BACKGROUND: Avelumab, a monoclonal antibody targeting PD-L1, is currently approved in the USA in combination with axitinib for the first-line treatment of patients with aRCC. This analysis evaluated the relationship between potential covariates, including avelumab exposure, and the efficacy endpoints progression-free survival (PFS; by blinded independent central review per Response Evaluation Criteria in Solid Tumors [RECIST] criteria) and objective response (OR; per RECIST) in patients with aRCC. METHODS: Exposure metrics for all patients in JAVELIN Renal 101 who received avelumab 10 mg/kg every 2 weeks (Q2W) in combination with axitinib were derived from a population pharmacokinetic model (N=434). E-R analysis for PFS was conducted using parametric time-to-event (TTE) methodology. The hazard distribution was tested using exponential, Weibull, log-normal, and log-logistic distributions. E-R analysis for OR was performed using generalized binomial logistic regression. For OR, the full model included the influence of all potential covariates, while the final model retained statistically significant covariates after stepwise backwards elimination (α=0.15). For PFS, covariates were included in the full model based on forward addition (α=0.05), and the final model was determined using backward elimination (α=0.01). Model evaluation included TTE-visual predictive checks, the likelihood ratio test, the Hosmer-Lemeshow test, and receiver operating characteristic curves. RESULTS: The best fit to the PFS data was the log-normal distribution. Avelumab exposure (cycle 1 day 15 trough concentration) was associated with probability of longer PFS in both univariate and multivariate regression models. In addition, the favorable-risk group, according to baseline Heng criteria, was associated with probability of longer PFS relative to patients with intermediate prognosis using Heng criteria. Similarly, increasing avelumab exposure was associated with a higher probability of achieving OR. However, several factors have confounded the interpretation of the causal relationship between exposure and PFS or OR, including the imbalance of Heng prognostic criteria across exposure quartiles, correlation among covariates, and that data were from a single-dose regimen. No relationship was found between incidence of ADA or baseline PD-L1 status and the efficacy endpoints PFS or OR. CONCLUSION: The E-R analyses were considered exploratory and no definite conclusions could be made on the impact of exposure on PFS or OR, as other variables confounded interpretation of the relationship. Overall, the exposure from avelumab 10 mg/kg IV Q2W in combination with axitinib was associated with a manageable and tolerable safety profile and demonstrated superior efficacy compared with sunitinib in terms of PFS in treatment-naive patients with aRCC. Citation Format: Carlo Bello, Satjit Brar, Joanna C. Masters, Akash Khandelwal, Ana M. Novakovic, Ana Ruiz-Garcia, Jennifer Hibma. Exposure-response (E-R) analysis of efficacy for avelumab in combination with axitinib in patients with advanced renal cell carcinoma (aRCC) in JAVELIN Renal 101 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1364.

The heritability of methylation patterns in tumor cells, as shown in recent studies, suggests that tumor heterogeneity and progression can be interpreted and predicted in the context of methylation changes. To elucidate methylation-based evolution trajectory in tumors, we introduce a novel computational method for methylation phylogeny reconstruction leveraging single cell bisulfite treated whole genome sequencing data (scBS-seq), incorporating additional copy number information inferred independently from matched single cell RNA sequencing (scRNA-seq) data, when available. We validate our method with the scBS-seq data of multi-regionally sampled colorectal cancer cells, and demonstrate that the cell lineages constructed by our method strongly correlate with original sampling regions. Our method consists of three components: (i) noise-minimizing site selection, (ii) likelihood-based sequencing error correction, and (iii) pairwise expected distance calculation for cells, all designed to mitigate the effect of noise and uncertainty due to data sparsity commonly observed in scBS-seq data. In (i), we present an integer linear program-based biclustering formulation to select a set of CpG-sites and cells so that the number of CpG-sites with non-zero coverage in the selected cells is maximized. This procedure filters out cells with read information in too few sites and CpG-sites with read information in too few cells. In (ii), we address the sequencing errors commonly encountered in currently available platforms with a maximum log likelihood approach to correct likely sequencing errors in scBS-seq reads, incorporating CpG-site copy number information in case it can be orthogonally obtained. Given the copy number and read information for a site in a cell, together with the overall sequencing error probability, we compute the log likelihood for all possible underlying allele statuses. If the mixed read statuses at the CpG-site for the cell are more likely due to sequencing error on homozygous alleles as opposed to the presence of alleles mixed methylation statuses, we correct the reads of the minority methylation status to the majority one. In (iii), we introduce a formulation to estimate distances between any pair of cells. As scBS-seq data is typically characterized by shallow read coverage, there is rarely read count evidence for two (or more, depending on CNV status) alleles at a CpG-site. Since allele-specific methylation has been shown to have increased frequency in cancer tissues, given the reads at a CpG-site, it is especially important to consider the possibility of unobserved alleles and their methylation status when determining the CpG-site9s possible methylation zygosities. Our method incorporates copy number information when available, and for each CpG-site in a cell, we compute a probability distribution across all possible methylation zygosities. Then, given specific distance values between pairs of distinct zygosities and the likelihood of each possible zygosity for each shared CpG-site in both cells, we compute the expected total distance between any pair of cells as the mean of expected distances across all shared CpG-sites. We leverage such pairwise distances in methylation phylogeny construction. Citation Format: Xuan C. Li, Yuelin Liu, Farid Rashidi, Salem Malikic, Stephen M. Mount, Eytan Ruppin, Kenneth Aldape, Cenk Sahinalp. Epigenomic tumor evolution modeling with single-cell methylation data profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB020.

