DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations.

Inferring gene regulatory networks (GRNs) allows us to obtain a deeper understanding of cellular function and disease pathogenesis. Recent advances in single-cell RNA sequencing (scRNA-seq) technology have improved the accuracy of GRN inference. However, many methods for inferring individual GRNs from scRNA-seq data are limited because they overlook intercellular heterogeneity and similarities between different cell subpopulations, which are often present in the data. Here, we propose a deep learning-based framework, DeepGRNCS, for jointly inferring GRNs across cell subpopulations. We follow the commonly accepted hypothesis that the expression of a target gene can be predicted based on the expression of transcription factors (TFs) due to underlying regulatory relationships. We initially processed scRNA-seq data by discretizing data scattering using the equal-width method. Then, we trained deep learning models to predict target gene expression from TFs. By individually removing each TF from the expression matrix, we used pre-trained deep model predictions to infer regulatory relationships between TFs and genes, thereby constructing the GRN. Our method outperforms existing GRN inference methods for various simulated and real scRNA-seq datasets. Finally, we applied DeepGRNCS to non-small cell lung cancer scRNA-seq data to identify key genes in each cell subpopulation and analyzed their biological relevance. In conclusion, DeepGRNCS effectively predicts cell subpopulation-specific GRNs. The source code is available at https://github.com/Nastume777/DeepGRNCS.

Novel Triazolopyridine-Based BRD4 Inhibitors as Potent HIV-1 Latency Reversing Agents.

Bromodomain-containing protein 4 (BRD4) inhibitors have been proven to be a promising option for anti-HIV-1 latency therapeutics. We herein describe the design, synthesis, and anti-HIV-1 latency bioevaluation of triazolopyridine derivatives as BRD4 inhibitors. Among them, compound 13d displayed favorable HIV-1 reactivation and prominent safety profile without triggering abnormal immune activation. It exerted strong synergism when combined with the PKC activator prostratin and has the same BRD4-targeting latency mechanism as observed with JQ1, by stimulating Tat-dependent HIV-1 elongation. Besides, it neither affected the antiviral efficacies of antiviral drugs nor caused secondary infections to uninfected cells and the latency reversing potency of 13d, in turn, was not affected by different classes of antiviral drugs.

Lung adenocarcinoma-related target gene prediction and drug repositioning.

Lung cancer is the leading cause of cancer deaths globally, and lung adenocarcinoma (LUAD) is the most common type of lung cancer. Gene dysregulation plays an essential role in the development of LUAD. Drug repositioning based on associations between drug target genes and LUAD target genes are useful to discover potential new drugs for the treatment of LUAD, while also reducing the monetary and time costs of new drug discovery and development. Here, we developed a pipeline based on machine learning to predict potential LUAD-related target genes through established graph attention networks (GATs). We then predicted potential drugs for the treatment of LUAD through gene coincidence-based and gene network distance-based methods. Using data from 535 LUAD tissue samples and 59 precancerous tissue samples from The Cancer Genome Atlas, 48,597 genes were identified and used for the prediction model building of the GAT. The GAT model achieved good predictive performance, with an area under the receiver operating characteristic curve of 0.90. 1,597 potential LUAD-related genes were identified from the GAT model. These LUAD-related genes were then used for drug repositioning. The gene overlap and network distance with the target genes were calculated for 3,070 drugs and 672 preclinical compounds approved by the US Food and Drug Administration. At which, bromoethylamine was predicted as a novel potential preclinical compound for the treatment of LUAD, and cimetidine and benzbromarone were predicted as potential therapeutic drugs for LUAD. The pipeline established in this study presents new approach for developing targeted therapies for LUAD.

A novel variant of SPAST in a pedigree with pure hereditary spastic paraplegia in Yunnan Province.

