encoded by long non-coding RNAs (lncRNA) have been increasingly discovered, however, complete functional characterization of these emerging proteins is scattered. Here, we show that LINC00493-encoded SMIM26, an understudied microprotein localized in mitochondria, is tendentiously downregulated in clear cell renal cell carcinoma (ccRCC) and correlated with poor overall survival. LINC00493 is recognized by RNA-binding protein PABPC4 and transferred to ribosomes for translation of a 95-amino-acid protein SMIM26. SMIM26, but not LINC00493, suppresses ccRCC growth and metastatic lung colonization by interacting with acylglycerol kinase (AGK) and glutathione transport regulator SLC25A11 via its N-terminus. This interaction increases the mitochondrial localization of AGK and subsequently inhibits AGK-mediated AKT phosphorylation. Moreover, the formation of the SMIM26-AGK-SCL25A11 complex maintains mitochondrial glutathione import and respiratory efficiency, which is abrogated by AGK overexpression or SLC25A11 knockdown. This study functionally characterizes the LINC00493-encoded microprotein SMIM26 and establishes its anti-metastatic role in ccRCC, and therefore illuminates the importance of hidden proteins in human cancers.

Diamond formation mechanism in chemical vapor deposition.

It is a key challenge to prepare large-area diamonds by using the methods of high-pressure high-temperature and normal chemical vapor deposition (CVD). The formation mechanism of thermodynamically metastable diamond compared to graphite in low-pressure CVD possibly implies a distinctive way to synthesize large-area diamonds, while it is an intriguing problem due to the limitation of in situ characterization in this complex growth environment. Here, we design a series of short-term growth on the margins of cauliflower-like nanocrystalline diamond particles, allowing us to clearly observe the diamond formation process. The results show that vertical graphene sheets and nanocrystalline diamonds alternatively appear, in which vertical graphene sheets evolve into long ribbons and graphite needles, and they finally transform into diamonds. A transition process from graphite (200) to diamond (110) verifies the transformation, and Ta atoms from hot filaments are found to atomically disperse in the films. First principle calculations confirm that Ta-added H- or O-terminated bilayer graphene spontaneously transforms into diamond. This reveals that in the H, O, and Ta complex atmosphere of the CVD environment, diamond is formed by phase transformation from graphite. This subverts the general knowledge that graphite is etched by hydrogen and sp3 carbon species pile up to form diamond and supplies a way to prepare large-area diamonds based on large-sized graphite under normal pressure. This also provides an angle to understand the growth mechanism of materials with sp2 and sp3 electronic configurations.

Advances in phosphoproteomics and its application to COPD.

INTRODUCTION: Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED: In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION: The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.

Enhanced sensitivity of dilute aqueous adrenaline solution with an asymmetric hexagonal ring structure in the terahertz frequencies.

Quantitative detection of neurotransmitters in aqueous environment is crucial for the early diagnosis of many neurological disorders. Terahertz waves, as a non-contact and non-labeling tool, have demonstrated large potentials in quantitative biosensing. Although the detection of trace-amount analyte has been achieved with terahertz metamaterials in the recent decades, most studies have been focused on dried samples. Here, a hexagonal asymmetric metamaterial sensor was designed and fabricated for aqueous solution sensing with terahertz waves in the reflection geometry. An absorption enhancement of 43 was determined from the simulation. Dilute adrenaline solutions ranging from 30 µM to 0.6 mM were measured on our sensor using a commercial terahertz time-domain spectroscopy system, and the effective absorption was found to be linearly correlated with the concentration (R2 = 0.81). Furthermore, we found that as the concentration becomes higher (>0.6 mM), a non-linear relationship starts to take place, which confirmed the previous theory on the extended solvation shell that can be probed on the picosecond scale. Our sensor, without the need of high-power and stable terahertz sources, has enabled the detection of subtle absorption changes induced by the solvation dynamics.

A novel PdC monolayer with fully dispersed Pd atoms and a rigid carbon backbone: an intrinsic versatile electrocatalyst for overall water splitting and the corresponding reverse reaction.

