Biomedical subjects

Jürgen Schmitz

Publications and source records attributed to Jürgen Schmitz.

At least 19 recordsLinked to original sources

PubMed2006

Evolution of small nucleolar RNAs in nematodes.

In contrast to mRNAs, which are templates for translating proteins, non-protein coding (npc) RNAs (also known as 'non-coding' RNA, ncRNA), exhibit various functions in different compartments and developmental stages of the cell. Small nucleolar RNAs (snoRNAs), one of the largest classes of npcRNAs, guide post-transcriptional modifications of other RNAs that are crucial for appropriate RNA folding as well as for RNA-RNA and RNA-protein interactions. Although snoRNA genes comprise a significant fraction of the eutherian genome, identifying and characterizing large numbers of them is not sufficiently accessible by classical computer searches alone. Furthermore, most previous investigations of snoRNAs yielded only limited indications of their evolution. Using data obtained by a combination of high-throughput cDNA library screening and computational search strategies based on a modified DNAMAN program, we characterized 151 npcRNAs, and in particular 121 snoRNAs, from Caenorhabditis elegans and extensively compared them with those in the related, Caenorhabditis briggsae. Detailed comparisons of paralog snoRNAs in the two nematodes revealed, in addition to trans-duplication, a novel, cis-duplication distribution strategy with insertions near to the original loci. Some snoRNAs coevolved with their modification target sites, demonstrating the close interaction of complementary regions. Some target sites modified by snoRNAs were changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs.

Animals↗

PubMed2006

An anthropoid-specific segmental duplication on human chromosome 1q22.

Segmental duplications (SDs) play a key role in genome evolution by providing material for gene diversification and creation of variant or novel functions. They also mediate recombinations, resulting in microdeletions, which have occasionally been associated with human genetic diseases. Here, we present a detailed analysis of a large genomic region (about 240 kb), located on human chromosome 1q22, that contains a tandem SD, SD1q22. This duplication occurred about 37 million years ago in a lineage leading to anthropoid primates, after their separation from prosimians but before the Old and New World monkey split. We reconstructed the hypothetical unduplicated ancestral locus and compared it with the extant SD1q22 region. Our data demonstrate that, as a consequence of the duplication, new anthropoid-specific genetic material has evolved in the resulting paralogous segments. We describe the emergence of two new genes, whose new functions could contribute to the speciation of anthropoid primates. Moreover, we provide detailed information regarding structure and evolution of the SD1q22 region that is a prerequisite for future studies of its anthropoid-specific functions and possible linkage to human genetic disorders.

Animals↗

PubMed2006

Retroposed elements as archives for the evolutionary history of placental mammals.

Reconstruction of the placental mammalian (eutherian) evolutionary tree has undergone diverse revisions, and numerous aspects remain hotly debated. Initial hierarchical divisions based on morphology contained many misgroupings due to features that evolved independently by similar selection processes. Molecular analyses corrected many of these misgroupings and the superordinal hierarchy of placental mammals was recently assembled into four clades. However, long or rapid evolutionary periods, as well as directional mutation pressure, can produce molecular homoplasies, similar characteristics lacking common ancestors. Retroposed elements, by contrast, integrate randomly into genomes with negligible probabilities of the same element integrating independently into orthologous positions in different species. Thus, presence/absence analyses of these elements are a superior strategy for molecular systematics. By computationally scanning more than 160,000 chromosomal loci and judiciously selecting from only phylogenetically informative retroposons for experimental high-throughput PCR applications, we recovered 28 clear, independent monophyly markers that conclusively verify the earliest divergences in placental mammalian evolution. Using tests that take into account ancestral polymorphisms, multiple long interspersed elements and long terminal repeat element insertions provide highly significant evidence for the monophyletic clades Boreotheria (synonymous with Boreoeutheria), Supraprimates (synonymous with Euarchontoglires), and Laurasiatheria. More importantly, two retropositions provide new support for a prior scenario of early mammalian evolution that places the basal placental divergence between Xenarthra and Epitheria, the latter comprising all remaining placentals. Due to its virtually homoplasy-free nature, the analysis of retroposon presence/absence patterns avoids the pitfalls of other molecular methodologies and provides a rapid, unequivocal means for revealing the evolutionary history of organisms.

Animals↗

PubMed2005

Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates.

Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model--the nucleotide composition--is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the "common ancestor" of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.

Animals↗

PubMed2005

Alu-SINE exonization: en route to protein-coding function.

The majority of more than one million primate-specific Alu elements map to nonfunctional parts of introns or intergenic sequences. Once integrated, they have the potential to become exapted as functional modules, e.g., as protein-coding domains via alternative splicing. This particular process is also termed exonization and increases protein versatility. Here we investigate 153 human chromosomal loci where Alu elements were conceivably exonized. In four selected examples, we generated, with the aid of representatives of all primate infraorders, phylogenetic reconstructions of the evolutionary steps presumably leading to exonization of Alu elements. We observed a variety of possible scenarios in which Alu elements led to novel mRNA splice forms and which, like most evolutionary processes, took different courses in different lineages. Our data show that, once acquired, some exonizations were lost again in some lineages. In general, Alu exonization occurred at various time points over the evolutionary history of primate lineages, and protein-coding potential was acquired either relatively soon after integration or millions of years thereafter. The course of these paths can probably be generalized to the exonization of other elements as well.