Background: Hereditary spastic paraplegia (HSP) is a rare group of genetically heterogeneous, neurodegenerative disorders. The aim of this study was to identify pathological candidate genes and variants in a large pedigree cohort of 11 purely HSP patients in Yunnan Province. Methods: Whole-exome sequencing (WES) was applied to 2 HSP patients and 1 control patient to screen out the candidate gene variants. Then, filtration and verification of these pathological variants were performed by Sanger sequencing. Results: After the raw data were filtered, two genes with novel variations (SPAST: c.1510 C>T, p.Gln504X, RefSeq.NM_199436; DNAJC16: c.718 C>T, p.Q240X, Ref Seq NM_015291) were identified. The accession numbers of the genes in the ClinVar database were SCV001573094 and SCV001573804, respectively. One gene with a reported single nucleotide polymorphism (CPT1C: rs150853576) was filtered as a candidate variant. Using Sanger sequencing, the novel SPAST gene (protein: Spastin) variant leading to a predicted premature termination and an 18% deletion of the SPAST/spastic paraplegia type 4 (SPG4) protein was confirmed to exist only in affected individuals. The candidate CPT1C and DNAJC16 variants were verified in almost all HSP patients, with one exception. Conclusions: Considering that the clinical symptoms and time of onset of HSP are highly heterogeneous, the SPAST as a genotype-phenotype cosegregated variant might be the causative gene of this pedigree, and the other two variants might present cumulative risks to the occurrence and progression of HSP. These three candidate genes with or without novel variants may be potential contributors to disease onset, and therefore useful diagnostic and therapeutic biomarkers. Further research is required to confirm the functions of these genes.

Reconstruction of human protein-coding gene functional association network based on machine learning.

Networks consisting of molecular interactions are intrinsically dynamical systems of an organism. These interactions curated in molecular interaction databases are still not complete and contain false positives introduced by high-throughput screening experiments. In this study, we propose a framework to integrate interactions of functional associated protein-coding genes from 31 data sources to reconstruct a network with high coverage and quality. For each interaction, 369 features were constructed including properties of both the interaction and the involved genes. The training and validation sets were built on the pathway interactions as positives and the potential negative instances resulting from our proposed semi-supervised strategy. Random forest classification method was then applied to train and predict multiple times to give a score for each interaction. After setting a threshold estimated by a Binomial distribution, a Human protein-coding Gene Functional Association Network (HuGFAN) was reconstructed with 20 383 genes and 1185 429 high confidence interactions. Then, HuGFAN was compared with other networks from data sources with respect to network properties, suggesting that HuGFAN is more function and pathway related. Finally, HuGFAN was applied to identify cancer driver through two famous network-based methods (DriverNet and HotNet2) to show its outstanding performance compared with other networks. HuGFAN and other supplementary files are freely available at https://github.com/xthuang226/HuGFAN.

Benzyl butyl phthalate (BBP) triggers the malignancy of acute myeloid leukemia cells via upregulation of PDK4.

Acute Myeloid Leukemia (AML) is a cancer of hematopoietic stem cells with a rapid progression. Recent studies indicated that endocrine disruptor chemicals (EDCs) are potential risk factors for AML progression. Our present data showed that an industrial endocrine disrupting chemical, Benzyl butyl phthalate (BBP), can promote the proliferation of AML cells and decrease their sensitivity to daunorubicin (DNR) and cytarabine (Ara-C) treatments. Further, BBP can increase the glucose consumption, lactate generation, and ATP levels of AML cells. Among the measured glycolysis-related genes, BBP can increase the expression of pyruvate dehydrogenase lipoamide kinase isozyme 4 (PDK4), a mitochondrial protein that regulates the tricarboxylic acid cycle (TCA) cycle. The inhibitor of PDK4 or its specific siRNA can attenuate BBP-induced cell proliferation and ATP generation, which suggested the essential roles of PDK4 in BBP-induced glycolysis and proliferation. Further, BBP can increase the mRNA stability of PDK4, while had no effect on its transcription and protein stability. miR-15b-5p can bind with the 3'UTR of PDK4 to decrease its mRNA stability, while BBP can decrease the expression of miR-15b-5p in AML cells. Collectively, our data showed that BBP can trigger the malignancy of AML cells via regulation of miR-15b-5p/PDK4 signals.

