Viral load, gene expression and mapping of viral integration sites in HPV16-associated HNSCC cell lines.

HPV-related HNSCC generally have a better prognosis than HPV-negative HNSCC. However, a subgroup of HPV-positive tumors with poor prognosis has been recognized, particularly related to smoking, EGFR overexpression and chromosomal instability. Viral integration into the host genome might contribute to carcinogenesis, as is shown for cervical carcinomas. Therefore, all HPV16-positive HNSCC cell lines currently available have been carefully analyzed for viral and host genome parameters. The viral integration status, viral load, viral gene expression and the presence of aneusomies was evaluated in the cell lines UD-SCC-2, UM-SCC-047, UM-SCC-104, UPCI:SCC090, UPCI:SCC152, UPCI:SCC154 and 93VU147T. HPV integration was examined using FISH, APOT-PCR and DIPS-PCR. Viral load and the expression of the viral genes E2, E6 and E7 were determined via quantitative PCR. All cell lines showed integration-specific staining patterns and signals indicating transcriptional activity using FISH. APOT- and DIPS-PCR identified integration-derived fusion products in six cell lines and only episomal products for UM-SCC-104. Despite the observed differences in viral load and the number of viral integration sites, this did not relate to the identified viral oncogene expression. Furthermore, cell lines exhibited EGFR expression and aneusomy (except UPCI:SCC154). In conclusion, all HPV16-positive HNSCC cell lines showed integrated and/or episomal viral DNA that is transcriptionally active, although viral oncogene expression was independent of viral copy number and the number of viral integration sites. Because these cell lines also contain EGFR expression and aneusomy, which are parameters of poor prognosis, they should be considered suitable model systems for the development of new antiviral therapies.

The T antigen locus of Merkel cell polyomavirus downregulates human Toll-like receptor 9 expression.

Establishment of a chronic infection is a key event in virus-mediated carcinogenesis. Several cancer-associated, double-stranded DNA (dsDNA) viruses act via their oncoproteins to downregulate Toll-like receptor 9 (TLR9), a key receptor in the host innate immune response that senses viral or bacterial dsDNA. A novel oncogenic virus, Merkel cell polyomavirus (MCPyV), has been recently identified that causes up to 80% of Merkel cell carcinomas (MCCs). However, it is not yet known whether this oncogenic virus also disrupts immune-related pathways. We find that MCPyV large T antigen (LT) expression downregulates TLR9 expression in epithelial and MCC-derived cells. Accordingly, silencing of LT expression results in upregulation of mRNA TLR9 levels. In addition, small T antigen (sT) also appears to inhibit TLR9 expression, since inhibition of its expression also resulted in an increase of TLR9 mRNA levels. LT inhibits TLR9 expression by decreasing the mRNA levels of the C/EBPß transactivator, a positive regulator of the TLR9 promoter. Chromatin immunoprecipitation reveals that C/EBPß binding at a C/EBPß response element (RE) in the TLR9 promoter is strongly inhibited by expression of MCPyV early genes and that mutation of the C/EBP RE prevents MCPyV downregulation of TLR9. A survey of BK polyomavirus (BKPyV), JC polyomavirus (JCPyV), KI polyomavirus (KIPyV), MCPyV, simian virus 40 (SV40), and WU polyomavirus (WUPyV) early genes revealed that only BKPyV and MCPyV are potent inhibitors of TLR9 gene expression. MCPyV LT targeting of C/EBP transactivators is likely to play an important role in viral persistence and potentially inhibit host cell immune responses during MCPyV tumorigenesis.

Comparative analysis of transforming properties of E6 and E7 from different beta human papillomavirus types.

The cutaneous beta human papillomavirus (beta HPV) types appear to be involved in skin carcinogenesis. However, only a few beta HPVs have been investigated so far. Here, we compared the properties of E6 and E7 oncoproteins from six uncharacterized beta HPVs (14, 22, 23, 24, 36, 49). Only HPV49 E6 and E7 immortalized primary human keratinocytes and efficiently deregulated the p53 and pRb pathways. Furthermore, HPV49 E6, similarly to E6 from the oncogenic HPV16, promoted p53 degradation.

