High-risk neuroblastoma is one of the most lethal childhood cancers. Half of these tumors are driven by MYCN gene amplification (MNA). Despite intensive chemo- and radiotherapy, only 40% of patients survive, and they often suffer from long-term side effects of these genotoxic treatments. Thus, less toxic and more efficacious therapies are needed. Here, we identified diphenyleneiodonium chloride (DPI) as tool compound that preferentially targeted MNA neuroblastoma. Using proteomic and metabolomic assays we investigated the DPI mode of action, finding that DPI could target alterations induced by MNA. These included cell cycle progression, DNA repair pathways, and profound changes in the expression of proteins participating in the mitochondrial electron transport chain. In addition, DPI also downregulated MYCN protein levels preferentially in MNA cells. Metabolic and biological assays suggested that alterations in mitochondrial function and the associated production of reactive oxygen species are critical DPI targets. DPI reduced the proliferation, survival, and malignant transformation of MNA neuroblastoma cells. DPI also shrank tumors and prevented metastatic spread in zebrafish models of neuroblastoma. These findings suggest that processes impacted by DPI could be valuable new targets for the development of non-genotoxic drugs against MNA neuroblastoma. ### Competing Interest Statement The authors have declared no competing interest.

In the development of proteins, aptamers, and molecular imprints for diagnostic purposes, a major goal is to obtain a molecule with both a high binding affinity and specificity for the target ligand. Cushing syndrome or Addison's disease can be diagnosed by cortisol level tests. We have previously characterized and solved the crystal structure of an anti-cortisol (17) Fab fragment having a high affinity to cortisol but also significant cross-reactivity to other glucocorticoids, especially the glucocorticoid drug prednisolone. We used native mass spectrometry (MS) to determine the binding affinities of nine steroid hormones to anti-cortisol (17) Fab, including steroidogenic precursors of cortisol. Based on the results, the number of hydroxyl groups in the structure of a steroid ligand plays a key role in the antigen recognition by the Fab fragment as the ligands with three hydroxyl groups, cortisol and prednisolone, had the highest affinities. The antibody affinity toward steroid hormones often decreases with a decrease in the number of hydroxyl groups in the structure. The presence of the hydroxyl group at position C11 increased the affinity more than did the other hydroxyl groups at positions C17 or C21. The binding affinities obtained by native MS were compared to the values determined by surface plasmon resonance (SPR), and the affinities were found to correlate well between these two techniques. Our study demonstrates that native MS with a large dynamic range and high sensitivity is a versatile tool for ligand binding studies of proteins.

Angewandte Chemie International EditionVolume 62, Issue 22 e202382211 Graphical AbstractFree Access Graphical Abstract: Angew. Chem. Int. Ed. 22/2023 First published: 12 May 2023 https://doi.org/10.1002/anie.202382211AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Volume62, Issue22May 22, 2023e202382211 RelatedInformation

Supplementary Figure S2 from TMPRSS2 Fusions with Oncogenic ETS Factors in Prostate Cancer Involve Unbalanced Genomic Rearrangements and Are Associated with HDAC1 and Epigenetic Reprogramming

Supplementary Figure Legends 1-5, Table Legends 1-6 from FZD4 as a Mediator of ERG Oncogene–Induced WNT Signaling and Epithelial-to-Mesenchymal Transition in Human Prostate Cancer Cells

Supplementary Table S4-S6 from TMPRSS2 Fusions with Oncogenic ETS Factors in Prostate Cancer Involve Unbalanced Genomic Rearrangements and Are Associated with HDAC1 and Epigenetic Reprogramming