A BODIPY-carbazole hybrid as a fluorescent probe: the design, synthesis, and discrimination of surfactants and the determination of the CMC values.

Surfactants play important roles in chemical industries and have become well-known environmental pollutants owing to their extensive use in different fields. In this work, we reported a fluorescent probe, namely, BDP-Zn2+ for the discrimination of four kinds of surfactants and the determination of CMC values. BDP-Zn2+ was composed of covalently linked BODIPY, carbazole, N,N-bis(2-pyridylmethyl)ethylenediamine (BPEA) and zinc ions to fabricate a novel push-pull molecular structure. Upon the addition of surfactants, the probe exhibited a turn-on fluorescence response and the emission was enhanced on increasing the surfactant concentrations. This indicated that the fluorescence intensity and the ratios of the emission at 607 nm to that at 514 nm as fingerprints could be used to identify the CMC values of the surfactants. Our current work provides an alternative method to efficiently discriminate different surfactants for the further studies of their physical and chemical functions.

In situ evolution of the active phase on stainless steel mesh toward a cost-effective bifunctional electrode for energy storage and conversion.

Developing low-cost, efficient and stable electrode materials is a major challenge of energy storage and conversion. Here, we report a facile, cost-effective and scaled-up self-sacrificing strategy for transforming commercial stainless steel into highly active and ultrastable electrodes for supercapacitors and the hydrogen evolution reaction. The modified stainless steel displays superior electrochemical activity as well as excellent cycling durability.

Down regulation of G protein-coupled receptor 137 expression inhibits proliferation and promotes apoptosis in leukemia cells.

BACKGROUND: G protein-coupled receptors (GPR) are involved in a wide range of physiological processes, some of which, however, can be hijacked by tumor cells. Over-expression of G protein-coupled receptors 137 (GPR137) are associated with the growth of tumor cells, but under-expression of GPR137 has shown to inhibit cell proliferation in several different types of cancers. Currently, the role of GPR137 in leukemia is still unclear. In this study, the effect of under-expression of GPR137 on inhibiting the proliferation of leukemia cells is explored, to identify a novel target for leukemia treatment. MATERIALS AND METHODS: In this study, lentivirus-mediated RNA interference (RNAi) was employed to investigate the role of GPR137 in two leukemia cell lines K562 and HL60. The gene expression of GPR137 was analyzed by RT-PCR and its protein expression was determined by Western blot. Flow cytometry and Annexin V/7-AAD Apoptosis Detection Kit was used respectively in cell cycle and apoptosis analysis. The protein expression of CyclinD1, CDK4, BCL-2 and caspase-3 were also determined. RESULTS: There was high level of constitutive expression of GPR137 in leukemia cancer cell lines K562 and HL60. Lentivirus-mediated RNAi could significantly down-regulate gene and protein expression of GPR137 in both cell lines. Down regulation of GPR137 was associated with the reduction in proliferation rate and colony forming capacity. In addition, down regulation of GPR137 arrested cells in the G0/G1 phase of cell cycle and induced apoptosis in both leukemia cell lines K562 and HL60. CONCLUSIONS: The expression of GPR137 is associated with the proliferation of leukemia cell lines. Down regulation of GPR137 could inhibit proliferation and promote apoptosis in leukemia cells, which makes it a promising bio-marker and therapeutic target to treat patients with leukemia.

Knockdown of immature colon carcinoma transcript 1 induces suppression of proliferation, S-phase arrest and apoptosis in leukemia cells.

