MDTips: a multimodal-data-based drug-target interaction prediction system fusing knowledge, gene expression profile, and structural data.

MOTIVATION: Screening new drug-target interactions (DTIs) by traditional experimental methods is costly and time-consuming. Recent advances in knowledge graphs, chemical linear notations, and genomic data enable researchers to develop computational-based-DTI models, which play a pivotal role in drug repurposing and discovery. However, there still needs to develop a multimodal fusion DTI model that integrates available heterogeneous data into a unified framework. RESULTS: We developed MDTips, a multimodal-data-based DTI prediction system, by fusing the knowledge graphs, gene expression profiles, and structural information of drugs/targets. MDTips yielded accurate and robust performance on DTI predictions. We found that multimodal fusion learning can fully consider the importance of each modality and incorporate information from multiple aspects, thus improving model performance. Extensive experimental results demonstrate that deep learning-based encoders (i.e. Attentive FP and Transformer) outperform traditional chemical descriptors/fingerprints, and MDTips outperforms other state-of-the-art prediction models. MDTips is designed to predict the input drugs' candidate targets, side effects, and indications with all available modalities. Via MDTips, we reverse-screened candidate targets of 6766 drugs, which can be used for drug repurposing and discovery. AVAILABILITY AND IMPLEMENTATION: https://github.com/XiaoqiongXia/MDTips and https://doi.org/10.5281/zenodo.7560544.

Multimodal reasoning based on knowledge graph embedding for specific diseases.

MOTIVATION: Knowledge Graph (KG) is becoming increasingly important in the biomedical field. Deriving new and reliable knowledge from existing knowledge by KG embedding technology is a cutting-edge method. Some add a variety of additional information to aid reasoning, namely multimodal reasoning. However, few works based on the existing biomedical KGs are focused on specific diseases. RESULTS: This work develops a construction and multimodal reasoning process of Specific Disease Knowledge Graphs (SDKGs). We construct SDKG-11, a SDKG set including five cancers, six non-cancer diseases, a combined Cancer5 and a combined Diseases11, aiming to discover new reliable knowledge and provide universal pre-trained knowledge for that specific disease field. SDKG-11 is obtained through original triplet extraction, standard entity set construction, entity linking and relation linking. We implement multimodal reasoning by reverse-hyperplane projection for SDKGs based on structure, category and description embeddings. Multimodal reasoning improves pre-existing models on all SDKGs using entity prediction task as the evaluation protocol. We verify the model's reliability in discovering new knowledge by manually proofreading predicted drug-gene, gene-disease and disease-drug pairs. Using embedding results as initialization parameters for the biomolecular interaction classification, we demonstrate the universality of embedding models. AVAILABILITY AND IMPLEMENTATION: The constructed SDKG-11 and the implementation by TensorFlow are available from https://github.com/ZhuChaoY/SDKG-11. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Polarization-sensitive narrowband infrared photodetection triggered by optical Tamm state engineering.

Polarization-sensitive narrowband photodetection at near-infrared (NIR) has attracted significant interest in optical communication, environmental monitoring, and intelligent recognition system. However, the current narrowband spectroscopy heavily relies on the extra filter or bulk spectrometer, which deviates from the miniaturization of on-chip integration. Recently, topological phenomena, such as the optical Tamm state (OTS), provided a new solution for developing functional photodetection, and we experimentally realized the device based on 2D material (graphene) for the first time to the best of our knowledge. Here, we demonstrate polarization-sensitive narrowband infrared photodetection in OTS coupled graphene devices, which are designed with the aid of the finite-difference time-domain (FDTD) method. The devices show narrowband response at NIR wavelengths empowered by the tunable Tamm state. The full width at half maximum (FWHM) of the response peak reaches ∼100 nm, and it can potentially be improved to ultra-narrow of about 10 nm by increasing the periods of dielectric distributed Bragg reflector (DBR). The responsivity and response time of the device reaches 187 mA/W and ∼290 µs at 1550 nm, respectively. Furthermore, the prominent anisotropic features and high dichroic ratios of ∼4.6 at 1300 nm and ∼2.5 at 1500 nm are achieved by integrating gold metasurfaces.