Summary Stress at the work place was declared by the World Health Organization as a worldwide epidemic. The stress caused by work appears when the balance between one’s own possibilities and the environment demands is disturbed, which leads to a poor mental state. The fact is that the majority of dentists find they are under constant stress, which is caused by the nature of dental work. Literature describes dentistry as an extremely stressful profession. The main stressors include the tendency toward technical perfection, the causation of pain in patients, the lack of patient cooperation during dental treatment, the failure to maintain the given appointments. Adequate education and preparation, even during dental studies, non-neglect of symptoms and difficulties at the work place, adequate and timely response to the identification of the cause and its elimination or balancing, have a key role in solving this great problem in modern dentistry.

Simple Summary Vulvar squamous cell carcinoma (VSCC) is the most common form of vulvar malignancy, and its incidence has increased in recent years. For better diagnosis and prognostication, and to expand available treatment options, molecular characterization of VSCC is crucial. We sought to identify aberrations in DNA methylation in VSCC, as this has been implicated in the development of several cancers. To this end, we performed genome-wide methylation sequencing on a set of VSCC and normal vulvar tissue using the Infinium MethylationEPIC BeadChip array. We detected 199 genes to be differentially methylated in VSCC compared to normal vulvar tissue. Of these, 194 genes were hyper-methylated, which leads to a loss of function of the genes. As most of these genes are involved in transcription regulator activity, our results suggest that disruption of this process plays an important role in VSCC development. Abstract DNA methylation is the most widely studied mechanism of epigenetic modification, which can influence gene expression without alterations in DNA sequences. Aberrations in DNA methylation are known to play a role in carcinogenesis, and methylation profiling has enabled the identification of biomarkers of potential clinical interest for several cancers. For vulvar squamous cell carcinoma (VSCC), however, methylation profiling remains an under-studied area. We sought to identify differentially methylated genes (DMGs) in VSCC, by performing Infinium MethylationEPIC BeadChip (Illumina) array sequencing, on a set of primary VSCC (n = 18), and normal vulvar tissue from women with no history of vulvar (pre)malignancies (n = 6). Using a false-discovery rate of 0.05, beta-difference (Δβ) of ±0.5, and CpG-island probes as cut-offs, 199 DMGs (195 hyper-methylated, 4 hypo-methylated) were identified for VSCC. Most of the hyper-methylated genes were found to be involved in transcription regulator activity, indicating that disruption of this process plays a vital role in VSCC development. The majority of VSCCs harbored amplifications of chromosomes 3, 8, and 9. We identified a set of DMGs in this exploratory, hypothesis-generating study, which we hope will facilitate epigenetic profiling of VSCCs. Prognostic relevance of these DMGs deserves further exploration in larger cohorts of VSCC and its precursor lesions.

Background In head and neck oncological surgery the goal is to achieve a complete tumor resection with acceptable remaining function and appearance. For oral cavity squamous cell carcinoma (OCSCC) only 15% of the resections are reported as adequate. Since 2013, we have performed intraoperative assessment of resection margins (IOARM) in our institute, based on palpation and visual inspection of the resected specimens by pathologist and surgeon. This has resulted in an improvement of adequate resection margins from 15% to 50%, underlining the importance of IOARM. However, this method is subjective, labor intensive, and logistically challenging. Objective Our aim is to develop an objective method for fast and reliable IOARM based on Raman spectroscopy (RS). Methods RS is a non-destructive objective optical technique that provides information about the molecular composition of tissues. It can discriminate between healthy tissue and tumors. We developed a prototype Raman instrument employing a fiber-optic needle probe. The fiber-optic needle is driven into the OCSCC specimen, from the resection surface towards the tumor. Based on the Raman spectra collected along the insertion path, the location of the tumor border can be determined. From this the resection margin can be determined. Results First tests of the method show that the instrument accurately predicts the achieved resection margins. Per location the measurement and assessment takes 5 seconds. Conclusions This development signifies an important step towards a fast and objective IOARM. The fast measurement time enables an objective inspection of the margins achieved at a large number of locations of the resection surface.