Immature colon carcinoma transcript 1 (ICT1), a human mitochondrial translation release factor, is a ribosome-dependent codon-independent peptidyl-tRNA hydrolase. ICT1-deficiency has been recognized as a cell growth inhibitor of hepatoblastoma and glioblastoma multiforme. To explore the role of ICT1 in human leukemia, 2 short hairpin RNAs (shRNAs) targeting ICT1 sequences were designed in leukemia U937 cells. The successful infection of ICT1 in the U937 cells was observed under a fluorescence microscope and further quantified by western blotting and quantitative real-time PCR (qRT-PCR) analysis. Tetrazolium dye (MTT) assay revealed a significant decrease in proliferation of ICT1-knockdown U937 cells on the fourth and fifth day as compared with the control. Depletion of ICT1 resulted in an increase in S phase and sub-G1 (representing cell apoptosis) fractions. Annexin V-APC/7-AAD staining assay confirmed that knockdown of ICT1 played a crucial role in boosting early and late apoptotic programs in U937 cells. Downregulation of ICT1 also altered cyclin A2 transcription expression, caspase-3 activity and p21 protein expression. Additionally, decreased levels of heat shock protein 27 (HSP27) phosphorylation at Ser78 was correlated with knockdown of ICT1 in U937 cells. Thus, we concluded that the regulatory role of ICT1 in leukemia may be used as a potential therapeutic target for the treatment of leukemia.

Knockdown of eukaryotic translation initiation factor 3 subunit D (eIF3D) inhibits proliferation of acute myeloid leukemia cells.

Various eukaryotic translation initiation factors (eIFs) have been implicated in carcinoma development. Eukaryotic translation initiation factor 3 subunit D (eIF3D) has recently been shown to regulate the growth of several types of human cancer cells. However, the function of eIF3D in acute myeloid leukemia (AML) remains unclear. In this study, we investigated the expression of eIF3D in three AML cell lines and a lymphoblast cell line, and found that eIF3D was expressed in all four leukemia cell lines. To explore the role of eIF3D in AML cell proliferation, lentivirus-mediated RNA interference was applied to knock down the expression of eIF3D in U937 cells. The expression of eIF3D was significantly downregulated in U937 cells after eIF3D knockdown, as confirmed by quantitative real-time PCR (qRT-PCR) and Western blot analysis. Knockdown of eIF3D significantly inhibited proliferation of U937 cells. Furthermore, flow cytometry analysis revealed that eIF3D silencing induced cell cycle arrest at the G2/M phase, ultimately leading to apoptosis. Our results indicate that eIF3D plays a key role in the proliferation of AML cells, and suggest that eIF3D silencing might be a potential therapeutic strategy for leukemia.

Boronic acid-based chemical sensors for saccharides.

During the past decades, the interaction between boronic acids-functionalized sensors and saccharides is of great interest in the frontier domain of the interdiscipline concerning both biology and chemistry. Various boronic acid-based sensing systems have been developed to detect saccharides and corresponding derivatives in vitro as well as in vivo, which embrace unimolecular sensors, two-component sensing ensembles, functional assemblies, and boronic acid-loaded nanomaterials or surfaces. New sensing strategies emerge in endlessly with excellent selectivity and sensitivity. In this review, several typical sensing systems were introduced and some promising examples were highlighted to enable the deep insight of saccharides sensing on the basis of boronic acids.

Assembly of BODIPY-carbazole dyes with liposomes to fabricate fluorescent nanoparticles for lysosomal bioimaging in living cells.

Two BODIPY-carbazole dye based fluorescent probes BCA and BCAS were designed, synthesized and encapsulated by liposomes to obtain fluorescent nanoparticles BCA-FNP and BCAS-FNP. The fluorescence imaging showed that BCA-FNP was membrane-permeable and capable of localizing lysosomes in living cells.

Boronlectin/Polyelectrolyte Ensembles as Artificial Tongue: Design, Construction, and Application for Discriminative Sensing of Complex Glycoconjugates from Panax ginseng.

