DeepHPV: a deep learning model to predict human papillomavirus integration sites.

Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism. Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: huzheng1998@163.com, liangjiuxing@m.scnu.edu.cn, lizheyzy@163.com.

DeepEBV: a deep learning model to predict Epstein-Barr virus (EBV) integration sites.

MOTIVATION: Epstein-Barr virus (EBV) is one of the most prevalent DNA oncogenic viruses. The integration of EBV into the host genome has been reported to play an important role in cancer development. The preference of EBV integration showed strong dependence on the local genomic environment, which enables the prediction of EBV integration sites. RESULTS: An attention-based deep learning model, DeepEBV, was developed to predict EBV integration sites by learning local genomic features automatically. First, DeepEBV was trained and tested using the data from the dsVIS database. The results showed that DeepEBV with EBV integration sequences plus Repeat peaks and 2-fold data augmentation performed the best on the training dataset. Furthermore, the performance of the model was validated in an independent dataset. In addition, the motifs of DNA-binding proteins could influence the selection preference of viral insertional mutagenesis. Furthermore, the results showed that DeepEBV can predict EBV integration hotspot genes accurately. In summary, DeepEBV is a robust, accurate and explainable deep learning model, providing novel insights into EBV integration preferences and mechanisms. AVAILABILITYAND IMPLEMENTATION: DeepEBV is available as open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepEBV.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles.

From initial human papillomavirus (HPV) infection and precursor stages, the development of cervical cancer takes decades. High-sensitivity HPV DNA testing is currently recommended as primary screening method for cervical cancer, whereas better triage methodologies are encouraged to provide accurate risk management for HPV-positive women. Given that virus-driven genomic variation accumulates during cervical carcinogenesis, we designed a 39 Mb custom capture panel targeting 17 HPV types and 522 mutant genes related to cervical cancer. Using capture-based next-generation sequencing, HPV integration status, somatic mutation and copy number variation were analyzed on 34 paired samples, including 10 cases of HPV infection (HPV+), 10 cases of cervical intraepithelial neoplasia (CIN) grade and 14 cases of CIN2+ (CIN2: n = 1; CIN2-3: n = 3; CIN3: n = 9; squamous cell carcinoma: n = 1). Finally, the machine learning algorithm (Random Forest) was applied to build the risk stratification model for cervical precursor lesions based on CIN2+ enriched biomarkers. Generally, HPV integration events (11 in HPV+, 25 in CIN1 and 56 in CIN2+), non-synonymous mutations (2 in CIN1, 12 in CIN2+) and copy number variations (19.1 in HPV+, 29.4 in CIN1 and 127 in CIN2+) increased from HPV+ to CIN2+. Interestingly, 'common' deletion of mitochondrial chromosome was significantly observed in CIN2+ (P = 0.009). Together, CIN2+ enriched biomarkers, classified as HPV information, mutation, amplification, deletion and mitochondrial change, successfully predicted CIN2+ with average accuracy probability score of 0.814, and amplification and deletion ranked as the most important features. Our custom capture sequencing combined with machine learning method effectively stratified the risk of cervical lesions and provided valuable integrated triage strategies.

A comparison of the characteristics and atrazine adsorption capacity of co-pyrolysed and mixed biochars generated from corn straw and sawdust.

The biochar used in this study was prepared from corn straw and sawdust mixed in a ratio of 1:1 (m/m) at temperatures of 300 °C and 800 °C, which adopted the methods of co-pyrolysis (BC300A and BC800A) and mixing of single biochar (BC300B and BC800B). The obtained biochar was characterized by SEM, BET and FTIR analysis. Adsorption properties, including the atrazine adsorption kinetics and isotherms of the four kinds of biochar to atrazine, were investigated. The results showed that a pseudo-second order kinetic model was suitable for describing the adsorption of atrazine by BC800B because its R2 value is greater than the pseudo-first order model. The adsorption capacity (qe) of BC800B, blended from the two single biochars produced at 800 °C, is 37.2 mg g-1, which is better than that of the other three species. This value is 4-6 times the qe values of BC300A, BC300B and BC800A, which are 6.74 mg g-1, 7.77 mg g-1 and 5.26 mg g-1, respectively. At higher pyrolysis temperature, the pore structure of biochar is more developed, the specific surface area is larger, and the species and number of surface functional groups are also significantly different. At the same time, the results also showed that the order of mixing and pyrolysis affected the characteristics and adsorption capacity of biochar. This study reveals the atrazine adsorption mechanism of four kinds of biochar and provides information about the potential of these types of materials for the removal of atrazine in the aquatic environment.

Non-homologous dsODN increases the mutagenic effects of CRISPR-Cas9 to disrupt oncogene E7 in HPV positive cells.

