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Biomedical subjects

Christoph Grunau

Publications and source records attributed to Christoph Grunau.

10 recordsLinked to original sources

Epigenetic and metabolic reprogramming of innate immune cells establishes immunological memory in the Schistosomiasis vector snail Biomphalaria glabrata.

Innate immune memory enables non-vertebrates to mount faster and more effective immune responses upon re-exposure to a previously encountered pathogen, yet its cellular and molecular bases remain poorly understood. The freshwater snail Biomphalaria glabrata, intermediate host of the human parasite Schistosoma mansoni, provides a powerful model to investigate this phenomenon. Here, we show that innate immune memory in B. glabrata is carried by hemocytes and relies on profound metabolic and epigenetic reprogramming initiated during primary infection. Using an integrative multi-omics approach combining transcriptomics, chromatin accessibility profiling, whole-genome bisulfite sequencing and targeted metabolomics, we reveal that the first parasite encounter induces a stable rewiring of hemocyte metabolism and chromatin landscape. This reprogramming primes hemocytes for a massive and rapid transcriptional response upon secondary challenge, characterized by an immune shift toward highly specific humoral effector pathways. Metabolic analyses demonstrate an early switch toward aerobic glycolysis, altered tricarboxylic acid cycle activity and amino acid metabolism, consistent with a Warburg-like metabolic state previously described in vertebrate trained immunity. Notably, metabolic and epigenetic remodeling occurs primarily during the primary infection and remains stable upon secondary exposure, suggesting that immune memory is encoded prior to pathogen re-encounter. Together, our results identify conserved metabolic and epigenetic mechanisms underlying innate immune memory in a non-vertebrate host and provide direct evidence that hemocyte-mediated innate immune memory in B. glabrata shares core features with trained immunity described in vertebrates.

Animals↗

Mapping of the juxtacentromeric heterochromatin-euchromatin frontier of human chromosome 21.

Euchromatin and heterochromatin are functional compartments of the genome. However, little is known about the structure and the precise location of the heterochromatin-euchromatin boundaries in higher eukaryotes. Constitutive heterochromatin in centromeric regions is associated with (1) specific histone methylation patterns, (2) high levels of DNA methylation, (3) low recombination frequency, and (4) the repression of transcription. All of this contrasts with the permissive structure of euchromatin found along chromosome arms. On the sequence level, the transition between these two domains consists most often of patchworks of segmental duplications. We present here a comprehensive analysis of gene expression, DNA methylation in CpG islands, distribution of histone isoforms, and recombination activity for the juxtacentromeric (or pericentromeric) region of the long arm of human chromosome 21. We demonstrate that most HapMap data are reliable within this region. We show that high linkage disequilibrium between pairs of SNPs extends 719-737 kb from the centromeric alpha-satellite. In the same region we find a peak of histone isoforms H3K9Me3 and H3K27Me (715-822 kb distal to the alpha-satellite). In normal somatic cells, CpG islands proximal to this peak are highly methylated, whereas distal CpG islands are not or very little methylated. This methylation profile undergoes dramatic changes in cancer cells and during spermatogenesis. As a consequence, transcription from heterochromatic genes is activated in the testis, and aberrant gene activation can occur during neoplastic transformation. Our data indicate that the frontier between the juxtacentromeric heterochromatic domain and euchromatic domain of the long arm of chromosome 21 is marked by a heterochromatic peak located approximately 750 kb distal to the alpha-satellite.

Chromatin Immunoprecipitation↗

Frequent DNA hypomethylation of human juxtacentromeric BAGE loci in cancer.

The BAGE (B melanoma antigens) sequence family contains 15 nearly identical sequences that are in the juxtacentromeric regions of chromosomes 9, 13, 18, and 21. BAGE loci are expressed in male germ tissue and in a high percentage of cancers and cancer cell lines. We analyzed the DNA methylation state of the sequences in or near the promoters of the BAGE loci by a quantitative bisulfite and PCR-based assay (multiplex COBRA) using MboI and HphI in 18 somatic tissue samples, 4 testis and 4 sperm samples, and 48 tumors and tumor cell lines. In 94% of the control somatic tissue samples, DNA was highly methylated in the analyzed regions. In contrast, 98% of tumor DNA samples displayed hypomethylation. Also, DNA from testes and sperm was hypomethylated in at least one of the BAGE loci. BAGE transcripts were observed in only 47% of the analyzed tumor samples. Consequently, we propose BAGE hypomethylation as a new, highly informative epigenetic biomarker for the diagnosis of cancer, whose hypomethylation in cancer may be causally related to that of juxtacentromeric satellite DNA.

Antigens, Neoplasm↗

Cyclin D1 gene activation in human myeloma cells is independent of DNA hypomethylation or histone hyperacetylation.