The electrocatalytic overall water splitting and the corresponding reverse reaction play a vital role in future renewable energy systems and, hence, are frontiers of catalysis research. In this work, we identify a heretofore unknown two-dimensional palladium carbide using the structure swarm intelligence algorithm. The proposed monolayer, named α-PdC, consists of fully dispersed Pd atoms and a rigid carbon backbone, exhibiting high mechanical, dynamical, and thermal stability with desirable electrical conductivity. Further calculations show that the proposed monolayer is an intrinsic multifunctional electrocatalyst. It possesses an excellent catalytic performance toward the hydrogen evolution reaction (HER), the oxygen evolution reaction (OER), and the oxygen reduction reaction (ORR) with low overpotentials. Specifically, the overpotential for the HER is only -0.01 V, and the significantly low activation energy barrier (0.16 eV) on α-PdC elucidates the fast kinetics. Moreover, α-PdC could also be highly active towards the OER and ORR with comparable overpotentials (0.38 and 0.27 V, respectively). This study identifies an intrinsic versatile electrocatalyst with potential applications in the fields of energy conversion and storage.

New advances in quantitative proteomics research and current applications in asthma.

INTRODUCTION: Asthma is the most common chronic respiratory disease and has been declared a global public health problem by the World Health Organization. Due to the high heterogeneity and complexity, asthma can be classified into different 'phenotypes' and it is still difficult to assess the phenotypes and stages of asthma by traditional methods. In recent years, mass spectrometry-based proteomics studies have made significant progress in sensitivity and accuracy of protein identification and quantitation, and are able to obtain differences in protein expression across samples, which provides new insights into the mechanisms and classification of asthma. AREAS COVERED: In this article, we summarize research strategies in quantitative proteomics, including labeled, label-free and targeted quantification, and highlight the advantages and disadvantages of each. In addition, new applications of quantitative proteomics and the current status of research in asthma have also been discussed. In this study, online resources such as PubMed and Google Scholar were used for literature retrieval. EXPERT OPINION: The application of quantitative proteomics in asthma has an important role in identifying asthma subphenotypes, revealing potential pathogenesis and therapeutic targets. But the proteomic studies on asthma are not sufficient, as most of them are in the phase of biomarker discovery.

Tunable electronic and optical properties in buckling a non-lamellar B3S monolayer.

We propose a novel polymorph of a hexagonal B3S monolayer by combing structure swarm intelligence and first-principles calculations. Phonon spectrum analysis and ab initio molecular dynamics simulation indicate that the new structure is dynamically and thermally stable. Furthermore, the structure is mechanically stable and has a satisfactory elastic modulus. Our results show that the B3S monolayer is a semiconductor with strong visible-light optical absorption. More importantly, the electronic properties of the structure are tunable via surface functionalization. For example, hydrogenation or fluorination could transform the monolayer from the semiconducting to metallic state. On the other hand, surface oxidation could significantly enhance both carrier mobility and near-infrared optical absorption. Furthermore, we also discovered that the monolayer possesses satisfactory storage capacity for H2.

A hidden human proteome encoded by 'non-coding' genes.

It has been a long debate whether the 98% 'non-coding' fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting. We found that these new proteins deviated from the canonical proteins with various physical and chemical properties, and emerged mostly in primates during evolution. We further deduced the protein functions by the assays of translation efficiency, RNA folding and intracellular localizations. As the new protein UBAP1-AST6 is localized in the nucleoli and is preferentially expressed by lung cancer cell lines, we biologically verified that it has a function associated with cell proliferation. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting a resource for annotating new human proteins.

Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy.

Mitochondria are involved in many crucial cellular processes. Maintaining healthy mitochondria is essential for cellular homeostasis. Parkin-dependent mitophagy plays an important role in selectively eliminating damaged mitochondria in mammalian cells. However, mechanisms of Parkin-dependent mitophagy remain elusive. In this research, we performed data-independent acquisition-based quantitative mitochondrial proteomics to study the proteomic alterations of carbonyl cyanide m-chlorophenylhydrazone (CCCP)-induced Parkin-mediated mitophagy. We identified 222 differentially expressed proteins, with 76 upregulations and 146 downregulations, which were potentially involved in mitophagy. We then demonstrated that annexin A7 (ANXA7), a calcium-dependent phospholipid-binding protein, can translocate to impaired mitochondria upon CCCP treatment, where it played a pivotal part in the process of Parkin-dependent mitophagy via interacting with BASP1. As a mitochondrial uncoupling agent, CCCP indirectly regulated ANXA7 and BASP1 to induce Parkin-dependent mitophagy.

Changes in Bemisia tabaci feeding behaviors caused directly and indirectly by cucurbit chlorotic yellows virus.

