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DNA 5-hydroxymethylcytosine (5hmC) modification is known to be associated with gene transcription and frequently used as a mark to investigate dynamic DNA methylation conversion during mammalian development and in human diseases. However, the lack of genome-wide 5hmC profiles in different human tissue types impedes drawing generalized conclusions about how 5hmC is implicated in transcription activity and tissue specificity. To meet this need, we describe the development of a 5hmC tissue map by characterizing the genomic distributions of 5hmC in 19 human tissues derived from ten organ systems. Subsequent sequencing results enabled the identification of genome-wide 5hmC distributions that uniquely separates samples by tissue type. Further comparison of the 5hmC profiles with transcriptomes and histone modifications revealed that 5hmC is preferentially enriched on tissue-specific gene bodies and enhancers. Taken together, the results provide an extensive 5hmC map across diverse human tissue types that suggests a potential role of 5hmC in tissue-specific development; as well as a resource to facilitate future studies of DNA demethylation in pathogenesis and the development of 5hmC as biomarkers., DNA 5-hydroxymethylcytosine (5hmC) modification is associated with gene transcription and used as a mark of mammalian development. Here the authors report a comprehensive 5hmC tissue map and analysis of 5hmC genomic distributions in 19 human tissues derived from 10 organ systems, thus providing insights into the role of 5hmC in tissue-specific development.

Purpose: 5-Hydroxymethylcytosine (5-hmC) is an epigenetic marker of open chromatin and active gene expression. We profiled 5-hmC with Nano-hmC-Seal technology using 10 ng of plasma-derived cell-free DNA (cfDNA) in blood samples from patients with neuroblastoma to determine its utility as a biomarker. Experimental Design: For the Discovery cohort, 100 5-hmC profiles were generated from 34 well children and 32 patients (27 high-risk, 2 intermediate-risk, and 3 low-risk) at various time points during the course of their disease. An independent Validation cohort encompassed 5-hmC cfDNA profiles (n = 29) generated from 21 patients (20 high-risk and 1 intermediate-risk). Metastatic burden was classified as high, moderate, low, or none per Curie metaiodobenzylguanidine scores and percentage of tumor cells in bone marrow. Genes with differential 5-hmC levels between samples according to metastatic burden were identified using DESeq2. Results: Hierarchical clustering using 5-hmC levels of 347 genes identified from the Discovery cohort defined four clusters of samples that were confirmed in the Validation cohort and corresponded to high, high-moderate, moderate, and low/no metastatic burden. Samples from patients with increased metastatic burden had increased 5-hmC deposition on genes in neuronal stem cell maintenance and epigenetic regulatory pathways. Further, 5-hmC cfDNA profiles generated with 1,242 neuronal pathway genes were associated with subsequent relapse in the cluster of patients with predominantly low or no metastatic burden (sensitivity 65%, specificity 75.6%). Conclusions: cfDNA 5-hmC profiles in children with neuroblastoma correlate with metastatic burden and warrants development as a biomarker of treatment response and outcome.

PURPOSE Whole-genome profiles of the epigenetic modification 5-hydroxymethylcytosine (5-hmC) are robust diagnostic biomarkers in adult patients with cancer. We investigated if 5-hmC profiles would serve as novel prognostic markers in neuroblastoma, a clinically heterogeneous pediatric cancer. Because this DNA modification facilitates active gene expression, we hypothesized that 5-hmC profiles would identify transcriptomic networks driving the clinical behavior of neuroblastoma. PATIENTS AND METHODS Nano-hmC-Seal sequencing was performed on DNA from Discovery (n = 51), Validation (n = 38), and Children’s Oncology Group (n = 20) cohorts of neuroblastoma tumors. RNA was isolated from 48 tumors for RNA sequencing. Genes with differential 5-hmC or expression between clusters were identified using DESeq2. A 5-hmC model predicting outcome in high-risk patients was established using linear discriminant analysis. RESULTS Comparison of low- versus high-risk tumors in the Discovery cohort revealed 577 genes with differential 5-hmC. Hierarchical clustering of tumors from the Discovery and Validation cohorts using these genes identified two main clusters highly associated with established prognostic markers, clinical risk group, and outcome. Genes with increased 5-hmC and expression in the favorable cluster were enriched for pathways of neuronal differentiation and KRAS activation, whereas genes involved in inflammation and the PRC2 complex were identified in the unfavorable cluster. The linear discriminant analysis model trained on high-risk Discovery cohort tumors was prognostic of outcome when applied to high-risk tumors from the Validation and Children’s Oncology Group cohorts (hazard ratio, 3.8). CONCLUSION 5-hmC profiles may be optimal DNA-based biomarkers in neuroblastoma. Analysis of transcriptional networks regulated by these epigenomic modifications may lead to a deeper understanding of drivers of neuroblastoma phenotype.