High-performance nanofiltration concentrate treatment by a five-chamber bioelectrochemical system.

A combination of bioelectrochemical systems and electrodialysis has been considered an effective strategy for removing salts from the nanofiltration (NF) concentrate of electroplating wastewater; however, the recovery efficiency of multivalent metals is low. Herein, a new process based on microbial electrolysis desalination and chemical-production cell with five chambers (MEDCC-FC) has been proposed for the simultaneous desalination and recovery of the multivalent metals from NF concentrate. The MEDCC-FC was found to be significantly superior to the MEDCC with the monovalent selective cation exchange membrane (MEDCC-MSCEM) and MEDCC with the cation exchange membrane (MEDCC-CEM), in terms of the elevated desalination efficiency, multivalent metal recovery efficiency, current density, and coulombic efficiency, and decreased energy consumption and membrane fouling. Within 12 h, the MEDCC-FC provided the desirable outcome, indicated by a maximum current density of 6.88 ± 0.06 A/m2, desalination efficiency of 88 ± 10%, metals recovery efficiency of >58%, and total energy consumption of 1.17 ± 0.11 kWh for the per kg total dissolved solids removal. Mechanistic studies revealed that the integration of CEM and MSCEM in the MEDCC-FC promoted the separation and recovery of multivalent metal. These findings revealed that the proposed MEDCC-FC was promising in treating NF concentrate of electroplating wastewater towards advantages of effectiveness, economic viability, and flexibility.

Large-area long-wave infrared broadband all-dielectric metasurface absorber based on markless laser direct writing lithography.

Scalable and low-cost manufacturing of broadband absorbers for use in the long-wave infrared region are of enormous importance in various applications, such as infrared thermal imaging, radiative cooling, thermal photovoltaics and infrared sensor. In recent years, a plethora of broadband absorption metasurfaces made of metal nano-resonators with plasmon resonance have been synthesized. Still, their disadvantages in terms of complex structure, production equipment, and fabrication throughput, limit their future commercial applications. Here, we propose and experimentally demonstrate a broadband large-area all-dielectric metasurface absorber comprised of silicon (Si) arrys of square resonators and a silicon nitride (Si3N4) film in the long-wave infrared region. The multiple Mie resonance modes generated in a single-size Si resonator are utilized to enhance the absorption of the Si3N4 film to achieve broadband absorption. At the same time, the transversal optical (TO) phonon resonance of Si3N4 and the Si resonator's magnetic dipole resonance are coupled to achieve a resonator size-insensitive absorption peak. The metasurface absorber prepared by using maskless laser direct writing technology displays an average absorption of 90.36% and a peak absorption of 97.55% in the infrared region of 8 to 14 µm, and still maintains an average absorption of 88.27% at a inciedent angle of 40°. The experimentally prepared 2 cm × 3 cm patterned metasurface absorber by markless laser direct writing lithography (MLDWL) exhibits spatially selective absorption and the thermal imaging of the sample shows that the maximum temperature difference of 17.3 °C can exist at the boundary.

Probing mid-infrared surface interface states based on thermal emission.

Probing mid-infrared surface wave radiation remains a big challenge for a long time. The lack of convenient and quick mid-infrared surface wave radiation probing methods limits the development of the integrated mid-infrared materials and devices. In this work, we propose a scheme to construct and probe the mid-infrared surface wave radiation of interface state in the waveguide through thermal emission. A superlattice composed of alternately placed periodic meta-crystals is designed to construct an array of interfaces to realize the interface states through the transverse electrical waveguide modes with a tolerance in structural parameters. By heating the structure, we employ angular resolved thermal emission spectroscopy to directly and quickly verify the dispersion of mid-infrared interface states, which have specific frequencies, angles, and polarizations. Moreover, we establish a thermal imaging microscopy to probe the local waveguide interface state directly for the first time. This proposed infrared probing method based on thermal emission can be generalized to probe the mid-infrared surface wave in other systems, such as surface plasmon waves in graphene or surface phonon waves in two-dimensional materials in the mid-infrared range.

