Liquid biopsies are emerging as an alternative source for pediatric cancer biomarkers with potential applications during all stages of patient care, from diagnosis to long-term follow-up. While developments within this field are reported, these mainly focus on dedicated items such as a specific liquid biopsy matrix, analyte, and/or single tumor type. To the best of our knowledge, a comprehensive overview is lacking. Here, we review the current state of liquid biopsy research for the most common non-central nervous system pediatric solid tumors. These include neuroblastoma, renal tumors, germ cell tumors, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma and other soft tissue sarcomas, and liver tumors. Within this selection, we discuss the most important or recent studies involving liquid biopsy-based biomarkers, anticipated clinical applications, and the current challenges for success. Furthermore, we provide an overview of liquid biopsy-based biomarker publication output for each tumor type based on a comprehensive literature search between 1989 and 2023. Per study identified, we list the relevant liquid biopsy-based biomarkers, matrices (e.g., peripheral blood, bone marrow, or cerebrospinal fluid), analytes (e.g., circulating cell-free and tumor DNA, microRNAs, and circulating tumor cells), methods (e.g., digital droplet PCR and next-generation sequencing), the involved pediatric patient cohort, and proposed applications. As such, we identified 344 unique publications. Taken together, while the liquid biopsy field in pediatric oncology is still behind adult oncology, potentially relevant publications have increased over the last decade. Importantly, steps towards clinical implementation are rapidly gaining ground, notably through validation of liquid biopsy-based biomarkers in pediatric clinical trials.

Our skin is home to a diverse community of commensal microorganisms integral to cutaneous function. However, microbial dysbiosis and barrier perturbation increase the risk of local and systemic infection. Staphylococcus aureus is a particularly problematic bacterial pathogen, with high levels of antimicrobial resistance and direct association with poor healing outcome. Innovative approaches are needed to selectively kill skin pathogens, such as S aureus, without harming the resident microbiota. In this study, we provide important data on the selectivity and efficacy of an S aureus-targeted endolysin (XZ.700) within the complex living skin/wound microbiome. Initial cross-species comparison using Nanopore long-read sequencing identified the translational potential of porcine rather than murine skin for human-relevant microbiome studies. We therefore performed an interventional study in pigs to assess the impact of endolysin administration on the microbiome. XZ.700 selectively inhibited endogenous porcine S aureus in vivo, restoring microbial diversity and promoting multiple aspects of wound repair. Subsequent mechanistic studies confirmed the importance of this microbiome modulation for effective healing in human skin. Taken together, these findings strongly support further development of S aureus-targeted endolysins for future clinical management of skin and wound infections.

PURPOSE: High-dose chemotherapy (HDCT) is one of the salvage therapy options for patients with relapsed/refractory germ cell tumors (rGCT) after failure of first-line chemotherapy. We aimed to identify circulating biomarkers predicting clinical response and outcome of HDCT. METHODS: Baseline and on-treatment plasma samples from 69 HDCT-treated and 26 conventional-dose chemotherapy (CDCT)-treated GCT patients were analyzed by shallow whole-genome sequencing. Tumor fraction (TF) and copy-number alterations (CNAs) were determined using ichorCNA, compared with miR-371a-3p levels, and correlated with progression-free survival (PFS) and overall survival (OS). CNA profiles from external tissue GCT cohorts were used for validation. RESULTS: TF was detectable in 75.4% of baseline plasma of HDCT patients. High TF was strongly associated with worse OS in HDCT-treated nonseminomas ( P = .021). This was confirmed in the CDCT cohort ( P = .039), where shorter median OS was observed in high-TF patients compared with the HDCT cohort. Conversely, miR-371a-3p levels were not prognostic. Plasma CNA profiling confirmed the high frequency of chromosome 3p gain in rGCT cases and revealed other alterations linked to poor HDCT outcomes, including 9q and 11q gains and 6q loss. These CNAs were enriched in a cluster predominantly composed of GCT with extra-embryonic histology (yolk sac and choriocarcinoma). Unsupervised clustering of CNA profile of plasma identified 13 patients in this high-risk cluster, who had significantly worse PFS and OS compared with other rGCT cases. CONCLUSION: Analysis of cell free DNA provides valuable prognostic information in rGCTs. High baseline TF and specific CNA patterns linked to extra-embryonic histology identify patients at higher risk of poor outcomes. HDCT seems to be more effective than CDCT in high-TF patients. These minimally invasive biomarkers could refine risk stratification and guide selection of salvage therapies in rGCTs.

Backgrounds/Objectives: Skin wound healing is a physiological process orchestrated by epithelial and mesenchymal cells able to restore tissue continuity by re-organizing themselves and the ECM. This research study aimed to develop an optimized in vitro experimental model of full-thickness skin, to address molecular and morphological modifications occurring in the re-epithelization and wound healing process. Methods: Wound healing starting events were investigated within an experimental window of 8 days at the molecular level by gene expression and immunofluorescence of key epidermal and dermal biomarkers. To mirror the behavior of infected wounds, the established wound healing model was then colonized with S. aureus, and the efficacy of a novel antibacterial agent, XZ.700, was investigated. Viable counts (CFU/tissue), IF, and ultrastructural analysis (SEM) were performed to evaluate S. aureus colonization inside and around the wound bed in an experimental window of 3 h of colonization and 24 h of treatment. Results: Endolysin showed an efficacy in counteracting bacterial growth and invasion within the wound bed, reducing the S. aureus load compared to its placebo, thanks to its selective antimicrobial activity interfering with biofilm formation. Conclusions: The preclinical in vitro infected wound model on FT-kin showed interesting applications to assess the repair efficacy of dermo-pharmaceutical and cosmetic formulations.

Background Human germ cell tumors (GCTs) occur in infants, children, and adults, and present as germinomatous and/or non-germinomatous (embryonal carcinoma (EC), teratoma, yolk sac tumor (YST), and choriocarcinoma) histologies at gonadal or extragonadal locations. Accurate subtyping is crucial for prognosis and treatment, but current clinical biomarkers lack sensitivity and specificity (serum proteins), or require a tissue biopsy (for histological and immunohistochemical characterization). Hence, less-invasive and improved subtype-specific biomarkers have significant potential for clinical utility. Methods We conducted an integrated DNA methylation analysis (450K/EPIC array) from 16 (three original and 13 published) datasets, including 719 GCTs, 109 healthy testis, and 221 healthy peripheral blood samples. Unsupervised hierarchical clustering, UMAP, and Heidelberg Central Nervous System tumor methylation classification were implemented for GCT global methylation profiling, followed by differential methylation analysis for in silico GCT subtype-specific biomarker identification, and methylation-sensitive restriction enzyme-based qPCR for in vitro and in vivo biomarker validation. Results We demonstrate that GCTs contain unique methylation profiles based on their histology, regardless of tumor location and the patient’s age or sex. Per GCT histology, we identify numerous differentially methylated regions as potential biomarkers. As proof of concept, two YST-specific (APC and DPP7) and two EC-specific (GATA4 and FBRS) biomarkers are validated in tumor DNA, of which DPP7 is also detectable in GCT serum-derived cell-free DNA. Conclusions We present a method for in silico identification and subsequent in vitro and in vivo validation of GCT subtype-specific methylation-derived liquid biopsy-based biomarkers with potential to complement the limitations of current biomarkers. Our bioinformatic pipeline is easily transferrable encouraging additional applications in pan(pediatric)-cancer studies beyond GCTs.