Effective and cheap methods and techniques for the safe removal of hexavalent chromate from the environment are in increasingly high demand. High concentrations of hexavalent chromate have been shown to have numerous harmful effects on human biology. We show that the E. coli molybdate-binding protein ModA is a genetically encoded tool capable of removing chromate from aqueous solutions. Although previously reported to not bind chromate, we show that ModA binds chromate tightly and is capable of removing chromate to levels well below current US federal standards.

8032 Background: The epigenetic mark 5-methylcytosines (5mC) have been associated with poor prognosis and survival in multiple myeloma (MM), but the prognostic role of 5-hydroxymethylcytosines (5hmC) as marks of tissue-specific enhancers generated from 5mC through active demethylation is unknown. We showed that 5hmC can be profiled in circulating cell-free DNA (cfDNA) and is associated with relapse/death in another lymphoproliferative disorder diffuse large B-cell lymphoma. To date, no study has investigated genome-wide 5hmC profiles in cfDNA for its prognostic significance in MM. Methods: A total of 354 newly diagnosed MM patients at the University of Chicago Medical Center were prospectively enrolled between 2010-2017. Blood samples were collected at the time of diagnosis. Patients were followed through 31 December 2020 (avg. follow-up = 77.8 mths). We collected baseline clinical, laboratory, and cytogenetic data from electronic medical records. Vital status was ascertained in 351 of the 354 patients (deaths = 73) using the National Death Index. We profiled genome-wide 5hmC in cfDNA using the 5hmC-Seal and next-generation sequencing. The 5hmC-Seal data were mapped to the human genome reference (hg19) and annotated to gene bodies. Overall survival (OS) was defined as time from diagnosis until death from any cause. We used Cox proportional hazards model and the elastic net regularization to identify genes with modified 5hmC levels that are associated with OS. Patients were randomly divided into a training set (n = 264) and testing set (n = 87). Results: The median age at diagnosis was 61.8 years and 47% (n = 165) were males. We used the differential 5hmC enrichment levels of a preliminary four-gene marker panel (i.e., YPEL1, VIPR2, PLAC8L1, and CYP2D6) to compute a weighted prognostic score (wp-score). In the training set (deaths = 55), MM patients with high wp-score had worse OS (Hazard Ratio [HR] = 2.2, 95% Confidence Interval [CI]: 1.3-3.9; p = 0.004). The same trend was observed in the testing set (deaths = 18) (HR = 3.5, 95% CI: 1.1-10.6; p = 0.02). The 5hmC-based wp-score remained significantly associated with OS after controlling for standard prognostic factors, suggesting that 5hmC-based wp-score for this 4-gene panel is an independent prognostic factor for MM. We also explored population-specific 5hmC and wp-score. We found that 5hmC profiles in cfDNA differ between Blacks (n = 117) and Whites (n = 234). In addition, 5hmC marker genes associated with OS differ between Blacks (13 genes) and Whites (20 genes). Conclusions: Our results suggest that 5hmC in cfDNA at the time of diagnosis correlate with OS in MM and the 5hmC marker genes associated with OS differ between Blacks and Whites. These findings suggest that a plasma-derived cfDNA 5hmC-modified gene panel holds promise as a noninvasive approach for predicting prognosis in MM and may be integrated in clinical practice to improve precision care.

