Classification of Brain Tumors by Nanopore Sequencing of Cell-Free DNA from Cerebrospinal Fluid.

BACKGROUND: Molecular brain tumor diagnosis is usually dependent on tissue biopsies or resections. This can pose several risks associated with anesthesia or neurosurgery, especially for lesions in the brain stem or other difficult-to-reach anatomical sites. Apart from initial diagnosis, tumor progression, recurrence, or the acquisition of novel genetic alterations can only be proven by re-biopsies. METHODS: We employed Nanopore sequencing on cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) and analyzed copy number variations (CNV) and global DNA methylation using a random forest classifier. We sequenced 129 samples with sufficient DNA. These samples came from 99 patients and encompassed 22 entities. Results were compared to clinical diagnosis and molecular analysis of tumor tissue, if available. RESULTS: 110/129 samples were technically successful, and 50 of these contained detectable circulating tumor DNA (ctDNA) by CNV or methylation profiling. ctDNA was detected in samples from patients with progressive disease but also from patients without known residual disease. CNV plots showed diagnostic and prognostic alterations, such as C19MC amplifications in embryonal tumors with multilayered rosettes or Chr.1q gains and Chr.6q losses in posterior fossa group A ependymoma, respectively. Most CNV profiles mirrored the profiles of the respective tumor tissue. DNA methylation allowed exact classification of the tumor in 22/110 cases and led to incorrect classification in 2/110 cases. Only 5/50 samples with detected ctDNA contained tumor cells detectable through microscopy. CONCLUSIONS: Our results suggest that Nanopore sequencing data of cfDNA from CSF samples may be a promising approach for initial brain tumor diagnostics and an important tool for disease monitoring.

Current status and future prospects of nanomedicine for arsenic trioxide delivery to solid tumors.

Despite having a rich history as a poison, arsenic and its compounds have also gained a great reputation as promising anticancer drugs. As a pioneer, arsenic trioxide has been approved for the treatment of acute promyelocytic leukemia. Many in vitro studies suggested that arsenic trioxide could also be used in the treatment of solid tumors. However, the transition from bench to bedside turned out to be challenging, especially in terms of the drug bioavailability and concentration reaching tumor tissues. To address these issues, nanomedicine tools have been proposed. As nanocarriers of arsenic trioxide, various materials have been examined including liposomes, polymer, and inorganic nanoparticles, and many other materials. This review gives an overview of the existing strategies of delivery of arsenic trioxide in cancer treatment with a focus on the drug encapsulation approaches and medicinal impact in the treatment of solid tumors. It focuses on the progress in the last years and gives an outlook and suggestions for further improvements including theragnostic approaches and targeted delivery.

Medulloblastoma in children with Fanconi anemia: Association with FA-D1/FA-N, SHH type and poor survival independent of treatment strategies.

BACKGROUND: Outcome of children with medulloblastoma (MB) and Fanconi Anemia (FA), an inherited DNA repair deficiency, has not been described systematically. Treatment is complicated by high vulnerability to treatment-associated side effects, yet structured data are lacking. This study aims at giving a comprehensive overview about clinical and molecular characteristics of pediatric FA MB patients. METHODS: Clinical data including detailed information on treatment and toxicities of six previously unreported FA MB patients were supplemented with data of 16 published cases. RESULTS: We identified 22 cases of children with FA and MB with clinical data available. All MBs with subgroup reporting were SHH-activated (n=9), confirmed by methylation profiling in five patients. FA MB patients exclusively belonged to complementation groups FA-D1 (n=16) or FA-N (n=3). Patients were treated with postoperative chemotherapy only (50%) or radiotherapy (RT)±chemotherapy (27%). 23% did not receive adjuvant therapy. Excessive treatment-related toxicities were frequent. Severe hematological toxicity occurred in 91% of patients treated with alkylating chemotherapy, while non-alkylating agents and RT were less toxic. Median overall survival (OS) was 1 year (95%CI 0.3-1.8). 1-year-progression-free-survival (PFS) was 26.3±10.1% and 1-year-OS was 42.1±11.3%. Adjuvant therapy prolonged survival (1y-OS/1y-PFS 0%/0% without adjuvant therapy vs. 53.3±12.9%/33.3±12.2% with adjuvant therapy, p=0.006/p=0.086). CONCLUSIONS: MB in FA patients is strongly associated with SHH activation and FA-D1/FA-N. Despite the dismal prognosis, adjuvant therapy may prolong survival. Non-alkylating chemotherapy and RT are feasible in selected patients with careful monitoring of toxicities and dose adjustments. Curative therapy for FA MB-SHH remains an unmet medical need.

Metal-organic framework nanoparticles for arsenic trioxide drug delivery.

Arsenic trioxide is a double-edged sword: On the one hand it is known as a poison, on the other hand it is used as an anticancer drug. Though effective in the treatment of leukaemia, arsenic trioxide has not been able to be introduced into the treatment of solid tumour entities yet due to its dose-limiting toxicity. However, different in vitro and in vivo studies revealed arsenic trioxide to be a potent agent against different solid tumour entities, including atypical teratoid rhabdoid tumours (ATRT), a paediatric brain tumour entity with a very poor prognosis. To improve the pharmacokinetics and therapeutic efficacy of arsenic trioxide and to reduce its toxic side effects, we propose to use a metal-organic framework (MOF) as a drug carrier material. Herein we report on using a MOF called MFU-4l (Metal-Organic Framework Ulm University), consisting of Zn(ii) ions and bis(1H-1,2,3-triazolo[4,5-b],[4',5'-i])dibenzo[1,4]dioxin ligands, to deliver arsenic trioxide in a form of dihydrogen arsenite anions. The H2AsO3 - anions were introduced to the MOF in a nanoparticle formulation via a postsynthetic side ligand exchange. The prepared material was characterised by IR, TGA, XRPD, SEM-EDX, TEM, DLS, ICP-OES and adsorption analysis. The drug release studies at different pH values were carried out as well as cytotoxicity tests with different ATRT cell lines and non-tumorous-control cell lines. The MOF-based material was shown to be a promising candidate for arsenic trioxide drug delivery.