Second-generation antipsychotics induce cardiotoxicity by disrupting spliceosome signaling: Implications from proteomic and transcriptomic analyses.

Second-generation antipsychotics (SGAs) are first-line drugs that are prescribed for mental disorders in clinic. Severe cardiotoxicity has been widely reported and thus limits their clinical application. This study aimed to identify the common mechanism underlying SGAs-induced cardiotoxicity using dual-omics analyses. Balb/C mice were intraperitoneally injected with two representative SGAs, olanzapine (2.5 mg/kg) and clozapine (25 mg/kg), at clinically comparable doses for 0, 7, 14 and 21 days. Our results showed that both SGAs induced cardiomyocyte degeneration, inflammation infiltration, and cardiac fibrosis, all of which worsened with time. Proteomic analysis revelaed that 22 differentially expressed (DE) proteins overlapped in olanzapine and clozapine-treated hearts. These proteins were significantly enriched in muscle contraction, amino acid metabolism and spliceosomal assembly by GO term analysis and spliceosome signaling was among the top enriched pathways by KEGG analysis. Among the 22 DE proteins, three spliceosome signal proteins were validated in a dynamic detection, and their expression significantly correlated with the extent of SGAs-induced cardiac fibrosis. Following the spliceosome signaling dysregulation, RNA sequencing revealed that alternative splicing events in the mouse hearts were markedly enhanced by SGAs treatments, and the production of vast transcript variants resulted in dysregulation of multiple pathways that are critical for cardiomyocytes adaptation and cardiac remodeling. Pladienolide B, a specific inhibitor of mRNA splicing, successfully corrected SGAs-induced alternative splicing and significantly attenuated the secretion of pro-inflammatory factors and cell deaths induced by SGAs exposure. Our study concluded that the spliceosome signaling was a common pathway driving SGAs cardiotoxicity. Pharmacological inhibition of the spliceosome signaling represents a novel therapeutic strategy against SGAs cardiotoxicity.

Computational and Mass Spectrometry-Based Approach Identify Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in JMJD6.

The jumonji domain-containing protein 6 (JMJD6) gene catalyzes the arginine demethylation and lysine hydroxylation of histone and a growing list of its known substrate molecules, including p53 and U2AF65, suggesting a possible role in mRNA splicing and transcription in cancer progression. Mass spectrometry-based technology offers the opportunity to detect SNP variants accurately and effectively. In our study, we conducted a combined computational and filtration workflow to predict the nonsynonymous single nucleotide polymorphisms (nsSNPs) present in JMJD6, followed by a liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and validation. The computational approaches SIFT, PolyPhen-2, SNAP, I-Mutant 2.0, PhD-SNP, PANTHER, and SNPS&GO were integrated to screen out the predicted damaging/deleterious nsSNPs. Through the three-dimensional structure of JMJD6, H187R (rs1159480887) was selected as a candidate for validation. The validation experiments showed that the mutation of this nsSNP in JMJD6 obviously affected mRNA splicing or the transcription of downstream genes through the reduced lysyl-hydroxylase activity of its substrates, U2AF65 and p53, further indicating the accuracy of this prediction method. This research provides an effective computational workflow for researchers with an opportunity to select prominent deleterious nsSNPs and, thus, remains promising for examining the dysfunction of proteins.

Characterization and validation of long noncoding RNAs as new candidates in prostate cancer.