Human papillomavirus type 16 genetic variants: phylogeny and classification based on E6 and LCR.

Naturally occurring genetic variants of human papillomavirus type 16 (HPV16) are common and have previously been classified into 4 major lineages; European-Asian (EAS), including the sublineages European (EUR) and Asian (As), African 1 (AFR1), African 2 (AFR2), and North-American/Asian-American (NA/AA). We aimed to improve the classification of HPV16 variant lineages by using a large resource of HPV16-positive cervical samples collected from geographically diverse populations in studies on HPV and/or cervical cancer undertaken by the International Agency for Research on Cancer. In total, we sequenced the entire E6 genes and long control regions (LCRs) of 953 HPV16 isolates from 27 different countries worldwide. Phylogenetic analyses confirmed previously described variant lineages and subclassifications. We characterized two new sublineages within each of the lineages AFR1 and AFR2 that are robustly classified using E6 and/or the LCR. We could differentiate previously identified AA1, AA2, and NA sublineages, although they could not be distinguished by E6 alone, requiring the LCR for correct phylogenetic classification. We thus provide a classification system for HPV16 genomes based on 13 and 32 phylogenetically distinguishing positions in E6 and the LCR, respectively, that distinguish nine HPV16 variant sublineages (EUR, As, AFR1a, AFR1b, AFR2a, AFR2b, NA, AA1, and AA2). Ninety-seven percent of all 953 samples fitted this classification perfectly. Other positions were frequently polymorphic within one or more lineages but did not define phylogenetic subgroups. Such a standardized classification of HPV16 variants is important for future epidemiological and biological studies of the carcinogenic potential of HPV16 variant lineages.

Rapid lignin quantification for fungal wood pretreatment by ATR-FTIR spectroscopy.

Lignin determination in lignocellulose with the conventional two-step acid hydrolysis method is highly laborious and time-consuming. However, its quantification is crucial to monitor fungal pretreatment of wood, as the increase of acid-insoluble lignin (AIL) degradation linearly correlates with the achievable enzymatic saccharification yield. Therefore, in this study, a new attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy method was developed to track fungal delignification in an easy and rapid manner. Partial least square regression (PLSR) with cross-validation (CV) was applied to correlate the ATR-FTIR spectra with the AIL content (19.9 %-27.1 %). After variable selection and normalization, a PLSR model with a high coefficient of determination (RCV2 = 0.87) and a low root mean square (RMSECV = 0.60 %) were obtained despite the heterogeneous nature of the fungal solid-state fermentation. These results show that ATR-FTIR can reliably predict the AIL content in fungus-treated wood while being a high-throughput method. This novel method can facilitate the transition to the wood-based economy.

Follow-up of solid-state fungal wood pretreatment by a novel near-infrared spectroscopy-based lignin calibration model.

Lignin removal plays a crucial role in the efficient bioconversion of lignocellulose to fermentable sugars. As a delignification process, fungal pretreatment has gained great interest due to its environmental friendliness and low energy consumption. In our previous study, a positive linear correlation between acid-insoluble lignin degradation and the achievable enzymatic saccharification yield has been found, hereby highlighting the importance of the close follow-up of lignin degradation during the solid-state fungal pretreatment process. However, the standard quantification of lignin, which relies on the two-step acid hydrolysis of the biomass, is highly laborious and time-consuming. Vibrational spectroscopy has been proven as a fast and easy alternative; however, it has not been extensively researched on lignocellulose subjected to solid-state fungal pretreatment. Therefore, the present study examined the suitability of near-infrared spectroscopy (NIR) for the rapid and easy assessment of lignin content in poplar wood pretreated with Phanerochaete chrysosporium. Furthermore, the predictive power of the obtained calibration model and the recently published ATR-FTIR spectroscopy-based model were compared for the first time using the same fungus-treated wood data set. PLSR was used to correlate the NIR spectra to the acid-insoluble lignin contents (19.9%-27.1%) of pretreated wood. After normalization and second derivation, a PLSR model with a good coefficient of determination (RCV2 = 0.89) and a low root mean square error (RMSECV = 0.55%) were obtained despite the heterogeneous nature of the fungal solid-state fermentation. The performance of this PLSR model was comparably good to the one obtained by ATR-FTIR (RCV2 = 0.87) while it required more extensive spectral pre-processing. In conclusion, both methods will be highly useful for the high-throughput and user-friendly monitoring of lignin degradation in a solid-state fungal pretreatment-based biorefinery concept.