BACKGROUND: Plant viruses can affect vector's behaviors in order to enhance viral transmission. Cucurbit chlorotic yellows virus (CCYV) (genus Crinivirus) is an emergent RNA plant virus and is transmitted specifically by biotypes B and Q of tobacco whitefly, Bemisia tabaci (Gennadius), in a semipersistent manner. METHODS: We used the electrical penetration graph (EPG) to investigate the effect of CCYV on the feeding behaviors of B. tabaci biotypes B and Q. RESULTS: CCYV could affect, both directly and indirectly, the feeding behaviors of B. tabaci to various degrees, depending on biotypes and sexes of the insect. CCYV showed stronger direct effects on biotype Q than on biotype B in terms of increased non-phloem probing and phloem salivation. CCYV increased non-phloem probing and phloem salivation more on females than on males of biotype Q, and increased phloem salivation more on females than on males of biotype B. CCYV had stronger indirect effects, via virus-infested plants, on biotype B than on biotype Q by enhancing phloem sap ingestion and feeding bouts. CCYV increased non-phloem probing and feeding bouts more on males than on females of biotype B, and decreased phloem sap ingestion more on males than on females on biotype Q indirectly. CONCLUSIONS: The results clearly indicated that CCYV affects the feeding behaviors of B. tabaci, which may lead to increased ability of the B. tabaci for CCYV transmission.

Perfect planar tetra-coordinated MC6 monolayer: superior anode material for Li-ion battery.

In past decades, there have been great achievements on theoretical prediction and experimental fabrication of two-dimensional transition metal carbides. In this work, we report a hitherto unknown atomic-thin planar-structured transition metal carbide sheet denoted as MC6 (M = Cu, Ag, Au) via a structure-swarm intelligence algorithm. The proposed 2D crystals are both statically and dynamically stable, and could maintain their structure integrity at temperatures up to 1500 K. The calculated specific capacities of lithium-ion batteries employing such materials reach 1188 mA h g-1, which is 26.38% higher than previously reported highest MXene material with Mn+1Xn atomic configuration. Our results present the potential application of MC6 in Li-ion batteries.

A novel hydrogenated boron-carbon monolayer with high stability and promising carrier mobility.

Although immense research on the extension of the two-dimensional (2D) material family has been carried out, 2D materials with a satisfactory band gap, high carrier mobility, and outstanding thermodynamic stability under ambient conditions are still limited. In this work, using first principles calculations, we proposed new 2D ternary materials consisting of C, B, and H atoms, namely hexagonal-BCH (h-BCH) and tetragonal-BCH (t-BCH). Both phonon calculations and ab initio molecular dynamics simulations show that these proposed sheets are thermodynamically stable phases. The electronic structure calculations indicate that h-BCH and t-BCH sheets are semiconductors with a band gap of 2.66 and 2.22 eV, respectively. Remarkably, the h-BCH (t-BCH) sheet exhibits electron mobility as high as 7.41 × 103 (1.09 × 103) cm2 V-1 s-1, which is higher than that of the MoS2 monolayer, though the hole mobility is about one (two) order of magnitude lower. Equally important is the fact that the position of both the conduction and valence band edges of the h-BCH sheet matches well with the chemical reaction potential of H2/H+ and O2/H2O, giving a 2D photocatalyst as a potential candidate for overall visible-light-driven water splitting. Therefore, the designed h-BCH and t-BCH monolayers have promising applications in future electronics and photocatalysts.

Optimal Settings of Mass Spectrometry Open Search Strategy for Higher Confidence.

In most proteome mass spectrometry experiments, more than half of the mass spectra cannot be identified, mainly because of various modifications. The open search strategy allows for a larger precursor tolerance to utilize more spectra, especially those with post-translational modifications; however, thorough quality control based on independent information is lacking. Here, we used the "Suspicious Discovery Rate (SDR)" based on translatome sequencing (RNC-seq) as an independent source to reference the proteome open search results in steady-state cells. We found that the open search strategy increased the spectra utilization with the cost of increased suspicious identifications that lack translation evidence. We further found that restricting the peptide FDR below 0.1% efficiently controlled the suspicious identifications of open search methods and thus enhanced the confidence of the peptide identification with modifications comparable to the level of the traditional narrow window search. We then demonstrated the successful and validated identification of 27 single amino acid variations from the spectra of two cell lines using the open search strategy without a predefined database. These results validated the proper use of open search methods for higher-quality proteome identifications with information on post-translational modifications and single amino acid polymorphisms.