Genome editing tools targeting high-risk human papillomavirus (HPV) oncogene could be a promising therapeutic strategy for the treatment of HPV-related cervical cancer. We aimed to improve the editing efficiency and detect off-target effects concurrently for the clinical translation strategy by using CRISPR-Cas9 system co-transfected with 34nt non-homologous double-stranded oligodeoxynucleotide (dsODN). We firstly tested this strategy on targeting the Green Fluorescent Protein (GFP) gene, of which the expression is easily observed. Our results showed that the GFP+ cells were significantly decreased when using GFP-sgRNAs with dsODN, compared to using GFP-sgRNAs without donors. By PCR and Sanger sequencing, we verified the dsODN integration into the break sites of the GFP gene. And by amplicon sequencing, we observed that the indels% of the targeted site on the GFP gene was increased by using GFP-sgRNAs with dsODN. Next, we went on to target the HPV18 E7 oncogene by using single E7-sgRNA and multiplexed E7-sgRNAs respectively. Whenever using single sgRNA or multiplexed sgRNAs, the mRNA expression of HPV18 E7 oncogene was significantly decreased when adding E7-sgRNAs with dsODN, compared to E7-sgRNAs without donor. And the indels% of the targeted sites on the HPV18 E7 gene was markedly increased by adding dsODN with E7-sgRNAs. Finally, we performed GUIDE-Seq to verify that the integrated dsODN could serve as the marker to detect off-target effects in using single or multiplexed two sgRNAs. And we detected fewer on-target reads and off-target sites in multiplexes compared to the single sgRNAs when targeting the GFP and the HPV18 E7 genes. Together, CRISPR-Cas9 system co-transfected with 34nt dsODN concurrently improved the editing efficiency and monitored off-target effects, which might provide new insights in the treatment of HPV infections and related cervical cancer.

The comparison of ZFNs, TALENs, and SpCas9 by GUIDE-seq in HPV-targeted gene therapy.

Zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR-associated Cas9 endonucleases are three major generations of genome editing tools. However, no parallel comparison about the efficiencies and off-target activity of the three nucleases has been reported, which is critical for the final clinical decision. We for the first time developed the genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) method in ZFNs and TALENs with novel bioinformatics algorithms to evaluate the off-targets. By targeting human papillomavirus 16 (HPV16), we compared the performance of ZFNs, TALENs, and SpCas9 in vivo. Our data showed that ZFNs with similar targets could generate distinct massive off-targets (287-1,856), and the specificity could be reversely correlated with the counts of middle "G" in zinc finger proteins (ZFPs). We also compared the TALENs with different N-terminal domains (wild-type [WT]/αN/ßN) and G recognition modules (NN/NH) and found the design (αN or NN) to improve the efficiency of TALEN inevitably increased off-targets. Finally, our results showed that SpCas9 was more efficient and specific than ZFNs and TALENs. Specifically, SpCas9 had fewer off-target counts in URR (SpCas9, n = 0; TALEN, n = 1; ZFN, n = 287), E6 (SpCas9, n = 0; TALEN, n = 7), and E7 (SpCas9, n = 4; TALEN, n = 36). Taken together, we suggest that for HPV gene therapies, SpCas9 is a more efficient and safer genome editing tool. Our off-target data could be used to improve the design of ZFNs and TALENs, and the universal in vivo off-target detection pipeline for three generations of artificial nucleases provided useful tools for genome engineering-based gene therapy.

An effective vaginal gel to deliver CRISPR/Cas9 system encapsulated in poly (ß-amino ester) nanoparticles for vaginal gene therapy.

BACKGROUND: Gene therapy has held promises for treating specific genetic diseases. However, the key to clinical application depends on effective gene delivery. METHODS: Using a large animal model, we developed two pharmaceutical formulations for gene delivery in the pigs' vagina, which were made up of poly (ß-amino ester) (PBAE)-plasmid polyplex nanoparticles (NPs) based two gel materials, modified montmorillonite (mMMT) and hectorite (HTT). FINDINGS: By conducting flow cytometry of the cervical cells, we found that PBAE-GFP-NPs-mMMT gel was more efficient than PBAE-GFP-NPs-HTT gel in delivering exogenous DNA intravaginally. Next, we designed specific CRISPR/SpCas9 sgRNAs targeting porcine endogenous retroviruses (PERVs) and evaluated the genome editing efficacy in vivo. We discovered that PERV copy number in vaginal epithelium could be significantly reduced by the local delivery of the PBAE-SpCas9/sgRNA NPs-mMMT gel. Comparable genome editing results were also obtained by high-fidelity version of SpCas9, SpCas9-HF1 and eSpCas9, in the mMMT gel. Further, we confirmed that the expression of topically delivered SpCas9 was limited to the vagina/cervix and did not diffuse to nearby organs, which was relatively safe with low toxicity. INTERPRETATION: Our data suggested that the PBAE-NPs mMMT vaginal gel is an effective preparation for local gene therapy, yielding insights into novel therapeutic approaches to sexually transmitted disease in the genital tract. FUNDING: This work was supported by the National Science and Technology Major Project of the Ministry of science and technology of China (No. 2018ZX10301402); the National Natural Science Foundation of China (81761148025, 81871473 and 81402158); Guangzhou Science and Technology Programme (No. 201704020093); National Ten Thousand Plan-Young Top Talents of China, Fundamental Research Funds for the Central Universities (17ykzd15 and 19ykyjs07); Three Big Constructions-Supercomputing Application Cultivation Projects sponsored by National Supercomputer Center In Guangzhou; the National Research FFoundation (NRF) South Africa under BRICS Multilateral Joint Call for Proposals; grant 17-54-80078 from the Russian Foundation for Basic Research.