Cortisol is a steroid hormone that is produced by the adrenal gland. It is a primary stress hormone that increases glucose levels in the blood stream. High concentrations of cortisol in the body can be used as a biomarker for acute and chronic stress and related mental and physiological disorders. Therefore, the accurate quantification of cortisol levels in body fluids is essential for clinical diagnosis. In this article, we describe the isolation of recombinant anti-cortisol antibodies with high affinity for cortisol and discover their cross-reactivity with other glucocorticoids. To describe the cortisol binding site and elucidate the structural basis for the binding specificity, the high-resolution crystal structures of the anti-cortisol (17) Fab fragment in the absence of glucocorticoid (2.00 Å) and the presence of cortisol (2.26 Å), corticosterone (1.86 Å), cortisone (1.85 Å) and prednisolone (2.00 Å) were determined. To our knowledge, this is the first determined crystal structure of a cortisol-specific antibody. The recognition of cortisol is driven by hydrophobic interactions and hydrogen bonding at the protein-ligand interface coupled with a conformational transition. Comparison of ligand-free and ligand-bound structures showed that the side chains of residues Tyr58-H and Arg56-H can undergo local conformational changes at the binding site, most likely prior to the binding event via a conformational selection mechanism. Compared to other anti-steroid antibody-antigen complexes, (17) Fab possesses a structurally unique steroid binding site, as the H3 loop from the CDR area has only a minor contribution, but framework residues have a prominent contribution to hapten binding.

Supplementary Methods from Novel Theranostic Opportunities Offered by Characterization of Altered Membrane Lipid Metabolism in Breast Cancer Progression

Supplementary Figures 1-3 from FZD4 as a Mediator of ERG Oncogene–Induced WNT Signaling and Epithelial-to-Mesenchymal Transition in Human Prostate Cancer Cells

Supplementary Figures 4-6 from FZD4 as a Mediator of ERG Oncogene–Induced WNT Signaling and Epithelial-to-Mesenchymal Transition in Human Prostate Cancer Cells

We report on a controllable and specific functionalisation route for graphene field-effect transistors (GFETs) for the recognition of small physiologically active molecules. Key element is the noncovalent functionalisation of the graphene surface with perylene bisimide (PBI) molecules directly on the growth substrate. This Functional Layer Transfer enables the homogeneous self-assembly of PBI molecules on graphene, onto which antibodies are subsequently immobilised. The sensor surface was characterised by atomic force microscopy, Raman spectroscopy and electrical measurements, showing superior performance over conventional functionalisation after transfer. Specific sensing of small molecules was realised by monitoring the electrical property changes of functionalised GFET devices upon the application of methamphetamine and cortisol. The concentration dependent electrical response of our sensors was determined down to a concentration of 300 ng ml(-1) for methamphetamine.

Supplementary Figure Legends 1-5, Table Legends 1-6 from FZD4 as a Mediator of ERG Oncogene–Induced WNT Signaling and Epithelial-to-Mesenchymal Transition in Human Prostate Cancer Cells

Supplementary Data from High-Throughput Cell-Based Screening of 4910 Known Drugs and Drug-like Small Molecules Identifies Disulfiram as an Inhibitor of Prostate Cancer Cell Growth

Changes in lipid metabolism are an important but not well-characterized hallmark of cancer. On the basis of our recent findings of lipidomic changes in breast cancer, we investigated glycerol-3-phosphate acyltransferase (GPAM), a key enzyme in the lipid biosynthesis of triacylglycerols and phospholipids. GPAM protein expression was evaluated and linked to metabolomic and lipidomic profiles in a cohort of human breast carcinomas. In addition, GPAM mRNA expression was analyzed using the GeneSapiens in silico transcriptiomics database. High cytoplasmic GPAM expression was associated with hormone receptor negative status (p = 0.013). On the protein (p = 0.048) and mRNA (p = 0.001) levels, increased GPAM expression was associated with a better overall survival. Metabolomic analysis by GC-MS showed that sn-glycerol-3-phosphate, the substrate of GPAM, was elevated in breast cancer compared to normal breast tissue. LC-MS based lipidomic analysis identified significantly higher levels of phospholipids, especially phosphatidylcholines in GPAM protein positive tumors. In conclusion, our results suggest that GPAM is expressed in human breast cancer with associated changes in the cellular metabolism, in particular an increased synthesis of phospholipids, the major structural component of cellular membranes.