Ginsenoside is a large family of triterpenoid saponins from Panax ginseng, which possesses various important biological functions. Due to the very similar structures of these complex glycoconjugates, it is crucial to develop a powerful analytic method to identify ginsenosides qualitatively or quantitatively. We herein report an eight-channel fluorescent sensor array as artificial tongue to achieve the discriminative sensing of ginsenosides. The fluorescent cross-responsive array was constructed by four boronlectins bearing flexible boronic acid moieties (FBAs) with multiple reactive sites and two linear poly(phenylene-ethynylene) (PPEs). An "on-off-on" response pattern was afforded on the basis of superquenching of fluorescent indicator PPEs and an analyte-induced allosteric indicator displacement (AID) process. Most importantly, it was found that the canonical distribution of ginsenoside data points analyzed by linear discriminant analysis (LDA) was highly correlated with the inherent molecular structures of the analytes, and the absence of overlaps among the five point groups reflected the effectiveness of the sensor array in the discrimination process. Almost all of the unknown ginsenoside samples at different concentrations were correctly identified on the basis of the established mathematical model. Our current work provided a general and constructive method to improve the quality assessment and control of ginseng and its extracts, which are useful and helpful for further discriminating other complex glycoconjugate families.

Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification.

MOTIVATION: Cell fate specification plays a key role to generate distinct cell types during metazoan development. However, most of the underlying signaling networks at cellular level are not well understood. Availability of time lapse single-cell gene expression data collected throughout Caenorhabditis elegans embryogenesis provides an excellent opportunity for investigating signaling networks underlying cell fate specification at systems, cellular and molecular levels. RESULTS: We propose a framework to infer signaling networks at cellular level by exploring the single-cell gene expression data. Through analyzing the expression data of nhr-25 , a hypodermis-specific transcription factor, in every cells of both wild-type and mutant C.elegans embryos through RNAi against 55 genes, we have inferred a total of 23 genes that regulate (activate or inhibit) nhr-25 expression in cell-specific fashion. We also infer the signaling pathways consisting of each of these genes and nhr-25 based on a probabilistic graphical model for the selected five founder cells, 'ABarp', 'ABpla', 'ABpra', 'Caa' and 'Cpa', which express nhr-25 and mostly develop into hypodermis. By integrating the inferred pathways, we reconstruct five signaling networks with one each for the five founder cells. Using RNAi gene knockdown as a validation method, the inferred networks are able to predict the effects of the knockdown genes. These signaling networks in the five founder cells are likely to ensure faithful hypodermis cell fate specification in C.elegans at cellular level. AVAILABILITY AND IMPLEMENTATION: All source codes and data are available at the github repository https://github.com/xthuang226/Worm_Single_Cell_Data_and_Codes.git . CONTACT: zhuyuan@cug.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Marine drug Haishengsu increases chemosensitivity to conventional chemotherapy and improves quality of life in patients with acute leukemia.

BACKGROUND: Pharmacological management of acute leukemia remains a challenge. A seashell protein Haishengsu (HSS) has been found to exert anticancer activities in recent in vitro studies. The aim of this study was to determine whether the addition of HSS to the conventional chemotherapies would increase chemosensitivity and improves quality of life in patients with acute leukemia. METHODS: Two hundred and forty-eight patients with acute leukemia were enrolled in a double-blind, and placebo-controlled study. In addition to conventional chemotherapy, 142 patients received HSS and 106 received placebo. In an in vitro study, the expression of P-gp was evaluated by flow cytometry in a drug-resistant leukemia cell line (K562/ADM cells). Sorcin was examined by Western blot. RESULTS: The complete remission rates in the HSS treatment group were all higher than in the placebo group with non-relapsing leukemia and relapsed leukemia (p<0.05). Less patients in the HSS group experienced gastrointestinal side effects from chemotherapy, whereas more patients had increased food take and an increase in Karnofsky performance status (KPS) score (p<0.01). In vitro, the expression of P-gp and sorcin in the HSS treated cells were lower than in the control group cells (p<0.01). CONCLUSION: When added to conventional chemotherapy, HSS improves the complete remission rates and quality of life in patients with acute leukemia. The in vitro findings indicate that suppression of P-gp and sorcin genes in leukemia cells may be involved in the beneficial effects of HSS.