In vitro and in vivo growth inhibition of human cervical cancer cells via human papillomavirus E6/E7 mRNAs' cleavage by CRISPR/Cas13a system.

Sustained infection of high-risk human papillomavirus (HR-HPVs), especially HPV16 and HPV18, is a major cause of cervical cancer. E6 and E7 oncoproteins, encoded by the HPV genome, are critical for transformation and maintenance of malignant phenotypes of cervical cancer. Here, we used an emerging programmable clustered regularly interspaced short palindromic repeat (CRISPR)/Cas13a system to cleave HPV 16/18 E6/E7 messenger RNAs (mRNAs). The results showed that customized CRISPR/Cas13a system effectively and specifically knocked down HPV 16/18 E6/E7 mRNAs, inducing growth inhibition and apoptosis in HPV16-positive SiHa and HPV18-positive HeLa Cell lines, but not in HPV-negative C33A cell line. Simultaneously, we detected downregulation of E6/E7 oncoproteins and upregulation of tumor suppressor P53 and RB proteins. In addition, we used subcutaneous xenograft tumor growth assays to find that the weight and volume of tumors in the SiHa-16E6CR1 group knocked down by the CRISPR/Cas13a system were significantly lower than those in the SiHa-VECTOR group lacking crRNA. Our study demonstrated that targeting HPV E6/E7 mRNAs by the CRISPR/Cas13a system may be a candidate therapeutic strategy for HPV-related cervical cancer.

Overview of thioredoxin system and targeted therapies for acute leukemia.

The thioredoxin (Trx) system is a major antioxidant system for keeping the intracellular redox state in almost all forms of life, including Trx, Trx reductase (TrxR) and NADPH. It regulates many signaling pathways related to antioxidative action, growth promotion, anti-apoptosis, cell migration, inflammatory modulation, immune function, etc. The oxidative stress has been proved to promote cancer occurrence and the readjustment of Trx system. Considerable results have demonstrated overexpression of Trx in cancer cells, moreover, the overexpression of Trx is closely related to high risk of cancer recurrence and drug resistance. This review focuses on the relationship between Trx system and acute leukemia (AL). The crux of the development of any useful therapy is a knowledge of disease etiology and progression. The potential of thioredoxin system inhibitors as therapeutic agents for acute leukemia is highlighted. Furthermore, targeting Trx as an anti-leukemic strategy is clinically beneficial to AL patients.

Alleviation of atrazine toxicity to maize seedlings grown in soils with amendment of biochar derived from wheat under different temperatures.

The effects of different biotransformation temperatures (250, 550, and 850 °C) and different dose (0-1%) of biochar on the physiological characteristics of maize seedlings under the stress of atrazine were studied. The results show that atrazine significantly inhibits the growth of maize seedlings, while biochar can alleviate the toxicity of atrazine to seedlings. Compared with the low temperature of biochar, the addition of BC850, the germination rate of maize was significantly increased. The biochars prepared at higher temperatures and adding 1% dose could significantly increase the plant height, while the effect of biochar on root growth of maize seedlings was not significant. According to the data, with the increase of biochar application, the accumulation of atrazine in maize leaves and roots gradually decreased. At the maximum application rate of 1%, the content of atrazine in maize leaves decreased by 58.94%, 60.70%, and 62.75%. The content of atrazine in maize roots decreased by 52.93%, 54.57%, and 55.42%, respectively. Meanwhile, the addition of biochar could slightly increase the chlorophyll content, but the change was not significant statistically, while the content of chlorophyll b increases with the application amount. The content of malondialdehyde (MDA) in roots and leaves decreased first and the increased with the dose of biochar from 0 to 1%. Compared with the atrazine treatment, the content of MDA in leaves and roots decreased significantly, and the lipid peroxidation of maize significantly decreased. With the addition of three kinds of biochar, the soluble content of plant tissues increased gradually, BC550 biochar has the most noticeable remediation effect. Given the toxicity of atrazine in soil, the quality and yield of agricultural products, and the potential health risks to human beings, biochar can be the soil remediation product.