Mycophenolic acid (MPA) is an immunosuppressant drug commonly used to prevent organ rejection in transplanted patients. MPA monitoring is of great interest due to its small therapeutic window. In this work, a phage-displayed peptide library was used to select cyclic peptides that bind to the MPA-specific recombinant antibody fragment (Fab) and mimic the behavior of MPA. After biopanning, several phage-displayed peptides were isolated and tested to confirm their epitope-mimicking nature in phage-based competitive immunoassays. After identifying the best MPA mimetic (ACEGLYAHWC with a disulfide constrained loop), several immunoassay approaches were tested, and a recombinant fusion protein containing the peptide sequence with a bioluminescent enzyme, NanoLuc, was developed. The recombinant fusion enabled its direct use as the tracer in competitive immunoassays without the need for secondary antibodies or further labeling. A bioluminescent sensor, using streptavidin-coupled magnetic beads for the immobilization of the biotinylated Fab antibody, enabled the detection of MPA with a detection limit of 0.26 ng mL–1 and an IC50 of 2.9 ± 0.5 ng mL–1. The biosensor showed good selectivity toward MPA and was applied to the analysis of the immunosuppressive drug in clinical samples, of both healthy and MPA-treated patients, followed by validation by liquid chromatography coupled to diode array detection.

Plasmonic biosensing has emerged as the most sensitive label-free technique to detect various molecular species in solutions and has already proved crucial in drug discovery, food safety and studies of bio-reactions. This technique relies on surface plasmon resonances in ~50 nm metallic films and the possibility to functionalize the surface of the metal in order to achieve selectivity. At the same time, most metals corrode in bio-solutions, which reduces the quality factor and darkness of plasmonic resonances and thus the sensitivity. Furthermore, functionalization itself might have a detrimental effect on the quality of the surface, also reducing sensitivity. Here we demonstrate that the use of graphene and other layered materials for passivation and functionalization broadens the range of metals which can be used for plasmonic biosensing and increases the sensitivity by 3-4 orders of magnitude, as it guarantees stability of a metal in liquid and preserves the plasmonic resonances under biofunctionalization. We use this approach to detect low molecular weight HT-2 toxins (crucial for food safety), achieving phase sensitivity~0.5 fg/mL, three orders of magnitude higher than previously reported. This proves that layered materials provide a new platform for surface plasmon resonance biosensing, paving the way for compact biosensors for point of care testing.

Introduction Neuroblastoma (NB) is the most common solid tumour in children under the age of five and it is responsible for 15% of paediatric cancer deaths. MYCN amplification represents the most frequent genetic alterations in high-risk NB and it is associated with poor prognosis. Our aim was to identify vulnerable, therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma by using an integrative ‘-omics’ approach. Material and methods We used a panel of NB cell lines (SY5Y: non-amplified; NBLS: MYCN overexpression from a single gene copy; KCN, KCNR, Be2C: MYCN-amplified). Interaction proteomics was performed by immunoprecipitating MYCN protein complexes (Co-IP) followed by quantitative label-free mass spectrometry (Q-exactive and MaxQuant). Transcriptomic analysis of total RNA was performed by real-time PCR on an ABI Prism 7700 System (Applied Biosistems). Results and discussions MYCN interaction proteomics revealed that MYCN is physically interacting with TFAM, a mitochondrial transcription factor. Therefore, we demonstrated that MYCN is present in the mitochondria of NB cells by Western blot and confocal microscopy (MYCN-Alexa488 and MitoTracker-Red-CMXRos staining), and that MYCN may repress or activate mitochondrial genes in cells rendered MYCN deficient by siRNA. Moreover, we found that certain mitochondrial genes are downregulated in patients with MYCN-amplified neuroblastoma, and they correlate with poor patient survival (Kaplan-Meier analysis of 709 patients). In addition, we performed a high throughput drug screening (~4000 compounds) and we found that diphenyleneiodonium chloride (DPI) inhibits the viability of MYCN-expressing NB cells. Interestingly, DPI significantly downregulated MYCN expression in the mitochondria of NB cells, and in turn, modulated mitochondrial gene expression. Moreover, DPI treatment resulted in a mitochondrial superoxide-mediated apoptosis in MYCN-amplified cells. In addition, soft agar colony formation assay demonstrated the tumour suppressive effects of DPI, and NB zebrafish models showed that treatment with DPI significantly reduced the neuroblastoma tumour size in vivo. Conclusion In summary, we found a vulnerable node in the MYCN interactome and we demonstrated that DPI was able to reduce the MYCN level in the mitochondria of NB cells, to induce a ROS-mediated apoptosis in MYCN-amplified, and to reduce the size of the tumour in vivo. Therefore, DPI might serve as a potential novel drug to treat MYCN-amplified NB.