Background Differentiated oral intraepithelial dysplasia (DOIN) was described by Japanese pathologists in 2007 but is not recognized by the World Health Organization. As in the vulva and penis, differentiated dysplasia in the oral cavity is a diagnostic challenge. Objective We determined reliable histologic criteria for the diagnosis of DOIN and assessed the usefulness of cytokeratins (CK) 13 and 17, combined with proliferation marker KI67. The frequency of DOIN in oral squamous cell carcinoma (OSCC) was also estimated. Methods All OSCC cases from 2014 to 2017 were reviewed for the presence of dysplasia. For differentiated dysplasia, histologic features were studied in detail and diagnostic criteria were established. Interobserver agreement was measured. Immunohistochemistry with CK13 and CK17/Ki67 was performed. Results We noted DOIN in 69% of OSCC cases (143/207). The histologic changes of DOIN were conspicuous in only 27% of cases, whereas in 73% the changes were subtle. Immunohistochemistry with CK13 and CK17 correlated with the histology: loss of CK13 and expression of CK17 in dysplasia, combined with KI67 altered expression. Conclusions DOIN is more frequently associated with oral carcinoma than usual dysplasia. In most cases the histologic changes are subtle. In this study we have attempted to define the histologic criteria. Cytokeratins 13 and 17/KI67 can be useful to support the diagnosis, especially in cases with subtle histologic changes. Recognition of subtle dysplastic changes will lead to progress in knowledge and treatment. We hope that the World Health Organization will recognize DOIN in the future.

Background Oral cavity squamous cell carcinoma (OCSCC) is the most frequent head and neck cancer. Surgery is the mainstay treatment for patients with OCSCC. In case of bone involvement, the affected bone needs to be resected. Cancer-free bone resection margins (BRMs) are of crucial importance: patients with cancer-free BRMs have a 2 times higher chance of survival. Currently, there is no standard method for intraoperative assessment of BRMs. Bone margin status is only known after tissue decalcification, which takes 1 to 2 weeks. After that time reoperations are highly undesirable, because the surgical defect has healed. Therefore, it is crucial to achieve tumor-free resection surfaces, which requires the possibility of intraoperative assessment of BRMs. Objective The aim of this study was to investigate the potential of Raman spectroscopy (RS) for detection of OCSCC in bone resection surfaces during mandibulectomy. RS is a nondestructive objective optical technique that provides information about the molecular composition of tissues. Methods Raman mapping experiments were performed on fresh mandible resection specimens from patients treated with mandibulectomy for OCSCC. A tumor detection algorithm was created based on water concentration and the high-wavenumber range (2800 cm−1-3050 cm−1) of the Raman spectra. Results Results show that RS can detect OCSCC in bone resection surfaces with a high sensitivity (96%) and specificity (83%; 26 mapping experiments, 22 patients). Conclusions These results form the basis for further development of an RS tool as an objective method for intraoperative assessment of BRMs.

The emerging mycotoxin fusaproliferin is produced by Fusarium proliferatum and other related Fusarium species. Several fungi from other taxonomic groups were also reported to produce fusaproliferin or the deacetylated derivative, known as siccanol or terpestacin. Here, we describe the identification and functional characterization of the Fusarium proliferatum genes encoding the fusaproliferin biosynthetic enzymes: a terpenoid synthase, two cytochrome P450s, a FAD-oxidase and an acetyltransferase. With the exception of one gene encoding a CYP450 (FUP2, FPRN_05484), knock-out mutants of the candidate genes could be generated, and the production of fusaproliferin and intermediates was tested by LC-MS/MS. Inactivation of the FUP1 (FPRN_05485) terpenoid synthase gene led to complete loss of fusaproliferin production. Disruption of a putative FAD-oxidase (FUP4, FPRN_05486) did not only affect oxidation of preterpestacin III to terpestacin, but also of new side products (11-oxo-preterpstacin and terpestacin aldehyde). In the knock-out strains lacking the predicted acetyltransferase (FUP5, FPRN_05487) fusaproliferin was no longer formed, but terpestacin was found at elevated levels. A model for the biosynthesis of fusaproliferin and of novel derivatives found in mutants is presented.