Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes ...associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.
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•Comprehensive molecular profiling of 1,122 adult diffuse grade II, III, and IV gliomas•Telomere length and telomere maintenance defined by somatic alterations•DNA methylation profiling reveals subtypes of IDH mutant and IDH-wild-type glioma•Integrated molecular analysis of progression from low-grade to high-grade disease
Integration of a large sample size of glioma tumors with multidimensional ‘omic characterization and clinical annotation provides insights into molecular classification, telomere maintenance mechanisms, progression from low to high grade disease, driver mutations, and therapeutic options.
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This ...atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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•Cities possess a consistent “core” set of non-human microbes•Urban microbiomes echo important features of cities and city-life•Antimicrobial resistance genes are widespread in cities•Cities contain many novel bacterial and viral species
This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.
In a murine melanoma model, malignant transformation promoted by a sustained stress condition was causally related to increased levels of reactive oxygen species resulting in DNA damage and massive ...epigenetic alterations. Since the chromatin modifier Sirtuin-1 (SIRT1) is a protein attracted to double-stranded DNA break (DSB) sites and can recruit other components of the epigenetic machinery, we aimed to define the role of SIRT1 in melanomagenesis through our melanoma model. The DNA damage marker, γH2AX was found increased in melanocytes after 24 hours of deadhesion, accompanied by increased SIRT1 expression and decreased levels of its target, H4K16ac. Moreover, SIRT1 started to be associated to DNMT3B during the stress condition, and this complex was maintained along malignant progression.
was identified by ChIP-seq among the DNA sequences differentially associated with SIRT1 during deadhesion and was shown to be a common target of both, SIRT1 and DNMT3B. In addition,
was found downregulated from pre-malignant melanocytes to metastatic melanoma cells. Treatment with DNMT inhibitor 5AzaCdR reversed the
expression. Sirt1 stable silencing increased
mRNA expression and led to down-regulation of MYC targets, such as Cdkn1a, Bcl2 and Psen2, whose upregulation is associated with human melanoma aggressiveness and poor prognosis. We demonstrated a novel role of the stress responsive protein SIRT1 in malignant transformation of melanocytes associated with deadhesion.
was identified as a new SIRT1 target gene. SIRT1 promoted
silencing, which led to increased activity of MYC oncogene contributing to melanoma progression.
Abstract
Meningiomas are mostly benign CNS tumors; however, a subset of these tumors may become atypical or malignant. The standard of care to monitor patients after diagnosis requires serial MRI ...assessments, which have limited value in distinguishing malignant tumors from benign disease. Therefore, the discovery of noninvasive methodologies that reflect meningioma tumor burden and its dynamic evolution in real-time is highly desirable. Liquid biopsy (LB) could be used to fine-tune surveillance and treatment with minimal risk to patients. Evidence of circulating tumor cells and cell-free (cf) tumor DNA in the blood has been shown in several tumor types; however, limited progress has been made for brain tumors with known biomarkers, possibly due to the unlikelihood of capturing point mutations in circulating DNA fragments. On the other hand, DNA methylation signatures are maintained even in small DNA fragments, which suggests that DNA methylation is an attractive marker to be studied in liquid biopsy of brain cancers. In order to identify DNA methylation-based biomarkers, we used archival serum and matching tissue specimens from primary (n=10) and recurrent (n=4) meningiomas. From isolated cfDNA from meningiomas and epileptic patients (n=5) as a control, we generated epigenetic data using Illumina Human EPIC array. cfDNA fragment size distribution revealed peaks with 150~200bp on average. We identified 482 CpGs (FDR<0.001) differentially methylated between primary meningiomas and controls, of which 294 (61%) show a DNA methylation profile similar to the epigenome of the matched tumor tissue. Overall, we observed that recurrent samples are hypermethylated (56%) compared to primary. From this pilot data, we were able to investigate the LB methylome of meningioma patients and identify potential markers to detect tumor cells in the serum of these patients, which could eventually allow clinicians to monitor impending disease progression and recurrence.