Ewing sarcoma (EwS) is an aggressive pediatric bone cancer in need of more effective therapies than currently available. Most research into novel targeted therapeutic approaches is focused on the fusion oncogene EWSR1-FLI1, which is the genetic hallmark of this disease. In this study, a broad range of 3,325 experimental compounds, among them FDA approved drugs and natural products, were screened for their effect on EwS cell viability depending on EWS-FLI1 expression. In a network-based approach we integrated the results from drug perturbation screens and RNA sequencing, comparing EWS-FLI1-high (normal expression) with EWS-FLI1-low (knockdown) conditions, revealing novel interactions between compounds and EWS-FLI1 associated biological processes. The top candidate list of druggable EWS-FLI1 targets included genes involved in translation, histone modification, microtubule structure, topoisomerase activity as well as apoptosis regulation. We confirmed our in silico results using viability and apoptosis assays, underlining the applicability of our integrative and systemic approach. We identified differential sensitivities of Ewing sarcoma cells to BCL-2 family inhibitors dependent on the EWS-FLI1 regulome including altered MCL-1 expression and subcellular localization. This study facilitates the selection of effective targeted approaches for future combinatorial therapies of patients suffering from Ewing sarcoma.

BACKGROUND:Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance.METHODS:We applied RNA sequencing (RNA-seq) and interaction proteomics coupled with network-based systems level analysis to identify targetable vulnerabilities of MYCN-mediated retinoid resistance. We altered MYCN expression levels in a MYCN-inducible neuroblastoma cell line to facilitate or block retinoic acid (RA)-mediated neuronal differentiation. The relevance of differentially expressed genes and transcriptional regulators for neuroblastoma outcome were then confirmed using existing patient microarray datasets.RESULTS:We determined the signalling networks through which RA mediates neuroblastoma differentiation and the inhibitory perturbations to these networks upon MYCN overexpression. We revealed opposing regulation of RA and MYCN on a number of differentiation-relevant genes, including LMO4, CYP26A1, ASCL1, RET, FZD7 and DKK1. Furthermore, we revealed a broad network of transcriptional regulators involved in regulating retinoid responsiveness, such as Neurotrophin, PI3K, Wnt and MAPK, and epigenetic signalling. Of these regulators, we functionally confirmed that MYCN-driven inhibition of transforming growth factor beta (TGF-β) signalling is a vulnerable node of the MYCN network and that multiple levels of cross-talk exist between MYCN and TGF-β. Co-targeting of the retinoic acid and TGF-β pathways, through RA and kartogenin (KGN; a TGF-β signalling activating small molecule) combination treatment, induced the loss of viability of MYCN-amplified retinoid-resistant neuroblastoma cells.CONCLUSIONS:Our approach provides a powerful precision oncology tool for identifying the driving signalling networks for malignancies not primarily driven by somatic mutations, such as paediatric cancers. By applying global omics approaches to the signalling networks regulating neuroblastoma differentiation and stemness, we have determined the pathways involved in the MYCN-mediated retinoid resistance, with TGF-β signalling being a key regulator. These findings revealed a number of combination treatments likely to improve clinical response to retinoid therapy, including co-treatment with retinoids and KGN, which may prove valuable in the treatment of high-risk MYCN-amplified neuroblastoma.