Ultralow loss graphene-based hybrid plasmonic waveguide with deep-subwavelength confinement.

In this paper, we theoretically propose a novel graphene-based hybrid plasmonic waveguide (GHPW) consisting of a low-index rectangle waveguide between a high-index cylindrical dielectric waveguide and the substrate with coated graphene on the surface. The geometric dependence of the mode characteristics on the proposed structure is analyzed in detail, showing that the proposed GHPW has a low loss and consequently a relatively long propagation distance. For TM polarization, highly confined modes guided in the low-index gap region between the graphene and the high-index GaAs and the normalized modal area is as small as 0.0018 (λ2/4) at 3 THz. In addition to enabling the building of high-density integration of the proposed structure are examined by analyzing crosstalk in a directional coupler composed of two GHPWs. This structure also exhibits ultra-low crosstalk when a center-to-center separation between adjacent GHPWs is 32µm, which shows great promise for constructing various terahertz integrated devices.

D-carbon: Ab initio study of a novel carbon allotrope.

By means of ab initio computations and the global minimum structure search method, we have investigated structural, mechanical, and electronic properties of D-carbon, a crystalline orthorhombic sp3 carbon allotrope (space group Pmma [ D2h5 ] with 6 atoms per cell). Total-energy calculations demonstrate that D-carbon is energetically more favorable than the previously proposed T6 structure (with 6 atoms per cell) as well as many others. This novel phase is dynamically, mechanically, and thermally stable at zero pressure and more stable than graphite beyond 63.7 GPa. D-carbon is a semiconductor with a bandgap of 4.33 eV, less than diamond's gap (5.47 eV). The simulated X-ray diffraction pattern is in satisfactory agreement with previous experimental data in chimney or detonation soot, suggesting its possible presence in the specimen.

Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes.

Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the exosomes secreted by three human HCC cell lines, including the non-motile Hep3B cell, and the motile 97H and LM3 cells. More than 1400 exosomal proteins were confidently quantified in each MS analysis with highly biological reproducibility. We justified that 469 and 443 exosomal proteins represented differentially expressed proteins (DEPs) in the 97H/Hep3B and LM3/Hep3B comparisons, respectively. These DEPs focused on sugar metabolism-centric canonical pathways per ingenuity pathway analysis, which was consistent with the gene ontology analysis on biological process enrichment. These pathways included glycolysis I, gluconeogenesis I and pentose phosphate pathways; and the DEPs enriched in these pathways could form a tightly connected network. By analyzing the relative abundance of proteins and translating mRNAs, we found significantly positive correlation between exosomes and cells. The involved exosomal proteins were again focusing on sugar metabolism. In conclusion, motile HCC cells tend to preferentially export more sugar metabolism-associated proteins via exosomes that differentiate them from non-motile HCC cells.

PIK3C2A is a gene-specific target of microRNA-518a-5p in imatinib mesylate-resistant gastrointestinal stromal tumor.

Imatinib mesylate resistance occurs in some patients with gastrointestinal stromal tumors (GISTs) during the course of treatment. In this study, we investigated the relationship between microRNAs (miRNAs) and imatinib-resistant GISTs, and the effect of miR-518a-5p on PIK3C2A in imatinib-resistant GISTs. A total of 20 matched-pair GIST samples from imatinib-resistant patients were included in the study. Each of the paired tumor specimens were from the same patient who had surgical removal of GISTs preimatinib and postimatinib treatment. Seven pairs of tissues were resected for microarray analysis, and the remaining 13 pairs were utilized for miRNAs analysis. Target genes were selected based on bioinformatics from multiple biological databases. Luciferase reporter assays were used to confirm the binding of miR-518a-5p to PIK3C2A 3'UTR. GIST882R-NC, 882R-miR-518a-5p-OE, and 882R-miR-518a-5p-KD cell lines were constructed using lentiviral vectors. miR-518a-5p and PIK3C2A expression in 882R-NC, 882R-OE, and 882R-KD cells was assessed by real-time PCR and western blotting. A cell counting kit was used to detect the influence of miR-518a-5p to cell proliferation. TUNEL staining was applied to detect the influence of miR-518a-5p to cell apoptosis. Microarray analysis showed that miR-518a-5p was downregulated in imatinib-resistant GISTs, and the expression of miR-518a-5p was confirmed with good concordance between real-time PCR and miRNA microarray results. Luciferase reporter assays indicated that miR-518a-5p bound to the PIK3C2A 3'UTR. Compared with 882R-OE, PIK3C2A expression was significantly increased in 882R-KD cells. MiR-518a-5p reduced 882R proliferation and promoted 882R apoptosis. In conclusion, PIK3C2A is a gene-specific target of miR-518a-5p in imatinib mesylate-resistant GISTs. Low expression of miR-518a-5p is likely to upregulate PIK3C2A and affect the cellular response to the drug, causing resistance to imatinib in GISTs.