Citation Format: Thais S. Sabedot, Tathiane M. Malta, James Snyder, Tobias Walbert, Ian Lee, Steven Kalkanis, Ana Valeria Castro, Houtan Noushmehr. DNA methylation-based liquid biopsy detects primary and recurrent meningioma 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 A12.
Abstract
BACKGROUND: Several mechanisms involved in gene regulation are altered in cancer. Cataloging these alterations can lead to a better understanding of tumorigenesis. In addition, the ...alterations can be used to classify patients with similar clinical features and thereby lead to better targeted treatment. Epigenetics (e.g. DNA methylation) is the process by which cells define gene regulation and aberrant DNA methylation patterns have been observed in many cancer types. Alterations in non-promoter (intergenic regions) have been shown to be tightly associated with functional genomic elements such as enhancers or transcription factor binding. In order to identify altered candidate functional elements associated with specific gene or pathways, we developed a method to integrate enhancer, DNA methylation and gene expression data, using tumor and non-tumor data.
METHOD: Using epigenome-wide platform (Illumina 850K), CpG probes were separated into promoters and intergenic regions. The intragenic CpGs were further filtered by overlapping with known functional enhancer database from multiple studies. The nearest genes to each CpG enhancer is further stratified based on differential gene expression. Each CpG/gene pair is classified as methylated or unmethylated by sample, using a 50% methylation cutoff. The mean expression of the methylated samples is calculated and pairs with lower than the bottom 10% (1.28 standard deviation) of the mean expression in the unmethylated group of samples are selected. Finally, CpG/gene pairs with at least 75% of the methylated samples have expression values lower than the mean expression in the unmethylated group of samples are classified as epigenetically silenced. CpG/gene pairs unmethylated and upregulated are called as epigenetically active. By separating samples into different epigenetically deregulated states (silenced or active), we can further characterize each sample by evaluating the association or enrichment for specific clinical features such as outcome, treatment, age at diagnosis, etc.
RESULTS: As a proof of concept, we applied our method across the TCGA PanCan cohort to identify potential enhancers regulating genes encoding subunits of the SWI/SNF protein complex. Our method was able to detect several deregulated enhancers associated with SWI/SNF genes specifically altered in each tumor type, independent of mutation. We validated the results using Hi-C data from primary cancer cell lines.
Citation Format: Thais S. Sabedot, Seth H. Cassel, Galen F. Gao, Caleb A. Lareau, Andrew Cherniack, Alexander Lazar, Cigall Kadoch, Houtan Noushmehr. Bioinformatic method to define epigenetically regulated enhancer elements associated with cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 907.
Abstract
Meningiomas are mostly benign CNS tumors however, a subset of these tumors may become atypical or malignant. The standard of care to monitor patients after diagnosis requires serial MRI ...assessments, which have limited value in distinguishing malignant tumors from benign disease. Therefore the discovery of non-invasive methodologies that reflect meningioma tumor burden and its dynamic evolution in real-time is highly desirable. Liquid biopsy (LB) could be used to fine-tune surveillance and treatment with minimal risk to patients. Evidence of circulating tumor cells and cell-free (cf) tumor DNA in the blood has been shown in several tumor types however, limited progress has been made for brain tumors with known biomarkers; possibly due to the unlikelihood of capturing point mutations in circulating DNA fragments. On the other hand, DNA methylation signatures are maintained even in small DNA fragments, which suggests that DNA methylation is an attractive biomarker to be studied in liquid biopsy of brain cancers. In order to identify DNA methylation-based biomarkers using archival serum and tissue specimens, we generated and analyzed the epigenome (Illumina Human EPIC array) of patients with meningioma (including primary (n=6); recurrent (n=8)) and non-meningioma (including non-tumor patients (n=5), pituitary tumor (n=13), colorectal cancer (n=2) and other CNS diseases (n=6), such as inflammatory tissue and radiation necrosis). cfDNA fragment size distribution revealed peaks with 150~200bp on average. By randomly selecting 70% of our cohort as a discovery set, we identified 500 CpGs (FDR<0.05) differentially methylated between meningiomas and non-meningiomas, which show a DNA methylation profile similar to the matched meningioma tissue. Then, we trained a random-forest machine learning using the same signature and applied the model to the remaining 30% samples (validation set) from our cohort. The model was able to correctly classify samples into meningioma and non-meningiomas with a sensitivity of 100% and specificity of 100%. From this pilot data, we were able to investigate the LB methylome of meningioma patients and identify potential markers to detect tumor cells in the serum of these patients, which could eventually allow clinicians to monitor impending disease progression and recurrence.