Alu Elements↗

PubMed2005

Isolation and generation of clinical-grade dendritic cells using the CliniMACS system.

Dendritic cells (DC) can either be generated from progenitors such as stem cells or CD14+ monocytes, or isolated directly from the blood. Blood-derived DC are present as at least two distinct populations-myeloid and plasmacytoid DC. Here we describe methods for the clinical-grade isolation of blood DC and DC precursors using the CliniMACS. We describe the isolation of ultra-pure monocytes in order to generate large numbers of monocyte-derived DC, and also new methods for the direct isolation of blood DC. Isolation of blood DC in large numbers means that natural DC with different properties can be investigated for their clinical function for the first time.

Cell Differentiation↗

PubMed2004

Does the AD7c-NTP locus encode a protein?

AD7c-NTP, the only known protein entirely encoded by tandem and nested cassettes of Alu repetitive elements, is reportedly over-expressed in brains of Alzheimer's disease patients [de la Monte et al., J. Clin. Invest. 15 (1997)]. Based on these findings a commercial diagnostic assay ("7c Gold"/"AlzheimAlert" ) has been developed. We analyzed the published cDNA sequence and compared it to corresponding EST clones as well as the genomic sequences of human and chimpanzee. We come to the conclusion that the existence of the gene and in particular the predicted protein is inconsistent with EST and genomic data. Previously published data need to be reassessed.

Alu Elements↗

PubMed2004

A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for the South American order Xenarthra, also termed Edentata (armadillos, anteaters, and sloths). Investigating this order, we discovered a novel high-copy-number family of tRNA derived SINEs in the nine-banded armadillo Dasypus novemcinctus, a species that successfully crossed the Central American land bridge to North America in the Pliocene. A specific computer algorithm was developed, and we detected and extracted 687 specific SINEs from databases. Termed DAS-SINEs, we further divided them into six distinct subfamilies. We extracted tRNA(Ala)-derived monomers, two types of dimers, and three subfamilies of chimeric fusion products of a tRNA(Ala) domain and an approximately 180-nt sequence of thus far unidentified origin. Comparisons of secondary structures of the DAS-SINEs' tRNA domains suggest selective pressure to maintain a tRNA-like D-arm structure in the respective founder RNAs, as shown by compensatory mutations. By analysis of subfamily-specific genetic variability, comparison of the proportion of direct repeats, and analysis of self-integrations as well as key events of dimerization and deletions or insertions, we were able to delineate the evolutionary history of the DAS-SINE subfamilies.

Animals↗

PubMed2004

A novel class of mammalian-specific tailless retropseudogenes.

In addition to their central function in protein biosynthesis, tRNAs also play a pervasive role in genome evolution and architecture because of their extensive ability to serve as templates for retroposition. Close to half of the human genome consists of discernible transposable elements, a vast majority of which are derived from RNA via reverse transcription and genomic integration. Apart from the presence of direct repeats (DRs) that flank the integrated sequence of retroposons, genomic integrations are usually marked by an oligo(A) tail. Here, we describe a novel class of retroposons that lack A-tails and are therefore termed tailless retropseudogenes. Analysis of approximately 2500 tRNA-related young tailless retropseudogene sequences revealed that they comprise processed and unprocessed (pre-)tRNAs, 3'-truncated in their loop regions, or truncated tRNA-derived SINE RNAs. Surprisingly, their mostly nonrandom integration is dependent on the priming of reverse transcription at sites determined by their 3'-terminal 2-18 nucleotides and completely independent from oligoadenylation of the template RNA. Thus, tailless retropseudogenes point to a novel, variant mechanism for the biogenesis of retrosequences.

Animals↗

PubMed2004

From "junk" to gene: curriculum vitae of a primate receptor isoform gene.

Exonization of Alu retroposons awakens public opinion, particularly when causing genetic diseases. However, often neglected, alternative "Alu-exons" also carry the potential to greatly enhance genetic diversity by increasing the transcriptome of primates chiefly via alternative splicing.Here, we report a 5' exon generated from one of the two alternative transcripts in human tumor necrosis factor receptor gene type 2 (p75TNFR) that contains an ancient Alu-SINE, which provides an alternative N-terminal protein-coding domain. We follow the primate evolution over the past 63 million years to reconstruct the key events that gave rise to a novel receptor isoform. The Alu integration and start codon formation occurred between 58 and 40 million years ago (MYA) in the common ancestor of anthropoid primates. Yet a functional gene product could not be generated until a novel splice site and an open reading frame were introduced between 40 and 25 MYA on the catarrhine lineage (Old World monkeys including apes).