Background: 5-Hydroxymethylcytosine (5-hmC) is an epigenetic marker of open chromatin and active gene expression. The level of 5-hmC expression serves as a biomarker in adults with cancer, and we recently demonstrated the prognostic significance of tumor whole-genome 5-hmC profiling in children with neuroblastoma. Here, we used Nano-hmC-Seal technology to profile 5-hmC in circulating cell-free DNA (cfDNA) in blood samples from patients with neuroblastoma and age-matched healthy children. Methods: Plasma was collected from 32 children with neuroblastoma at various time points during therapy and 34 well children. 5-hmC sequencing was performed using 100ng of cfDNA extracted from plasma. Metastatic disease burden was classified as high, moderate, low, or none based on Curie MIBG scores, the percentage of tumor cells in bone marrow samples, and/or measurable disseminated soft tissue disease. Results: One hundred cfDNA 5-hmC profiles were generated from 27 high-risk, 3 intermediate-risk, and 2 low-risk patients and 34 well controls. Hierarchical clustering based on 5-hmC levels of 347 genes separated the samples into three main clusters corresponding to high, moderate, and low/no disease burden in the bone, bone marrow, and/or soft tissue. Using functional gene pathways, two subsets of patients within the low/no cluster were revealed that correlated with low tumor burden or no clinically detectable metastatic disease (sensitivity 70%, specificity 76.9%). 5-hmC profiles tracked closely with changes in disease status in 15 patients with serial samples. Samples from patients with a detectable tumor burden had genes with elevated 5-hmC in pathways of neuronal stem cell maintenance and the epigenetic regulatory complexes PRC2 and CTCF/cohesion. Conclusions: cfDNA 5-hmC profiles correlate with disease burden in children with neuroblastoma and may serve as sensitive biomarkers of treatment response. Analysis of transcriptional networks regulated by these epigenomic modifications may lead to a deeper understanding of the pathways that drive resistance to treatment. Citation Format: Mark A. Applebaum, Erin K. Barr, Jason Karpus, Meritxell Oliva, Alexandre Chlenski, Helen R. Salwen, Emma Wilkinson, Marija Dobratic, Elizabeth A. Sokol, Barbara E. Stranger, Chuan He, Susan L. Cohn. 5-Hydroxymethylcytosine profiles in circulating cell-free DNA are biomarkers of disease burden in children with neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr B02.

Background: Biomarkers currently used for prognostic stratification or predicting survival in patients with newly diagnosed multiple myeloma (MM) either lack good sensitivity and specificity or require invasive bone marrow biopsies. Aberrant DNA methylation has been associated with poor prognosis and survival in MM. We recently identified a gene panel modified with 5-hydroxymethylcotosine (5hmC), a mark of gene activation, in circulating cell-free DNA (cfDNA) that is associated with relapse or death in patients with diffuse large B-cell lymphoma, another lymphoproliferative disorder. To date, no study has investigated 5hmC in cfDNA for its prognostic significance in MM. Methods: Starting in 2010, we prospectively enrolled patients who were newly diagnosed with MM at The University of Chicago Medical Center. Blood samples were collected at the time of diagnosis. The current report includes data from 184 MM patients. Mortality was ascertained using medical records and the National Death Index. Follow-up was through December 2017, with an average follow-up length of 41.64 months (deceased, n=31; alive, n=153). We profiled genome-wide 5hmC in cfDNA by first using the nano-hmC-Seal technique to construct DNA libraries, which were subjected to next-generation sequencing, mapped to the human genome, and annotated to ~22,000 gene bodies. Cox proportional hazards model and the elastic net regularization, controlling for age, gender, and population, were used to detect 5hmC marker genes associated with overall survival (OS) after diagnosis. Results: For the 184 patients, median age at diagnosis was 61.7 years and 48% (n=88) were males. The differential 5hmC enrichment levels of a preliminary eight-gene marker panel were used to compute a weighted prognostic score (wp-score). In multivariate Cox models, patients with high wp-score had worse OS (Hazard Ratio [HR] = 8.2; 95% Confidence Interval [CI], 2.9-23.4, p < 0.0001), compared with those in the low risk group. Some of the eight 5hmC-midified marker genes have been previously implicated in MM survival. For example, GTF2I (encoding general transcription factor IIi), a known prosurvival gene in MM, showed a single-gene HR of 0.3 (95% CI, 0.1-0.7, p=0.002). The 5hmC-based wp-score outperformed (sensitivity=0.74, specificity=0.84) standard prognostic indices (e.g., albumin, beta-2 microglobulin, and risk classification by cytogenetics) in predicting patients at risk for inferior survival. We are validating the gene panel in an independent cohort of ~150 MM patients. The results will be presented. Conclusions: These findings suggest that 5hmC in cfDNA at the time of diagnosis correlate with OS and outperform standard clinical prognostic indices. Our novel findings, if confirmed, suggest that a plasma-derived cfDNA 5hmC-modified gene panel holds promise as a noninvasive approach for predicting prognosis in MM and may be integrated in clinical practice to improve precision care of MM. This abstract is also being presented as Poster A40. Citation Format: Brian C.-H. Chiu, Zhou Zhang, Jason Karpus, Benjamin Derman, Chang Zeng, Elizabeth Stepniak, Rudy Chiu, John Spinelli, Andrzej Jakubowiak, Chuan He, Wei Zhang. Genome-wide 5-hydroxymethylcytosine profiles in circulating cell-free DNA and survival in patients with multiple myeloma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR03.