Human OCTN2 (SLC22A5) is down-regulated in virus- and nonvirus-mediated cancer.

The expression of carnitine plasma membrane transporter OCTN2 was evaluated in virus and nonvirus-mediated cancer. Both OCTN2 mRNA and protein levels were reduced in keratinocytes retrotransduced with HPV16 E6 and E7 compared with the control. The OCTN2 expression was reduced also in keratinocytes retrotransduced with the sole HPV16 E6. A similar down-regulation of OCTN2 mRNA level was observed in a naturally HPV16-infected cancer cell line, CaSki, harbouring several copies of HPV16 whole genome. The mechanism of down-regulation is not related to p53 transcriptional activity because in SAOS (p53-null) cell line, the restoration of p53 expression did not rescue OCTN2 expression. The treatment of keratinocytes retrotransduced with HPV16 E6 and E7 with 5-aza-cytidine rescued the OCTN2 expression, indicating that the mechanism of down-regulation is linked to DNA methylation. Low levels of mRNA expression of OCTN2 were found also in several nonvirus-related epithelial cancer cell lines. The treatment of those cell lines with 5-aza-cytidine again rescued the expression of OCTN2 as well. These data demonstrate for the first time that the OCTN2 transporter is generally down-regulated in virus and nonvirus-mediated epithelial cancers, probably via methylation of its promoter region.

Modeling the Physicochemical Properties of Natural Deep Eutectic Solvents.

Natural deep eutectic solvents (NADES) are mixtures of naturally derived compounds with a significantly decreased melting point owing to specific interactions among the constituents. NADES have benign properties (low volatility, flammability, toxicity, cost) and tailorable physicochemical properties (by altering the type and molar ratio of constituents); hence, they are often considered to be a green alternative to common organic solvents. Modeling the relation between their composition and properties is crucial though, both for understanding and predicting their behavior. Several efforts have been made to this end. This Review aims at structuring the present knowledge as an outline for future research. First, the key properties of NADES are reviewed and related to their structure on the basis of the available experimental data. Second, available modeling methods applicable to NADES are reviewed. At the molecular level, DFT and molecular dynamics allow density differences and vibrational spectra to be interpreted, and interaction energies to be computed. Additionally, properties at the level of the bulk medium can be explained and predicted by semi-empirical methods based on ab initio methods (COSMO-RS) and equation of state models (PC-SAFT). Finally, methods based on large datasets are discussed: models based on group-contribution methods and machine learning. A combination of bulk-medium and dataset modeling allows qualitative prediction and interpretation of phase equilibria properties on the one hand, and quantitative prediction of melting point, density, viscosity, surface tension, and refractive index on the other. Multiscale modeling, combining molecular and macroscale methods, is expected to strongly enhance the predictability of NADES properties and their interaction with solutes, and thus yield truly tailorable solvents to accommodate (bio)chemical reactions.

Of enzyme use in cost-effective high solid simultaneous saccharification and fermentation processes.