BACKGROUND: Long noncoding RNAs (lncRNAs) have been proved to be an important regulator in gene expression. In almost all kinds of cancers, lncRNAs participated in the process of pathogenesis, invasion, and metastasis. Meanwhile, compared with the large amounts of patients, there is rare knowledge about the role of lncRNAs in prostate cancer (PCa). MATERIAL/METHOD: In this study, lncRNA expression profiles of prostate cancer were detected by Agilent microarray chip, 5 pairs of case and control specimens were involved in. Differentially expressed lncRNAs were screened out by volcano plot for constructing lncRNA-miRNA-mRNA central network. Then, the top ten up-regulated and down-regulated lncRNAs were validated by qRT-PCR in another 5 tumor specimens and 7 para-cancerous/benign contrasts. Furthermore, we searched for the survival curve of the top 10 upregulated and downregulated lncRNAs. RESULTS: A total of 817 differentially expressed lncRNAs were filtered out by the criteria of fold change (FC) and t-test p < 0.05. Among them, 422 were upregulated, whereas 395 were downregulated in PCa tissues. Gene ontology and KEGG pathway analyses showed that many lncRNAs were implicated in carcinogenesis. lnc-MYL2-4:1 (FC = 0.00141, p = 0.01909) and NR_125857 (FC = 59.27658, p = 0.00128) had the highest magnitude of change. The subsequent qPCR confirmed the expression of NR_125857 was in accordance with the clinical samples. High expression of PCA3, PCAT14 and AP001610.9 led to high hazard ratio while low expression of RP11-279F6.2 led to high hazard ratio. CONCLUSIONS: Our study detected a relatively novel complicated map of lncRNAs in PCa, which may have the potential to investigate for diagnosis, treatment and follow-up in PCa. Our study revealed the expression of NR_125857 in human PCa tissues was most up-regulated. Further studies are needed to investigate to figure out the mechanisms in PCa.

Complement Inhibitor CRIg/FH Ameliorates Renal Ischemia Reperfusion Injury via Activation of PI3K/AKT Signaling.

Complement activation is involved in the pathogenesis of ischemia reperfusion injury (IRI), which is an inevitable process during kidney transplantation. Therefore, complement-targeted therapeutics hold great potential in protecting the allografts from IRI. We observed universal deposition of C3d and membrane attack complex in human renal allografts with delayed graft function or biopsy-proved rejection, which confirmed the involvement of complement in IRI. Using FB-, C3-, C4-, C5-, C5aR1-, C5aR2-, and C6-deficient mice, we found that all components, except C5aR2 deficiency, significantly alleviated renal IRI to varying degrees. These gene deficiencies reduced local (deposition of C3d and membrane attack complex) and systemic (serum levels of C3a and C5a) complement activation, attenuated pathological damage, suppressed apoptosis, and restored the levels of multiple local cytokines (e.g., reduced IL-1ß, IL-9, and IL-12p40 and increased IL-4, IL-5, IL-10, and IL-13) in various gene-deficient mice, which resulted in the eventual recovery of renal function. In addition, we demonstrated that CRIg/FH, which is a targeted complement inhibitor for the classical and primarily alternative pathways, exerted a robust renoprotective effect that was comparable to gene deficiency using similar mechanisms. Further, we revealed that PI3K/AKT activation, predominantly in glomeruli that was remarkably inhibited by IRI, played an essential role in the CRIg/FH renoprotective effect. The specific PI3K antagonist duvelisib almost completely abrogated AKT phosphorylation, thus abolishing the renoprotective role of CRIg/FH. Our findings suggested that complement activation at multiple stages induced renal IRI, and CRIg/FH and/or PI3K/AKT agonists may hold the potential in ameliorating renal IRI.

Tailoring Hexagonal Gibbsite Single Crystal Nanoplatelets for Ethylene Polymerization and Nanocomposite Formation on MAO-Free Heterogeneous Bis(imino)pyridine Iron(II) Catalyst.

Ultrathin single crystal γ-Al(OH)3 (Gibbsite) nanoplatelets with average thickness <20 nm and length <800 nm, pretreated with trimethylaluminum (TMA), represent highly efficient activators and supports bis(imino)pyridine iron (II) (FeBIP) complex to produce high density polyethylene (HDPE) as well as gibbsite/HDPE nanocomposites in exceptionally high yields. Opposite to both methylaluminoxane (MAO)-activated homogeneous FeBIP catalyst and heterogenous silica-supported single site catalysts, no addition of MAO is required. At low TMA/Fe = 50 molar ratio, the superior catalyst activity (up to 6500 kg mol-1 h-1 bar-1 ) of FeBIP@TMA@Gibbsite is paralleled by controlled polyethylene particle growth without encountering reactor-fouling problems typical for homogeneous catalysts. TMA@Gibbsite is compared with other AlR3 @Gibbsite activators. The Al/Fe molar ratio governs catalyst activity as well as molar mass, molar mass distribution, and thermal properties of polyethylene. Moreover, hexagonal gibbsite nanoplatelets are uniformly dispersed in polyethylene to yield agglomerate-free polyethylene/gibbsite nanocomposites.