A plasma microRNA panel for early detection of colorectal cancer.

Colonoscopy remains the standard screening method for detecting colorectal cancer (CRC) at an early stage. However, many people avoid having a colonoscopy because of the fear for its potential complications. Our study aimed to identify plasma microRNAs for preliminarily screening CRC in general population, so that some unnecessary colonoscopies can be avoided. We investigated plasma microRNA expression in three independent cohorts including the discovery (n = 80), training (n = 112), and validation (n = 49) phases recruited at two medical centers. Microarrays were used for screening 723 microRNAs in 80 plasma samples to identify candidate microRNAs. Quantitative reverse-transcriptase PCR was performed on the 161 training and validation plasma samples to evaluate the candidate microRNAs discovered from microarrays. A logistic regression model was constructed based on the training cohort and then verified by using the validation dataset. Area under the receiver operating characteristic curve (AUC) was used to evaluate the diagnostic accuracy. We identified a panel of miR-409-3p, miR-7, and miR-93 that yielded high diagnostic accuracy in discriminating CRC from healthy group (AUC: 0.866 and 0.897 for training and validation dataset, respectively). Moreover, the diagnostic performance of the microRNA panel persisted in nonmetastasis CRC stages (Dukes' A-B, AUC: 0.809 and 0.892 for training and validation dataset, respectively) and in metastasis CRC stages (Dukes' C-D, AUC: 0.917 and 0.865 for training and validation dataset, respectively). In conclusion, our study reveals a plasma microRNA panel that has potential clinical value in early CRC detection and would play a critical role on preliminarily screening CRC in general population.

The prognostic value of EGFR overexpression and amplification in Esophageal squamous cell Carcinoma.

BACKGROUND: In view of the prominent role in cancer cell biology and alteration in substantial numbers of ESCC, defining EGFR molecular characteristics relevant to patient prognosis is of great importance. Therefore, we analyzed the protein expression and gene copy variation of the epithelial growth factor receptor (EGFR) in Chinese esophageal squamous cell carcinoma (ESCC) and explored the possible associations with various features of the tumors and survival of the patients. METHODS: Sections were made from tissue microarray composed of 96 ESCC, and examined for EGFR expression by means of immunohistochemistry (IHC) and for EGFR gene amplification by means of fluorescence in situ hybridization (FISH). The results of IHC were evaluated with six different reported scoring systems. Correlation with clinical features and survival was evaluated using chi-square test and Kaplan-Meier analysis. RESULTS: EGFR overexpression according to scoring system 1 significantly correlated with advanced lymph node involvement (P = 0.046), patient disease specific free survival (DFS) (P = 0.006) and overall survival (OS) (P = 0.007). No such association was observed using other 5 scoring systems (P > 0.05 ). EGFR amplification was associated with lymph node metastasis (P = 0.028), but not correlated with DFS and OS until 20 months. CONCLUSIONS: EGFR IHC overexpression evaluated by scoring system 1 might be suitable to be used in predicting patients survival in ESCC. EGFR gene amplification showed delayed prognostic information after 20 months.

Two-dimensional silicon monolayers generated on c-BN(111) substrate.

Silicene, a buckled two-dimensional honeycomb structure of silicon, has been experimentally synthesized on very few substrates. Furthermore, synthesizing silicene with a Dirac point is another hot research area. However, only silicene grown on Ag(111) has been reported to have a Dirac point, which has lowered the expectations of researchers. Here, three Si monolayer structures, a Si chain-type structure, a two-dimensional hexagonal close packed compound structure, and a two-dimensional hexagonal close packed structure, are generated on a c-BN(111) substrate using a particle-swarm optimization algorithm implemented in CALYPSO code. Band structure calculations show that all three structures exhibit a metallic nature. In particular, due to the absolutely flat conformation of the latter two structures, a linear dispersion exists near the Fermi energy level, indicating that charge carriers can transport like massless Dirac fermions. Our results open an alternative way of searching for other two-dimensional silicon monolayers with Dirac points.