Assessment of targeted therapy opportunities in sinonasal cancers using patient-derived functional tumor models.

Malignant tumors derived from the epithelium lining the nasal cavity region are termed sinonasal cancers, a highly heterogeneous group of rare tumors accounting for 3 - 5 % of all head and neck cancers. Progress with next-generation molecular profiling has improved our understanding of the complexity of sinonasal cancers and resulted in the identification of an increasing number of distinct tumor entities. Despite these significant developments, the treatment of sinonasal cancers has hardly evolved since the 1980s, and an advanced sinonasal cancer presents a poor prognosis as targeted therapies are usually not available. To gain insights into potential targeted therapeutic opportunities, we performed a multiomics profiling of patient-derived functional tumor models to identify molecular characteristics associated with pharmacological responses in the different subtypes of sinonasal cancer. METHODS: Patient-derived ex vivo tumor models representing four distinct sinonasal cancer subtypes: sinonasal intestinal-type adenocarcinoma, sinonasal neuroendocrine carcinoma, sinonasal undifferentiated carcinoma and SMARCB1 deficient sinonasal carcinoma were included in the analyses. Results of functional drug screens of 160 anti-cancer therapies were integrated with gene panel sequencing and histological analyses of the tumor tissues and the ex vivo cell cultures to establish associations between drug sensitivity and molecular characteristics including driver mutations. RESULTS: The different sinonasal cancer subtypes display considerable differential drug sensitivity. Underlying the drug sensitivity profiles, each subtype was associated with unique molecular features. The therapeutic vulnerabilities correlating with specific genomic background were extended and validated with in silico analyses of cancer cell lines representing different human cancers and with reported case studies of sinonasal cancers treated with targeted therapies. CONCLUSION: The results demonstrate the importance of understanding the differential biology and the molecular features associated with the different subtypes of sinonasal cancers. Patient-derived ex vivo tumor models can be a powerful tool for investigating these rare cancers and prioritizing targeted therapeutic strategies for future clinical development and personalized medicine.

Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia.

Genomic analyses have redefined the molecular subgrouping of pediatric acute lymphoblastic leukemia (ALL). Molecular subgroups guide risk-stratification and targeted therapies, but outcomes of recently identified subtypes are often unclear, owing to limited cases with comprehensive profiling and cross-protocol studies. We developed a machine learning tool (ALLIUM) for the molecular subclassification of ALL in retrospective cohorts as well as for up-front diagnostics. ALLIUM uses DNA methylation and gene expression data from 1131 Nordic ALL patients to predict 17 ALL subtypes with high accuracy. ALLIUM was used to revise and verify the molecular subtype of 281 B-cell precursor ALL (BCP-ALL) cases with previously undefined molecular phenotype, resulting in a single revised subtype for 81.5% of these cases. Our study shows the power of combining DNA methylation and gene expression data for resolving ALL subtypes and provides a comprehensive population-based retrospective cohort study of molecular subtype frequencies in the Nordic countries.

Twelve Weeks of High-Intensity Interval Training Alters Adipose Tissue Gene Expression but Not Oxylipin Levels in People with Non-Alcoholic Fatty Liver Disease.

Lifestyle modifications, including increased physical activity and exercise, are recommended for non-alcoholic fatty liver disease (NAFLD). Inflamed adipose tissue (AT) contributes to the progression and development of NAFLD and oxylipins such as hydroxyeicosatetraenoic acids (HETE), hydroxydocosahexanenoic acids (HDHA), prostaglandins (PEG2), and isoprostanoids (IsoP), which all may play a role in AT homeostasis and inflammation. To investigate the role of exercise without weight loss on AT and plasma oxylipin concentrations in NAFLD subjects, we conducted a 12-week randomized controlled exercise intervention. Plasma samples from 39 subjects and abdominal subcutaneous AT biopsy samples from 19 subjects were collected both at the beginning and the end of the exercise intervention. In the AT of women, a significant reduction of gene expression of hemoglobin subunits (HBB, HBA1, HBA2) was observed within the intervention group during the 12-week intervention. Their expression levels were negatively associated with VO2max and maxW. In addition, pathways involved in adipocyte morphology alterations significantly increased, whereas pathways in fat metabolism, branched-chain amino acids degradation, and oxidative phosphorylation were suppressed in the intervention group (p < 0.05). Compared to the control group, in the intervention group, the ribosome pathway was activated, but lysosome, oxidative phosphorylation, and pathways of AT modification were suppressed (p < 0.05). Most of the oxylipins (HETE, HDHA, PEG2, and IsoP) in plasma did not change during the intervention compared to the control group. 15-F2t-IsoP significantly increased in the intervention group compared to the control group (p = 0.014). However, this oxylipin could not be detected in all samples. Exercise intervention without weight loss may influence the AT morphology and fat metabolism at the gene expression level in female NAFLD subjects.

