Publications by authors named "Christopher R Schmidt"

7 Publications

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The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing.

Sci Rep 2017 10 18;7(1):13459. Epub 2017 Oct 18.

Graduate School of Cancer Science and Policy, Cancer Biomedical Science, National Cancer Center, Gyeonggi-do, Republic of Korea.

While transcription as regulated by histones and their post-translational modifications has been well described, the function of histone variants in this process remains poorly characterized. Potentially important insight into this process pertain to the frequently occurring mutations of H3.3, leading to G34 substitutions in childhood glioblastoma and giant cell tumor of the bone (GCTB). In this study, we have established primary cell lines from GCTB patients and used them to uncover the influence of H3.3 G34W substitutions on cellular growth behavior, gene expression, and chromatin compaction. Primary cell lines with H3.3 G34W showed increased colony formation, infiltration and proliferation, known hallmarks of tumor development. Isogenic cell lines with H3.3 G34W recapitulated the increased proliferation observed in primary cells. Transcriptomic analysis of primary cells and tumor biopsies revealed slightly more downregulated gene expression, perhaps by increased chromatin compaction. We identified components related to splicing, most prominently hnRNPs, by immunoprecipitation and mass spectrometry that specifically interact with H3.3 G34W in the isogenic cell lines. RNA-sequencing analysis and hybridization-based validations further enforced splicing aberrations. Our data uncover a role for H3.3 in RNA processing and chromatin modulation that is blocked by the G34W substitution, potentially driving the tumorigenic process in GCTB.
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http://dx.doi.org/10.1038/s41598-017-13887-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647428PMC
October 2017

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

Nat Genet 2017 Jul 12;49(7):1052-1060. Epub 2017 Jun 12.

Division of Epigenomics and Cancer Risk Factors, DKFZ, Heidelberg, Germany.

Several mechanisms of action have been proposed for DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi), primarily based on candidate-gene approaches. However, less is known about their genome-wide transcriptional and epigenomic consequences. By mapping global transcription start site (TSS) and chromatin dynamics, we observed the cryptic transcription of thousands of treatment-induced non-annotated TSSs (TINATs) following DNMTi and HDACi treatment. The resulting transcripts frequently splice into protein-coding exons and encode truncated or chimeric ORFs translated into products with predicted abnormal or immunogenic functions. TINAT transcription after DNMTi treatment coincided with DNA hypomethylation and gain of classical promoter histone marks, while HDACi specifically induced a subset of TINATs in association with H2AK9ac, H3K14ac, and H3K23ac. Despite this mechanistic difference, both inhibitors convergently induced transcription from identical sites, as we found TINATs to be encoded in solitary long terminal repeats of the ERV9/LTR12 family, which are epigenetically repressed in virtually all normal cells.
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http://dx.doi.org/10.1038/ng.3889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005702PMC
July 2017

Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia.

Cancer Discov 2014 Mar 19;4(3):348-61. Epub 2013 Dec 19.

Divisions of 1Epigenomics and Cancer Risk Factors, 2Theoretical Bioinformatics, 3Biostatistics, and 4Molecular Genetics; 5Department of Translational Oncology, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ); 6Department of Medicine V, University of Heidelberg, Heidelberg; 7Department of Medicine, University of Freiburg Medical Center, Freiburg; 8Department of Internal Medicine III, University of Ulm, Ulm; 9The German Cancer Consortium, Germany; 10Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California; and 11Division of Hematology, The Ohio State University, Columbus, Ohio.

Although clonal selection by genetic driver aberrations in cancer is well documented, the ability of epigenetic alterations to promote tumor evolution is undefined. We used 450k arrays and next-generation sequencing to evaluate intratumor heterogeneity and evolution of DNA methylation and genetic aberrations in chronic lymphocytic leukemia (CLL). CLL cases exhibit vast interpatient differences in intratumor methylation heterogeneity, with genetically clonal cases maintaining low methylation heterogeneity and up to 10% of total CpGs in a monoallelically methylated state. Increasing methylation heterogeneity correlates with advanced genetic subclonal complexity. Selection of novel DNA methylation patterns is observed only in cases that undergo genetic evolution, and independent genetic evolution is uncommon and is restricted to low-risk alterations. These results reveal that although evolution of DNA methylation occurs in high-risk, clinically progressive cases, positive selection of novel methylation patterns entails coevolution of genetic alteration(s) in CLL.
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http://dx.doi.org/10.1158/2159-8290.CD-13-0349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134522PMC
March 2014

Altered regulation of DNA ligase IV activity by aberrant promoter DNA methylation and gene amplification in colorectal cancer.

Hum Mol Genet 2014 Apr 26;23(8):2043-54. Epub 2013 Nov 26.

Department of Epigenomics and Cancer Risk Factors and.