Tailoring Hydrocarbon Polymers and All-Hydrocarbon Composites for Circular Economy.

The world population will rapidly grow from 7 to 9 billion by 2050 and this will parallel a surging annual plastics consumption from today's 350 million tons to well beyond 1 billion tons. The switch from a linear economy with its throwaway culture to a circular economy with efficient reuse of waste plastics is therefore mandatory. Hydrocarbon polymers, accounting for more than half the world's plastics production, enable closed-loop recycling and effective product-stewardship systems. High-molar-mass hydrocarbons serve as highly versatile, cost-, resource-, eco- and energy-efficient, durable lightweight materials produced by solvent-free, environmentally benign catalytic olefin polymerization. Nanophase separation and alignment of unentangled hydrocarbon polymers afford 100% recyclable self-reinforcing all-hydrocarbon composites without requiring the addition of either alien fibers or hazardous nanoparticles. Recycling of durable hydrocarbons is far superior to biodegradation. The facile thermal degradation enables liquefaction and quantitative recovery of low molar mass hydrocarbon oil and gas. Teamed up with biomass-to-liquid and carbon dioxide-to-fuel conversions, powered by renewable energy, waste hydrocarbons serve as renewable hydrocarbon feedstocks for the synthesis of high molar mass hydrocarbon materials. Herein, an overview is given on how innovations in catalyst and process technology enable tailoring of advanced recyclable hydrocarbon materials meeting the needs of sustainable development and a circular economy.

Proteome-wide Mapping of Endogenous SUMOylation Sites in Mouse Testis.

SUMOylation is a reversible post-translational modification involved in various critical biological processes. To date, there is limited approach for endogenous wild-type SUMO-modified peptides enrichment and SUMOylation sites identification. In this study, we generated a high-affinity SUMO1 antibody to facilitate the enrichment of endogenous SUMO1-modified peptides from Trypsin/Lys-C protease digestion. Following secondary Glu-C protease digestion, we identified 53 high-confidence SUMO1-modified sites from mouse testis by using high-resolution mass spectrometry. Bioinformatics analyses showed that SUMO1-modified proteins were enriched in transcription regulation and DNA repair. Nab1 was validated to be an authentic SUMOylated protein and Lys479 was identified to be the major SUMOylation site. The SUMOylation of Nab1 enhanced its interaction with HDAC2 and maintained its inhibitory effect on EGR1 transcriptional activity. Therefore, we provided a novel approach to investigating endogenous SUMOylation sites in tissue samples.

Controlling Surface Plasmons Through Covariant Transformation of the Spin-Dependent Geometric Phase Between Curved Metamaterials.

General relativity uses curved space-time to describe accelerating frames. The movement of particles in different curved space-times can be regarded as equivalent physical processes based on the covariant transformation between different frames. In this Letter, we use one-dimensional curved metamaterials to mimic accelerating particles in curved space-times. The different curved shapes of structures are used to mimic different accelerating frames. The different geometric phases along the structure are used to mimic different movements in the frame. Using the covariant principle of general relativity, we can obtain equivalent nanostructures based on space-time transformations, such as the Lorentz transformation and conformal transformation. In this way, many covariant structures can be found that produce the same surface plasmon fields when excited by spin photons. A new kind of accelerating beam, the Rindler beam, is obtained based on the Rindler metric in gravity. Very large effective indices can be obtained in such systems based on geometric-phase gradient. This general covariant design method can be extended to many other optical media.