Quantification of the amphetamine content in seized street samples by Raman spectroscopy.

A Raman spectroscopy method for determining the drug content of street samples of amphetamine was developed by dissolving samples in an acidic solution containing an internal standard (sodium dihydrogen phosphate). The Raman spectra of the samples were measured with a CDD-Raman spectrometer. Two Raman quantification methods were used: (1) relative peak heights of characteristic signals of the amphetamine and the internal standard; and (2) multivariate calibration by partial least squares (PLS) based on second derivative of the spectra. For the determination of the peak height ratio, the spectra were baseline corrected and the peak height ratio (h(amphetamine at 994 cm(-1) )/h(internal standard at 880 cm(-1) )) was calculated. For the PLS analysis, the wave number interval of 1300-630 cm(-1) (348 data points) was chosen. No manual baseline correction was performed, but the spectra were differentiated twice to obtain their second derivatives, which were further analyzed. The Raman results were well in line with validated reference LC results when the Raman samples were analyzed within 2 h after dissolution. The present results clearly show that Raman spectroscopy is a good tool for rapid (acquisition time 1 min) and accurate quantitative analysis of street samples that contain illicit drugs and unknown adulterants and impurities.

Quantitative analysis of amorphous content of lactose using CCD-Raman spectroscopy.

A Raman spectroscopy method was developed for the quantification of the amorphous content of lactose. Both physical mixtures and spray-dried samples were used and the results were compared with the IMC determinations. Sample inhomogeneities were averaged out by collecting multiple spectra from each sample, and the total measurement time remained below 10 min due to the high sensitivity of the CCD-Raman spectrometer used in the measurements. The obtained calibration error (SEC) for the physical mixtures was 1.3% (w/w) in the 0-100% amorphous content range and was reduced to 0.2% (w/w) in the 0-10% range of more practical interest. The crystallization heat values of the spray-dried samples showed a linear correlation with the Raman quantifications in the amorphous content range of 0-80%, but saturated over the 80% concentration. This finding suggests a reference value of ca. 60 J/g for the spray-dried samples, instead of the crystallization heat of amorphous lactose (ca. 50 J/g) valid in the IMC determinations of physical mixtures.

Evaluation of the amorphous content of lactose by solution calorimetry and Raman spectroscopy.

Solution calorimetry can be used to determine the amorphous content of a compound when the solubility and dissolution rate of the compound in the chosen solvent are reasonably high. Sometimes, it can be difficult find a solvent in which a sample is freely soluble. The present study evaluated the use of solution calorimetry for the assessment of the amorphous content of a sample that is poorly soluble in a solvent. Physical mixtures of lactose and spray-dried lactose samples (the amorphous content varied from 0 to 100%) were analyzed by a solution calorimeter and the results were compared with Raman spectroscopy determinations. The heat of solvation of the samples was determined by solution calorimetry in organic solvents MeOH, EtOH, ACN, THF, acetone (400mg sample/100ml solvent). Lactose is virtually insoluble in ACN, THF and acetone and very slightly soluble in EtOH and MeOH. The amorphous content of the samples could not be determined by solution calorimetry in EtOH, ACN, THF or acetone. However, an excellent correlation was observed between the heat of solvation and the amorphous content of the samples in MeOH. Furthermore, the heat of solvation values of the samples in MeOH showed a linear correlation with the Raman quantifications. Therefore, our results demonstrate that solution calorimetry may represent a rapid and simple method for determining the amorphous content also in samples that are not freely soluble in the solvent.