OBJECTIVE: Overexpression of cyclin D1 is a common event in solid and hematological cancers. In multiple myeloma (MM), a B-cell hemopathy, one mechanism responsible for cyclin D1 expression is the translocation t(11;14)(q13;q32). But this translocation does not account for cyclin D1 gene activation in all MM. We have hypothesized that epigenetic events could regulate cyclin D1 gene transcription. METHODS: Using 6 MM cell lines representative of different cyclin D1 expression levels and exhibiting various chromosome 11 abnormalities, as well as normal B cells, we studied DNA methylation and histone acetylation of the cyclin D1 promoter. RESULTS: With the bisulfite sequencing technique, we have studied the DNA methylation status of the core minimal cyclin D1 promoter containing Sp1- and CRE-binding sites. Our results show that this region is not methylated in 6 human MM cell lines as well as in normal B lymphocytes, independently of cyclin D1 expression. Treatment with the DNA methyltransferase inhibitor 5-aza-deoxycytidine (5-Aza) had no effect on cyclin D1 gene transcription. Chromatin immunoprecipitation (ChIP) experiments indicated that acetylated histones H4 are located at both the active and inactive cyclin D1 promoter. Treatment with a histone deacetylase inhibitor, trichostatin A (TSA), had no effect on gene transcription, nor had combined TSA plus 5-Aza treatment. CONCLUSION: The cyclin D1 gene is silenced within the B lineage by a mechanism different from DNA methylation or histone deacetylation.

Acetylation↗

eL-DASionator: an LDAS upload file generator.

BACKGROUND: The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to use the "Lightweight DAS" server (LDAS). Onto this type of server, annotations can be uploaded as flat text files in a defined format. The popular Ensembl ContigView uses the same format for the transient upload and display of user data. RESULTS: In order to easily generate LDAS upload files we developed a software tool that is accessible via a web-interface http://atgc.lirmm.fr/eldasionator.html. Users can submit their DNA sequences of interest. Our program (i) aligns these sequences to the reference sequences of Ensembl, (ii) determines start and end positions of each sequence on the reference sequence, and (iii) generates a formatted annotation file. This file can be used to load any LDAS annotation server or it can be uploaded to the Ensembl ContigView. CONCLUSION: The eL-DASionator is an on-line tool that is intended for life-science researchers with little bioinformatics background. It conveniently generates LDAS upload files, and makes it possible to generate annotations in a standard format that permits comfortable sharing of this data.

Base Sequence↗

Non-Mendelian transmission of alleles at microsatellite loci: an example in Ixodes ricinus, the vector of Lyme disease.

Microsatellite loci are usually considered to be neutral co-dominant and Mendelian markers. We undertook to study the inheritance of five microsatellite loci in the European Lyme disease vector, the tick Ixodes ricinus. Only two loci appeared fully Mendelian while the three others displayed non-Mendelian patterns that highly frequent null alleles could not fully explain. At one locus, IR27, some phenomenon seems to hinder the PCR amplification of one allele, depending on its origin (maternal imprinting) and/or its size (short allele dominance). DNA methylation, which appeared to be a possible explanation of this amplification bias, was rejected by a specific test comparing the amplification efficiency that did not differ between unmethylated and experimentally methylated DNA. The role of allele size in heterozygous individuals was then revealed from the data available on field collected ticks and consistent with the results of a theoretical approach. These observations highlight the need for prudence while inferring reproductive systems (selfing rates), parentage or even allelic frequencies from microsatellite markers, in particular for parasitic organisms for which molecular approaches often represent the only way for population biology inferences.

Alleles↗

An improved version of the DNA Methylation database (MethDB).

Cytosine methylation is a characteristic property of prokaryotic and eukaryotic genomes. In the latter, it is indispensable for a healthy development of the organism and uncontrolled changes in the distribution of 5-methylcytosine (5mC) have been linked to severe disorders, in particular cancer. The growing scientific interest in DNA methylation has led to a considerable amount of data about this epigenetic phenomenon. In order to make these data readily available, we have established a dedicated database. The DNA Methylation database (MethDB) is currently the only public database for DNA methylation (http://www.methdb.net). This constantly growing database has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of September 4, 2002). About 14% of the data have not been published elsewhere. These data can be conveniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter new data into MethDB.

Animals↗

Identification and resolution of artifacts in bisulfite sequencing.

Bisulfite sequencing has become the most widely used application to detect 5-methylcytosine (5-MeC) in DNA, and provides a reliable way of detecting any methylated cytosine at single-molecule resolution in any sequence context. The process of bisulfite treatment exploits the different sensitivity of cytosine and 5-MeC to deamination by bisulfite under acidic conditions, in which cytosine undergoes conversion to uracil while 5-MeC remains unreactive. In this article, we address the more commonly encountered experimental artifacts associated with bisulfite sequencing, and provide methods for the detection and elimination of these artifacts. In particular, we focus on conditions that inhibit complete bisulfite-mediated conversion of cytosines in a target sequence, and demonstrate the necessity of complete protein removal from DNA samples prior to bisulfite treatment. We also include a brief summary of the experimental protocol for bisulfite treatment and tips for designing polymerase chain reaction (PCR) primers to amplify from bisulfite-treated DNA.

5-Methylcytosine↗

DNA Methylation Database "MethDB": a user guide.

The DNA Methylation Database (MethDB; http://www.methdb.net) is a public database dedicated to DNA methylation. It attempts to store all data about DNA methylation in a common source. MethDB can be searched in different ways, ranging from a simple browse mode to detailed queries for sequence-specific DNA methylation profiles and patterns, total methylation content data or environmental conditions that can influence the methylation state of DNA. Currently, the database contains 2570 values for methylation content and 5278 methylation patterns and profiles for a total of 83 genes or loci. MethDB is an annotated database, and the scientific community is invited to submit their own data (submit@methdb.de).

Computer Graphics↗