Background: Positron emission tomography (PET) is one of the current standard-of-care imaging techniques for evaluating extramedullary disease in multiple myeloma (MM); hypermetabolic focal lesions at diagnosis are associated with poor prognosis. Molecular analysis of circulating cell-free DNA (cfDNA) has potential to not only be a noninvasive test for measuring extramedullary disease to complement imaging, but also provide pathobiologic insights. We previously discovered that signatures of the epigenetic modification 5-hydroxyethylcytosine (5hmC) in cfDNA differ between MM and its precursor conditions and predict relapse risk for MM patients at the time of diagnosis. We evaluated differentially modified 5hmC genes between PET-negative and PET-positive patients at the time of MM diagnosis and assessed concordance of the cfDNA 5hmC profiles with PET. Methods: We prospectively enrolled patients with newly diagnosed MM at The University of Chicago Medical Center from 2010 to 2017. Patients enrolled in the study who underwent standard-of-care PET imaging within 30 days of a corresponding blood draw were evaluated. Blood samples were collected and processed immediately to separate plasma. We profiled 5hmC with DNA extracted from ~2 mL of plasma to construct the 5hmC-seal libraries using the nano-hmC-Seal technology, which then underwent next-generation sequencing. 5hmC sequencing data were mapped to the human genome and annotated to ~22,000 gene bodies. We compared genome-wide 5hmC loci between PET-positive and PET-negative patients with MM. We developed an eight gene-based weighted prognostic score (wp-score) for predicting overall survival by applying the elastic net regularization on Cox proportional hazards model. Next, we evaluated concordance between PET results and wp-score. Results: A total of 71 MM patients (age, 61.2±10.65 year; males n=42) had at least one PET scan performed and had cfDNA sequencing data available; 29 (36%) patients had an initial PET positive for MM and the remaining 52 had a negative PET. We found 14 differentially modified 5hmC genes between PET-positive and PET-negative patients at baseline (p Conclusions: Differential enrichment of 5hmC-modifications on gene body regions identified from 5hmC profiling of plasma cfDNA at the time of MM diagnosis differentiates patterns of PET imaging and adds complementary prognostic information to PET. These novel findings support the investigation of 5hmC in cfDNA as part of a multimodal approach to enhance prognostication in MM and potentially guide initial therapy. Citation Format: Benjamin Derman, Zhou Zhang, Jason Karpus, Chang Zeng, Elizabeth Stepniak, Diana West-Szymanski, Rudy Chiu, John Spinelli, Chuan He, Jagoda Jasielec, Andrzej Jakubowiak, Wei Zhang, Brian Chiu. Concordance of 5-hydroxymethylcytosine-modified genes from circulating cell-free DNA and positron emission tomography in multiple myeloma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A39.

Copper is a transition metal that plays critical roles in many life processes. Controlling the cellular concentration and trafficking of copper offers a route to disrupt these processes. Here we report small molecules that inhibit the human copper-trafficking proteins Atox1 and CCS, and so provide a selective approach to disrupt cellular copper transport. The knockdown of Atox1 and CCS or their inhibition leads to a significantly reduced proliferation of cancer cells, but not of normal cells, as well as to attenuated tumour growth in mouse models. We show that blocking copper trafficking induces cellular oxidative stress and reduces levels of cellular ATP. The reduced level of ATP results in activation of the AMP-activated protein kinase that leads to reduced lipogenesis. Both effects contribute to the inhibition of cancer cell proliferation. Our results establish copper chaperones as new targets for future developments in anticancer therapies.