Enzyme cost is considered to be one of the most significant factors defining the final product price in lignocellulose hydrolysis and fermentation. Enzyme immobilization and recycling can be a tool to decrease costs. However, high solid loading is a key factor towards high product titers, and recovery of immobilized enzymes from this thick liquid is often overlooked. This paper aims to evaluate the economic feasibility of immobilized enzymes in simultaneous saccharification and fermentation (SSF) of lignocellulose biomass in general, as well as the recuperation of magnetic immobilized enzymes (m-CLEAs) during high solid loading in simultaneous saccharification, detoxification and fermentation processes (SSDF) of lignocellulose biomass. Enzyme prices were obtained from general cost estimations by Klein-Marcuschamer et al. [Klein-Marcuschamer et al. (2012) Biotechnol. Bioeng. 109, 1083-1087]. During enzyme cost analysis, the influence of inoculum recirculation as well as a shortened fermentation time was explored. Both resulted in 15% decrease of final enzyme product price. Enzyme recuperation was investigated experimentally and 99.5 m/m% of m-CLEAs was recovered from liquid medium in one step, while 88 m/m% could still be recycled from a thick liquid with high solid concentrations (SSF fermentation broth). A mathematical model was constructed to calculate the cost of immobilized and free enzyme utilization and showed that, with current process efficiencies and commercial enzyme prices, the cost reduction obtained by enzyme immobilization can reach around 60% compared to free enzyme utilization, while lower enzyme prices will result in a lower percentage of immobilization related savings, but overall enzyme costs will decrease significantly. These results are applied in a case study, estimating the viability of shifting from sugar to lignocellulose substrate for a 100 t lactic acid fermentation batch. It was concluded that it will only be economically feasible if the enzymes are produced at the most optimistic variable cost and either the activity of the immobilized catalyst or the recovery efficiency is further increased.

Human papillomavirus type 16 E6 variants in France and risk of viral persistence.

BACKGROUND: Only a small portion of HPV 16 infections persist and can lead to cervical intraepithelial lesions and cancer. Factors that favour HPV persistence versus clearance are still poorly understood, but several studies have suggested that HPV intra-type variants may influence persistence and clinical outcome. The aim of this study was to assess the possible association between HPV 16 variants and the risk for viral persistence in the general population of France. METHODS: One hundred and forty two women infected with HPV 16 with normal cytology, without previous treatment for cervical lesions, and with a valid second follow-up visit 4 to 16 months later, were selected from patients participating in routine cervical cancer screening in the Reims HPV Primary Screening Cohort Study. HPV intra-type variants were determined by sequencing the HPV 16 E6 open reading frame, and were compared for viral persistence at the second visit using odds ratios (OR) to estimate relative risk. RESULTS: Although no statistically significant differences in risk for persistence were observed by the HPV 16 variant lineage, European variants containing the polymorphism 350 T (EUR-350 T) appeared to persist more often than those containing 350 G (EUR-350 G) (OR = 1.6, 95% CI = 0.8-3.4). CONCLUSIONS: No strong differences were observed in the risk of viral persistence for the HPV 16 variants that predominate in France.

Risks for persistence and progression by human papillomavirus type 16 variant lineages among a population-based sample of Danish women.

BACKGROUND: Little is known about factors determining HPV16 persistence and progression, but several studies have suggested that genetic variants may play a role. METHODS: HPV16-positive women with normal cytology in a large Danish cohort were reassessed for HPV16 status at 2 years and followed-up for cervical intraepithelial neoplasia 3 or worse (CIN3+) over 11 years through linkage with a national pathology database. Relative risks for clearance, persistence, and progression were compared with different HPV16 variant lineages based upon E6 gene sequencing. RESULTS: Sixty-two (23.7%) of 261 HPV16 infections were persistent at 2 years, and 32 (51.6%) persistent infections progressed to CIN3+. The majority of baseline infections belonged to the European lineage (97.3%), with EUR-350T and EUR-350G accounting for 61.3% and 36.0% of infections, respectively. At two years, the proportion of HPV16 infections that persisted was significantly higher for EUR-350T (28.2%) than EUR-350G (15.9%) variants (odds ratio = 2.06, 95% CI, 1.04-4.25). This increased risk for persistence was consistent both in the absence (OR = 2.16, 95% CI, 0.84-6.26) or presence (OR = 1.89, 95% CI, 0.76-5.15) of progression to CIN3+. Among persistent HPV16 infections, there was no significant difference in risk of progression to CIN3+ between EUR-350T and EUR-350G sub-lineages, which were both associated with a substantial absolute risk (>50%) of CIN3+. CONCLUSIONS: Significant differences in risk for persistence exist between the HPV16 variants that predominate in Europe. IMPACT: Understanding the genetic basis of HPV16 persistence and carcinogenicity may help unravel important interactions between HPV16 and the host immune system.