Histone H3K9 demethylase JMJD1A modulates hepatic stellate cells activation and liver fibrosis by epigenetically regulating peroxisome proliferator-activated receptor γ.

As a central event in liver fibrogenesis, hepatic stellate cell (HSC) transdifferentiation involves loss of regulation by adipogenic transcription factors such as peroxisome proliferator-activated receptor γ; (PPARγ), which is epigenetically silenced during HSC activation. We hypothesized that JMJD1A, an H3K9 demethylase involved in adipogenic metabolism, could regulate PPARγ. In human HSC cell line, rat primary HSCs, and carbontetrachloride-induced mouse liver fibrogenesis model, we down-regulated the expression of JMJD1A using small interfering or short hairpin RNAs, and overexpressed its wild-type and mutant. We analyzed the effects of JMJD1A manipulation on the histone di-methyl-H3K9 (H3k9me2) status of PPARγ gene and the expression of PPARγ and fibrosis markers using chromatin immunoprecipitation, real-time quantitative RT-PCR and Western blot, and also investigated the in vitro and in vivo consequences on liver fibrosis and necrosis by Masson or hematoxylin-eosin staining, respectively. JMJD1A knockdown in HSCs correlated with reinforced H3K9me2 in the PPARγ gene promoter, and its down-regulation in both mRNA and protein led to increased expression of fibrosis markers, which could be consistently rescued by JMJD1A overexpression. Jmjd1a knockdown in situ resulted in significantly increased expression of α-smooth muscle actin (P = 0.005) and Col1a (P = 0.036), strengthened production of collagens (P = 0.028), and remarkably enhanced necrosis (P = 0.007) 4 weeks after treatment. This study suggests JMJD1A as a novel epigenetic regulator that modulates HSC activation and liver fibrosis through targeting PPARγ gene expression.

Transcriptome and proteome of human hepatocellular carcinoma reveal shared metastatic pathways with significant genes.

Previously isolated pathways screened from individual genes were investigated at either the transcriptional or translational level; however, the consistency between the pathways screened at the gene expression levels was obscure in metastatic human hepatocellular carcinoma (HCC). To elucidate this question, we performed a transcriptomic (16,353 genes) and proteomic (7861 proteins) analysis simultaneously on six metastatic HCC cell lines against two nonmetastatic HCC cell lines, with all HBV traceable and close genetic-backgrounds for a comparative study. The quantitative and integrated results showed that significant genes were screened differentially with 351 transcripts from the transcriptome and 304 proteins from the proteome, with limited overlapping genes (7%). However, we discovered that these discrete 351 transcripts and 304 proteins screened share extrusive significant-pathways/networks with a 77% overlap, including active TGF-ß, RAS, NFκB, and Wnt, and inactive HNF4A, which are responsible for HCC metastasis. We conclude that the discrete, but significant genes predicted by either ome play intrinsically important roles in the linkage of responsible pathways shared by both omes in HCC metastasis.

Functional Proteomics Study Reveals SUMOylation of TFII-I is Involved in Liver Cancer Cell Proliferation.

SUMOylation has emerged as a new regulatory mechanism for proteins involved in multiple physiological and pathological processes. However, the detailed function of SUMOylation in liver cancer is still elusive. This study reveals that the SUMOylation-activating enzyme UBA2 is highly expressed in liver cancer cells and clinical samples. Silencing of UBA2 expression could to some extent suppress cell proliferation. To elucidate the function of UBA2, we used a large scale proteomics strategy to identify SUMOylation targets in HepG2 cells. We characterized 827 potential SUMO1-modified proteins that were not present in the control samples. These proteins were enriched in gene expression processes. Twelve candidates were validated as SUMO1-modified proteins by immunoprecipitation-Western blotting. We further characterized SUMOylated protein TFII-I that was identified in this study and determined that TFII-I was modified by SUMO1 at K221 and K240. PIAS4 was an E3 ligase for TFII-I SUMOylation, and SENP2 was responsible for deSUMOylating TFII-I in HepG2 cells. SUMOylation reduced TFII-I binding to its repressor HDAC3 and thus promoted its transcriptional activity. We further show that SUMOylation is critical for TFII-I to promote cell proliferation and colony formation. Our findings contribute to understanding the role of SUMOylation in liver cancer development.