Colorectal cancer (CRC) presents as a very heterogeneous disease which cannot sufficiently be characterized with the currently known genetic and epigenetic markers. To identify new markers for CRC we scrutinized the methylation status of 231 DNA repair-related genes by methyl-CpG immunoprecipitation followed by global methylation profiling on a CpG island microarray, as altered expression of these genes could drive genomic and chromosomal instability observed in these tumors. We show for the first time hypermethylation of MMP9, DNMT3A and LIG4 in CRC which was confirmed in two CRC patient groups with different ethnicity. DNA ligase IV (LIG4) showed strong differential promoter methylation (up to 60%) which coincided with downregulation of mRNA in 51% of cases. This functional association of LIG4 methylation and gene expression was supported by LIG4 re-expression in 5-aza-2'-deoxycytidine-treated colon cancer cell lines, and reduced ligase IV amounts and end-joining activity in extracts of tumors with hypermethylation. Methylation of LIG4 was not associated with other genetic and epigenetic markers of CRC in our study. As LIG4 is located on chromosome 13 which is frequently amplified in CRC, two loci were tested for gene amplification in a subset of 47 cases. Comparison of amplification, methylation and expression data revealed that, in 30% of samples, the LIG4 gene was amplified and methylated, but expression was not changed. In conclusion, hypermethylation of the LIG4 promoter is a new mechanism to control ligase IV expression. It may represent a new epigenetic marker for CRC independent of known markers.
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http://dx.doi.org/10.1093/hmg/ddt599DOI Listing
April 2014

Differential expression of the tumor suppressor A-kinase anchor protein 12 in human diffuse and pilocytic astrocytomas is regulated by promoter methylation.

J Neuropathol Exp Neurol 2013 Oct;72(10):933-41

From the Institute of Pathology, University Hospital Heidelberg (BG, MR, WW, PS); Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ) (CRS, LG, CD, PS, OP, CP); Department of Neuropathology, University of Heidelberg (DC); Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) (DC, WW); and Department of Neuroradiology, University of Heidelberg (MNV), Heidelberg; Edinger Institute, University Hospital Frankfurt a.M., Frankfurt (CZ, JZ, PNH, MM); and Division of Neurosurgical Research, Department of Neurosurgery, University of Heidelberg (BC); and Department of Neurooncology, Neurology Clinic and National Center for Tumor Diseases, University of Heidelberg (WW), Heidelberg, Germany; Department of Neurology, University Hospital Zurich, Zurich, Switzerland (MW); and Department of Neuropathology, Institute of Pathology and Neuropathology, Eberhard-Karls-University of Tübingen, Tübingen (RM, JS); and Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University, Mainz (PS), Germany.

The scaffold protein A-kinase anchor protein 12 (AKAP12) exerts tumor suppressor activity and is downregulated in several tumor entities. We characterized AKAP12 expression and regulation in astrocytomas, including pilocytic and diffusely infiltrating astrocytomas. We examined 194 human gliomas and 23 normal brain white matter samples by immunohistochemistry or immunoblotting for AKAP12 expression. We further performed quantitative methylation analysis of the AKAP12 promoter by MassARRAY® of normal brain, World Health Organization (WHO) grade I to IV astrocytomas, and glioma cell lines. Our results show that AKAP12 is expressed in a perivascular distribution in normal CNS, strongly upregulated in tumor cells in pilocytic astrocytomas, and weakly expressed in diffuse astrocytomas of WHO grade II to IV. Methylation analyses revealed specific hypermethylation of AKAP12α promoter in WHO grade II to IV astrocytomas. Restoration experiments using 5-aza-2'-deoxycytidine in primary glioblastoma cells decreased AKAP12α promoter methylation and markedly increased AKAP12α mRNA levels. In summary, we demonstrate that AKAP12 is differentially expressed in human astrocytomas showing high expression in pilocytic but low expression in diffuse astrocytomas of all WHO-grades. Our results further indicate that epigenetic mechanisms are involved in silencing AKAP12 in diffuse astrocytomas; however, a tumor suppressive role of AKAP12 in distinct astrocytoma subtypes remains to be determined.
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http://dx.doi.org/10.1097/NEN.0b013e3182a59a88DOI Listing
October 2013

HPV-related methylation signature predicts survival in oropharyngeal squamous cell carcinomas.

J Clin Invest 2013 Jun 1;123(6):2488-501. Epub 2013 May 1.

Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany.

High-risk types of human papilloma virus (HPV) are increasingly associated with oropharyngeal squamous cell carcinoma (OPSCC). Strikingly, patients with HPV-positive OPSCC are highly curable with ionizing radiation and have better survival compared with HPV-negative patients, but the underlying molecular mechanisms remain poorly understood. We applied an array-based approach to monitor global changes in CpG island hypermethylation between HPV-negative and HPV-positive OPSCCs and identified a specific pattern of differentially methylated regions that critically depends on the presence of viral transcripts. HPV-related alterations were confirmed for the majority of candidate gene promoters by mass spectrometric, quantitative methylation analysis. There was a significant inverse correlation between promoter hypermethylation of ALDH1A2, OSR2, GATA4, GRIA4, and IRX4 and transcript levels. Interestingly, Kaplan-Meier analysis revealed that a combined promoter methylation pattern of low methylation levels in ALDH1A2 and OSR2 promoters and high methylation levels in GATA4, GRIA4, and IRX4 promoters was significantly correlated with improved survival in 3 independent patient cohorts. ALDH1A2 protein levels, determined by immunohistochemistry on tissue microarrays, confirmed the association with clinical outcome. In summary, our study highlights specific alterations in global gene promoter methylation in HPV-driven OPSCCs and identifies a signature that predicts the clinical outcome in OPSCCs.
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http://dx.doi.org/10.1172/JCI67010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668826PMC
June 2013