Citation Format: Thais S. Sabedot, Tathiane M. Malta, Ruicong She, James Snyder, Tobias Walbert, Ian Lee, Steven Kalkanis, James Ewing, AnaValeria Castro, Houtan Noushmehr. Methylation-based liquid biopsy of meningioma primary and recurrent samples abstract. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 781.
Recurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform ...treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation levels in blood (serum and plasma) and tissue samples from 155 meningioma patients, compared to other central nervous system tumor and non-tumor entities. We discover DNA methylation markers unique to meningiomas and use artificial intelligence to create accurate and universal models for identifying and predicting meningioma recurrence, using either blood or tissue samples. Here we show that liquid biopsy is a potential noninvasive and reliable tool for diagnosing and predicting outcomes in meningioma patients. This approach can improve personalized management strategies for these patients.
Abstract
In a murine melanoma model of malignant transformation promoted by sustained stress, increased levels of reactive oxygen species were found to result in DNA damage and were related to ...massive epigenetic alterations. Since the chromatin modifier Sirtuin-1 (SIRT1) is a protein attracted to double-stranded DNA break (DSB) sites and can recruit other components of the epigenetic machinery, we aimed to define the role of SIRT1 in melanomagenesis through our melanoma model. The DNA damage marker, γH2AX was found increased in melanocytes after 24 hours of deadhesion, accompanied by increased SIRT1 expression and decreased levels of its target, H4K16ac. Moreover, SIRT1 started to be associated to DNMT3B during the stress condition, and this complex was maintained along malignant progression. Mxd1 was identified by ChIP-seq among the DNA sequences differentially associated with SIRT1 during deadhesion and was shown to be a common target of both, SIRT1 and DNMT3B. In addition, Mxd1 was found down-regulated from pre-malignant melanocytes to metastatic melanoma cells. Treatment with DNMT inhibitor 5AzaCdR reversed the Mxd1 expression. Sirt1 stable silencing increased Mxd1 mRNA expression and led to up-regulation of MYC targets, such as Cdkn1a, Bcl2 and Psen2, the upregulation of which is associated with human melanoma aggressiveness and poor prognosis. We demonstrated a novel role of the stress responsive protein SIRT1 in malignant transformation of melanocytes associated with deadhesion. Mxd1 was identified as a new SIRT1 target gene. SIRT1 promoted Mxd1 silencing, which led to increased activity of MYC oncogene contributing to melanoma progression.