Omics evidence: single nucleotide variants transmissions on chromosome 20 in liver cancer cell lines.

Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence. Herein, we proposed a transomics strategy to profile the expression status of human Chr.20 genes (555 in Ensembl v72). The data of transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that ∼80% of the coding genes on Chr.20 were detected with mRNA signals in three liver cancer cell lines, whereas of the proteome identified, only ∼45% of the Chr.20 coding genes were detected. The high amount of overlapping of identified genes in mRNA and RNC-mRNA (ribosome nascent-chain complex-bound mRNAs, translating mRNAs) and the consistent distribution of the abundance averages of mRNA and RNC-mRNA along the Chr.20 subregions in three liver cancer cell lines indicate that the mRNA information is efficiently transmitted from transcriptional to translational stage, qualitatively and quantitatively. Of the 457 genes identified in mRNAs and RNC-mRNA, 136 were found to contain SNVs with 213 sites, and >40% of these SNVs existed only in metastatic cell lines, suggesting them as the metastasis-related SNVs. Proteomics analysis showed that 16 genes with 20 SNV sites were detected with reliable MS/MS signals, and some SNVs were further validated by the MRM approach. With the integration of the omics data at the three expression phases, therefore, we are able to achieve the overall view of the gene expression of Chr.20, which is constructive in understanding the potential trend of encoding genes in a cell line and exploration of a new type of markers related to cancers.

Chromosome-8-coded proteome of Chinese Chromosome Proteome Data set (CCPD) 2.0 with partial immunohistochemical verifications.

We upgraded the preliminary CCPD 1.0 to CCPD 2.0 using the latest deep-profiling proteome (CCPD 2013) of three hepatocellular carcinoma (HCC) cell lines, namely, Hep3B, MHCC97H, and HCCLM3 (ProteomeXchange identifiers: PXD000529, PXD000533, and PXD000535). CCPD 2.0 totally covered 63.6% (438/689) of Chr. 8-coded proteins and 62.6% (439/701) of Chr. 8-coded protein-coding genes. Interestingly, we found that the missing proteins exhibited a tendency to form a cluster region in chromosomes, such as two ß-defensins clusters in Chr. 8, caused perhaps by their inflammation-related features. For the 41 Chr. 8-coded proteins being weakly or barely identified previously, we have performed an immunohistochemical (IHC) verification in 30 pairs of carcinoma/para-carcinoma HCC and 20 noncancerous liver tissues and confirmed their expressional evidence and occurrence proportions in tissue samples. We also verified 13 Chr. 8-coded HCC tumorigenesis-associated depleting or deficient proteins reported in CCPD 1.0 using IHC and screened 16 positive and 24 negative HCC metastatic potential-correlated proteins from large-scale label-free proteome quantitation data of CCPD 2013. Our results suggest that the selection of proper samples and the methodology to look for targeted missing proteins should be carefully considered in further verifications for the remaining Chr. 8-coded proteins.

Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP.

To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with varied metastatic potential qualitatively and quantitatively. The results provide a global view of gene expression profiles. The 9064 identified high confident proteins covered 50.2% of all gene products in the translatome. Those proteins with function of adhesion, development, reproduction, and so on are low abundant in transcriptome and translatome but absent in proteome. Taking the translatome as the background of protein expression, we found that the protein abundance plays a decisive role and hydrophobicity has a greater influence than molecular weight and isoelectric point on protein detectability. Thus, the enrichment strategy used for low-abundant transcription factors helped to identify missing proteins. In addition, those peptides with single amino acid polymorphisms played a significant role for the disease research, although they might negligibly contribute to new protein identification. The proteome raw and metadata of proteome were collected using the iProX submission system and submitted to ProteomeXchange (PXD000529, PXD000533, and PXD000535). All detailed information in this study can be accessed from the Chinese Chromosome-Centric Human Proteome Database.