ALL-tRNAseq enables robust tRNA profiling in tissue samples.

Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.

Predictive value of PCT and IL-6 for bacterial infection in children with cancer and febrile neutropenia.

PURPOSE: Only a third of children with cancer and febrile neutropenia (FN) have a proven bacterial infection; nevertheless, most children are hospitalized and treated with intravenous antibiotics. Several biomarkers have been proposed as predictive markers for bacterial infection in this population. We aimed to evaluate the role of interleukin-6 (IL-6) and procalcitonin (PCT) in diagnosing bacterial infection in children with cancer and FN. METHODS: The study population was derived from a prospective database (2006-2013, IL-8 study) comprising children with cancer who presented with FN. From stored plasma samples (taken at admission and/or at 12-24 h), we determined the PCT and IL-6 levels. Consequently, we explored their relation with the presence of bacterial infection (positive blood culture, radiologically documented infection or clinical bacterial focus). We predefined cutoff values at 60 ng/L for IL-6 and 0.25 ng/mL for PCT. RESULTS: Seventy-seven FN episodes in 55 children with cancer were included. In 18 episodes (23.4%), a bacterial infection was documented. Both at presentation and after 12-24 h, median values of IL-6 and PCT were significantly higher in patients with a bacterial infection compared to patients without a bacterial infection. With both biomarkers above cutoff values, sensitivity was 93% (with either one, this was even 100%). The identified group at low risk for bacterial infection comprised 41% of the population. CONCLUSION: PCT and IL-6 are promising markers in identifying bacterial infection in children with cancer and FN. In a subsequent project, we will incorporate these biomarkers in a risk assessment model that we will test prospectively in a clinical trial.

Lactate dehydrogenase levels and 18F-FDG PET/CT metrics differentiate between mediastinal Hodgkin's lymphoma and primary mediastinal B-cell lymphoma.

PURPOSE: This study aims to investigate whether clinical, laboratory, and fluorine-18-fluorodeoxyglucose (F-FDG) PET/CT findings can discriminate between mediastinal Hodgkin's lymphoma and primary mediastinal B-cell lymphoma (PMBCL). PATIENTS AND METHODS: This retrospective study included 56 patients (42 with mediastinal Hodgkin's lymphoma and 14 with PBMCL). Differences in clinical, laboratory, and F-FDG PET/CT metrics were assessed between Hodgkin's lymphoma and PMBCL. RESULTS: Lactate dehydrogenase (LDH) and F-FDG PET/CT-based maximum tumor diameter, lesion-to-liver ratio maximum standardized uptake value (SUVmax), and lesion-to-liver ratio peak standardized uptake value (SUVpeak) were all significantly higher (P<0.001) in PMBCL than in Hodgkin's lymphoma, and PMBCL also significantly more frequently (P=0.001) exhibited necrosis on F-FDG PET/CT than Hodgkin's lymphoma. LDH, maximum tumor diameter, lesion-to-liver ratio SUVmax, and lesion-to-liver ratio SUVpeak yielded areas under the receiver operating characteristic curve of 0.968 [95% confidence interval (CI): 0.923-1.000], 0.866 (95% CI: 0.765-0.968), 0.875 (95% CI: 0.776-0.975), and 0.874 (95% CI: 0.771-0.976), respectively. LDH (with cutoff of 236 U/l) achieved sensitivity and specificity of 81.6 and 100%, respectively; maximum tumor diameter (with cutoff of 9.98 cm) achieved sensitivity and specificity of 87.2 and 78.3%, respectively; lesion-to-liver ratio SUVmax (with cutoff of 7.12) achieved sensitivity and specificity of 94.9 and 64.3%, respectively; lesion-to-liver ratio SUVpeak (with cutoff of 11.45) achieved sensitivity and specificity of 97.4 and 64.3%, respectively; and the presence of necrosis achieved sensitivity and specificity of 78.6 and 74.4%, respectively, in discriminating PMBCL from Hodgkin's lymphoma. CONCLUSION: LDH levels and several F-FDG PET/CT findings (tumor size, presence of necrosis, and degree of F-FDG uptake) are helpful in discriminating mediastinal Hodgkin's lymphoma from PMBCL.