Citation Format: Fabiana M. Meliso, Danilo Micali, Camila T. Silva, Thais S. Sabedot, Simon G. Coetzee, Adrian Koch, Fabian B. Fahlbusch, Houtan Noushmehr, Regine Schneider-Stock, Miriam G. Jasiulionis. SIRT1 regulates Mxd1 throughout melanoma progression abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2413. doi:10.1158/1538-7445.AM2017-2413
Abstract
Central nervous system-related tumors release tumoral material into circulating blood and the cerebrospinal fluid (e.g. cell free DNA). The sampling of these biofluids, i.e. liquid biopsy ...(LB), may offer an opportunity for diagnosis, prognostication and response prediction in a constantly evolving and biologically and prognostically heterogeneous tumor, such as glioma, in real-time. In glioma-tumor tissue, genome-wide DNA methylation profiling has shown that epigenetic abnormalities play significant biological and clinical roles, making DNA methylome profiling attractive for LB application in these tumors. Thus far, studies of epigenetic LB (eLB) focused on targeted markers which have shown low sensitivity; however, this can be potentially circumvented by a comprehensive genome-wide CpG methylation profiling. Herein, we profiled the genome-wide CpG methylation landscape of matching serum/tissue from 22 patients who received surgical resection for a glioma diagnosis (15 IDH-mutant and 7 IDH-wildtype) and 4 who received surgical resection of the brain for a non-tumor brain related disease. We identified 199 glioma specific DNA methylation-serum based markers (Wilcoxon Rank Sum test, p-value < 0.001) that differentiated glioma from non-tumor brain tissues (diagnostic eLB). These eLB diagnostic markers were found to be enriched for CpG islands and depleted for open seas and shores. Interestingly, CpG methylation of MYC and CD34 promoters, previously described in the tissue, were detectable in the serum of glioma patients as part of the 199 CpG eLB signature. We also identified 987 eLB markers (Wilcoxon Rank Sum test, p-value < 0.01) that discriminated patients with IDH-mutant from IDH-wildtype (prognostic eLB). Among the initial cohort, comprised by 4 MGMT-unmethylated and 18 MGMT-methylated gliomas, we also identified 428 specific eLB markers that discriminated the MGMT status among the patients (predictive eLB). Harnessing DNA methylation data of The Cancer Genome Atlas (TCGA) consortium, derived from 10,000 primary and untreated tumor tissue samples, spanning 33 cancer types, we found our three eLB signatures (diagnostic, prognostic and predictive) to be highly specific to gliomas. Our results suggest that serum eLB profiling may be useful as a surrogate or complementary for tissue-based approach for diagnosis, prognostication and treatment prediction of gliomas. In addition, our eLB signatures can be applied as a real-time non-invasive approach to improve detection of glioma progression and recurrence. Once validated, the application of the eLB panels discovered in this study have the potential to significantly and positively improve the pre- and post-surgical quality of care for patients harboring gliomas.
Citation Format: Houtan Noushmehr, Thais S. Sabedot, Tathiane M. Malta, Kevin K. Nelson, James Snyder, Michael Wells, Maritza S. Mosella, Ana C. deCarvalho, Karam Asmaro, Lisa Scarpace, Adam M. Robin, Mark L. Rosenblum, Tom Mikkelsen, Jack Rock, Tobias Walbert, Ian Lee, Laila M. Poisson, Steven N. Kalkanis, Ana V. Castro. Pre-surgical identification of diagnostic, prognostic and predictive DNA methylation-based markers in serum (liquid biopsy) of patients harboring gliomas abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-234.
Abstract
Background
Early detection of increased aggressiveness of brain tumors is a major challenge in the field of neuro-oncology because of the inability of traditional imaging to uncover it. ...Isocitrate dehydrogenase (IDH)-mutant gliomas represent an ideal model system to study the molecular mechanisms associated with tumorigenicity because they appear indolent and non-glycolytic initially, but eventually a subset progresses toward secondary glioblastoma with a Warburg-like phenotype. The mechanisms and molecular features associated with this transformation are poorly understood.
Methods
We employed model systems for IDH1 mutant (IDH1mut) gliomas with different growth and proliferation rates in vivo and in vitro. We described the metabolome, transcriptome, and epigenome of these models in order to understand the link between their metabolism and the tumor biology. To verify whether this metabolic reprogramming occurs in the clinic, we analyzed data from The Cancer Genome Atlas.
Results
We reveal that the aggressive glioma models have lost DNA methylation in the promoters of glycolytic enzymes, especially lactate dehydrogenase A (LDHA), and have increased mRNA and metabolite levels compared with the indolent model. We find that the acquisition of the high glycolytic phenotype occurs at the glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP)-high molecular subtype in patients and is associated with the worst outcome.
Conclusion
We propose very early monitoring of lactate levels as a biomarker of metabolic reprogramming and tumor aggressiveness.
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