The capture of uranyl, UO2(2+), by a recently engineered protein (Zhou et al. Nat. Chem. 2014, 6, 236) with high selectivity and femtomolar sensitivity has been examined by a combination of density functional theory, molecular dynamics, and free-energy simulations. It was found that UO2(2+) is coordinated to five carboxylate oxygen atoms from four amino acid residues of the super uranyl binding protein (SUP). A network of hydrogen bonds between the amino acid residues coordinated to UO2(2+) and residues in its second coordination sphere also affects the protein's uranyl binding affinity. Free-energy simulations show how UO2(2+) capture is governed by the nature of the amino acid residues in the binding site, the integrity and strength of the second-sphere hydrogen bond network, and the number of water molecules in the first coordination sphere. Alteration of any of these three factors through mutations generally results in a reduction of the binding free energy of UO2(2+) to the aqueous protein as well as of the difference between the binding free energies of UO2(2+) and other ions (Ca(2+), Cu(2+), Mg(2+), and Zn(2+)), a proxy for the protein's selectivity over these ions. The results of our free-energy simulations confirmed the previously reported experimental results and allowed us to discover a mutant of SUP, specifically the GLU64ASP mutant, that not only binds UO2(2+) more strongly than SUP but that is also more selective for UO2(2+) over other ions. The predictions from the computations were confirmed experimentally.

International audience; The capture of uranyl, UO22+, by a recently engineered protein (Zhou et al. Nat. Chem.2014, 6, 236) with high selectivity and femtomolar sensitivity has been examined by a combination of density functional theory, molecular dynamics, and free-energy simulations. It was found that UO22+ is coordinated to five carboxylate oxygen atoms from four amino acid residues of the super uranyl binding protein (SUP). A network of hydrogen bonds between the amino acid residues coordinated to UO22+ and residues in its second coordination sphere also affects the protein’s uranyl binding affinity. Free-energy simulations show how UO22+ capture is governed by the nature of the amino acid residues in the binding site, the integrity and strength of the second-sphere hydrogen bond network, and the number of water molecules in the first coordination sphere. Alteration of any of these three factors through mutations generally results in a reduction of the binding free energy of UO22+ to the aqueous protein as well as of the difference between the binding free energies of UO22+ and other ions (Ca2+, Cu2+, Mg2+, and Zn2+), a proxy for the protein’s selectivity over these ions. The results of our free-energy simulations confirmed the previously reported experimental results and allowed us to discover a mutant of SUP, specifically the GLU64ASP mutant, that not only binds UO22+ more strongly than SUP but that is also more selective for UO22+ over other ions. The predictions from the computations were confirmed experimentally.

Copper represents one of the most important biological metal ions due to its role as a catalytic cofactor in a multitude of proteins. However, an excess of copper is highly toxic. Thus, copper is heavily regulated, and copper homeostasis is controlled by many metalloregulatory proteins in various organisms. Here we report a genetically encoded copper(I) probe capable of monitoring copper fluctuations inside living cells. We insert the copper regulatory protein Ace1 into a yellow fluorescent protein, which selectively binds copper(I) and generates improved copper(I) probes.

However, the biological function of carbon monoxide and itsrolesasacellularmessengerinmammaliancellshaverecentlyattracted significant interest. Studies have shown that mam-malian cells constantly generate carbon monoxide gasthrough the endogenous degradation of heme by a family ofconstitutive (HO-2) and inducible (HO-1) heme oxygenaseenzymes.

Aqueous sulphides, including hydrogen sulphide, have important roles in biological signalling and metabolic processes. Here we develop a selective sulphide-trapping strategy involving sulphide addition to an aldehyde; the resulting hemithioacetal undergoes a Michael addition with an adjacent unsaturated acrylate ester to form a thioacetal at neutral pH in aqueous solution. Employing this new strategy, two sulphide-selective fluorescent probes, SFP-1 and SFP-2, were synthesized on the basis of two different fluorophore templates. These probes exhibit an excellent fluorescence increase and an emission maximum shift (SFP-1) in response to Na(2)S and H(2)S in a high thiol background as found under physiological conditions. We show the utility of the probes for the selective detection of sulphides, and the capacity of our probes to monitor enzymatic H(2)S biogenesis and image free sulphide in living cells.