Natural killer cell immunotherapy against multiple myeloma: Progress and possibilities.

Multiple myeloma (MM) is a complex aggressive mature B-cell malignancy. Although with the wide application of chemotherapy drugs, it remains incurable and the vast majority of patients relapse. Natural killer (NK) cells, also known as CD56+ CD3- large granular lymphocytes, are cytotoxic innate immune cells against MM without prior sensitization steps. NK cell-based immunotherapy is extensively promising in a wide range of clinical settings. It is worthy of note that some novel drugs such as monoclonal antibodies (mAbs), proteasome inhibitors (PIs), and immunomodulators (IMiDs) directly or indirectly activate NK cells to enhance their antitumor activity, and the combined regimens significantly improve the prognosis of MM patients. In this review, we summarize recent findings that support a role for NK cells in the pathogenesis of MM and outline innovative approaches in the implementation of NK cell-based immunotherapy against MM.

Effects of multi-walled carbon nanotubes with various diameters on bacterial cellular membranes: Cytotoxicity and adaptive mechanisms.

The effect of multi-walled carbon nanotubes (MWNTs) with different diameters on the destruction degree toward cellular membranes of bacterial has been explored by investigating the viability of bacteria and the change of composition and surface properties in cellular membranes with the exposure of MWNTs. The atrazine degrading bacteria Acinetobacter lwoffii DNS32 (DNS32) is chosen as the model species and Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis) are selected as the comparison specie. Bacterial viability testing shows that MWNTs with smaller diameters generally display stronger toxicity to bacteria and also influenced by many factors including the electrostatic repulsion between MWNTs and bacteria and bacteria types. Interestingly, bacteria can self-regulate as an adaptive response to the toxicity of MWNTs, notably, DNS32 strain presents the adaptive responses when cultivated with MWNT60-100 through modification of fatty acids in cell membranes, but does not exhibit similar responses when exposed to MWNT10-20. This result may be related to the interference from MWNT10-20, which exceeds the cellular ability to self-repair. Transmission electron microscopy (TEM) images and flow cytometric analysis of bacteria exposed to MWNTs reveal that the destruction of cell membrane in the DNS32 strain is more serious than that in the B. subtilis, indicating that electrostatic repulsion between the material and bacteria leading to the decrease of direct contact may be the primary factor that reduces the impacts from MWNTs.

Nitrogen-functionalization biochars derived from wheat straws via molten salt synthesis: An efficient adsorbent for atrazine removal.

N-doped porous carbon sheets (NPCS) resulted from wheat straws are fabricated through using molten salts via the carbonization-functionalization progress, which show unique hierarchical structure, large pore volume and high surface area with affluent micropores. Results indicate that there exist many hierarchical pores consisting of the single carbon sheet with ultrathin nature, owing to the template role of molten salt mixtures at high temperature. Such superior structure can bring about desired performance of adsorption capacity of 82.8mg/g and quick adsorption rate of 1.43L/(gh) with an initial concentration of 35mg/L at 25°C. Langmuir and Freundlich models are adopted to interpret the adsorption behavior of atrazine and modified Freundlich and intraparticle diffusion (IPD) models are employed to characterize the dynamics of adsorption. Furthermore, nitrogen-functionalization biochars via molten salt synthesis should be further developed as a one-pot methodology to produce N-doped carbons, opening up a feasible approach for resource utilization of crop straws and other biomass wastes.

Hydroxyl radical scavenging mechanism of human erythrocytes by quercetin-germanium (IV) complex.

Quercetin is a popular flavonoid in plant foods, herbs, and dietary supplement. Germanium, a kind of trace elements, can enhance the body immunity. This study investigated the hydroxyl-radical-scavenging mechanism of the quercertin-germanium (IV) (Qu-Ge) complex to human erythrocytes, especially the effects on ultrastructure and mechanical properties of cell membrane, plasma membrane potential and intracellular free Ca(2+) concentration. Results showed that QuGe(2), a kind of the Qu-Ge complex, could reduce the oxidative damage of erythrocytes, change the cell-surface morphology, and partly recover the disruption of plasma membrane potential and intracellular free Ca(2+) level. Atomic force microscopy (AFM) was used to characterize the changes of the cell morphology, cell-membrane ultrastructure and biophysical properties at nanoscalar level. QuGe(2) has triggered the antioxidative factor to inhibit cellular damage. These results can improve the understanding of hydroxyl-radical-scavenging mechanism of human erythrocytes induced by the Qu-Ge complex, which can be potentially developed as a new antioxidant for treatment of oxidative damage.