Aggregates-Based Boronlectins with Pyrene as Fluorophore: Multichannel Discriminative Sensing of Monosaccharides and Their Applications.

Four-channel fluorescence assay toward six monosaccharides was achieved by employing two novel pyrene-functionalized boronlectins with flexible diboronic acid as receptors. The effects of pH values and aging time on the sensor properties were thoroughly evaluated by UV-vis, fluorescence spectroscopy and dynamic light scattering. We find that the fluorescence relative ratios were highly correlated with analyte concentrations at µM level. The flexibility of the receptors was perceived as an indispensable factor to produce diverse fluorescence signals toward different monosaccharides. Most importantly, integration of four fluorescence channels derived from the two sensors enables an excellent discrimination for all tested monosaccharides at a certain concentration or a concentration range via linear discriminant analysis (LDA). It is proposed that the multiple flexible linkers in the boronlectins could increase their self-adaptive capacity for different analytes, and facilitate the formation of stable boronlectin-sugar aggregate assemblies. In addition, practical sensing of glucose in the simulative blood and urine was illustrated to be feasible in the presence of interferences at physiological concentrations.

An integrative C. elegans protein-protein interaction network with reliability assessment based on a probabilistic graphical model.

In Caenorhabditis elegans, a large number of protein-protein interactions (PPIs) are identified by different experiments. However, a comprehensive weighted PPI network, which is essential for signaling pathway inference, is not yet available in this model organism. Therefore, we firstly construct an integrative PPI network in C. elegans with 12,951 interactions involving 5039 proteins from seven molecular interaction databases. Then, a reliability score based on a probabilistic graphical model (RSPGM) is proposed to assess PPIs. It assumes that the random number of interactions between two proteins comes from the Bernoulli distribution to avoid multi-links. The main parameter of the RSPGM score contains a few latent variables which can be considered as several common properties between two proteins. Validations on high-confidence yeast datasets show that RSPGM provides more accurate evaluation than other approaches, and the PPIs in the reconstructed PPI network have higher biological relevance than that in the original network in terms of gene ontology, gene expression, essentiality and the prediction of known protein complexes. Furthermore, this weighted integrative PPI network in C. elegans is employed on inferring interaction path of the canonical Wnt/ß-catenin pathway as well. Most genes on the inferred interaction path have been validated to be Wnt pathway components. Therefore, RSPGM is essential and effective for evaluating PPIs and inferring interaction path. Finally, the PPI network with RSPGM scores can be queried and visualized on a user interactive website, which is freely available at .

Prognostic value of PD-1 and TIM-3 on CD3+ T cells from diffuse large B-cell lymphoma.

OBJECTIVE: To investigate the expression of PD-1 and TIM-3 in CD3+ T cells in patients with diffuse large B-cell lymphoma (DLBCL). METHODS: A retrospective analysis was conducted on data from 46 patients with newly diagnosed DLBCL and 30 healthy people. Flow cytometry was used to detect the expression of PD-1 and TIM-3 before and after chemotherapy. RESULTS: Compared to healthy control, the expression of PD-1 and TIM-3 in patients with DLBCL was increased in CD3+ T cells. There is no significant change of PD-1 and TIM-3 in patients with stage I/II DLBCL, however, they were markedly increased in patients with stage III/IV DLBCL. The expression of PD-1 and TIM-3 elevated in DLBCL patients with B symptoms, IPI score >2 points and high level of LDH and Ki-67. After four courses of standard chemotherapy, PD-1 and TIM-3 expression level decreased. The treatment efficiency is higher in patients with low expression of PD-1 and TIM-3 than in patients with high PD-1 and TIM-3 expression. CONCLUSION: DLBCL patients have high expression level of PD-1 and TIM-3, which are related to DLBCL staging. PD-1 and TIM-3 expression levels are also related to the efficiency of chemotherapy. PD-1 and TIM-3 expression levels may be used as an indicator of chemotherapeutic efficacy in patients with DLBCL.