Animals↗

PubMed2004

Primate jumping genes elucidate strepsirrhine phylogeny.

Transposable elements provide a highly informative marker system for analyzing evolutionary histories. To solve controversially discussed topics in strepsirrhine phylogeny, we characterized 61 loci containing short interspersed elements (SINEs) and determined the SINE presence-absence pattern at orthologous loci in a representative strepsirrhine panel. This SINE monolocus study was complemented by a Southern blot analysis tracing multiple loci of two different strepsirrhine specific SINEs. The results thereof were combined with phylogenetic trees reconstructed on the basis of complete mitochondrial cytochrome b sequences from all recognized strepsirrhine genera. Here we present evidence for (i) a sister group relationship of Malagasy Chiromyiformes and Lemuriformes, (ii) Lorisidae being a monophyletic sister clade to the Galagidae, and (iii) common ancestry of African and Asian lorisids. Based on these findings, we conclude that strepsirrhines originated in Africa and that Madagascar and Asia were colonized by respective single immigration events. In agreement with paleocontinental data, the molecular analyses suggest a crossing of the Mozambique channel by rafting between the late Cretaceous and the middle Eocene, whereas Asia was most likely colonized between the early Eocene and the middle Oligocene on a continental route. Furthermore, one SINE integration links the two Lemuriformes families, Lemuridae and Indriidae, indicating a common origin of diurnality or cathemerality and a later reversal to nocturnality by the indriid genus Avahi.

Animals↗

PubMed2003

Origin and subset distribution of peripheral blood dendritic cells in patients with chronic graft-versus-host disease.

BACKGROUND: After allogeneic hematopoietic stem cell transplantation, donor T cells interact with an antigen-presenting cell environment that is distorted in number, level of activation, and origin. The role of antigen presentation in the development of chronic graft-versus host disease (cGVHD) is unknown. METHODS: The number and origin of peripheral blood immature myeloid (CD19- CD1c+) and plasmacytoid (BDCA-2+) dendritic cells (DCs) was determined in 30 patients at more than 100 days after allogeneic hematopoietic stem cell transplantation. RESULTS: Patients with cGVHD had significantly higher plasmacytoid DC numbers than individuals without this complication (9.1+/-2.0 x 10(6)/L versus 3.8+/-0.6 x 10(6)/L, =0.025). Chimerism studies demonstrated that DCs in patients with cGVHD were exclusively of donor origin, whereas persistence of host DCs was observed in some control patients. CONCLUSIONS: The antigen-presenting cell environment in patients with cGVHD, as represented by immature blood DCs, is of donor origin but distorted in terms of subset distribution.

Adolescent↗

PubMed2003

The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences.

The phylogeny of the Syndermata (Rotifera: Monogononta, Bdelloidea, Seisonidea; Acanthocephala: Palaeacanthocephala, Eoacanthocephala, Archiacanthocephala) is key to understanding the evolution of acanthocephalan endoparasitism from free-living ancestors. In the present study, maximum likelihood, distance/neighbor-joining, and maximum parsimony analyses have been carried out based on 18S rDNA data of 22 species (four new sequences). The results suggest a monophyletic origin of the Eurotatoria (Monogononta+Bdelloidea). Seison appears as the acanthocephalan sistergroup. Palaeacanthocephala split into an "Echinorhynchus"-and a "Leptorhynchoides"-group, the latter sharing a monophyletic origin with the Eoacanthocephala and Archiacanthocephala. As inferred from the phylogeny obtained acanthocephalan endoparasitism evolved from a common ancestor of Seison and Acanthocephala that lived epizoically on an early mandibulate. Probably, an acanthocephalan stem species invaded the mandibulate host, thus establishing an endoparasitic lifestyle. Subsequently, vertebrates (or gnathostomes) became part of the parasite's life cycle. In the stem line of the Archiacanthocephala, a terrestrial life cycle has evolved, with an ancestor of the Tracheata (Insecta, Myriapoda) acting as intermediate host.

Acanthocephala↗

PubMed2003

Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates).

Transpositions of primate-specific Alu elements were applied as molecular cladistic markers in a phylogenetic analysis of South American primates. Seventy-four human and platyrrhine loci containing intronic Alu elements were PCR screened in various New World monkeys and the human outgroup to detect the presence of orthologous retrotransposons informative of New World monkey phylogeny. Six loci revealed size polymorphism in the amplification pattern, indicating a shared derived character state due to the presence of orthologous Alu elements confirmed by subsequent sequencing. Three markers corroborate (1) New World monkey monophyly and one marker supports each of the following callitrichine relationships: (2) Callithrix and Cebuella are more closely related to each other than to any other callitrichine, (3) the callitrichines form a monophyletic clade including Callimico, and (4) the next living relatives to the callitrichines are Cebus, Saimiri, and Aotus.

Alu Elements↗

PubMed2003

A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates.

Short interspersed nuclear elements (SINEs) provide a near homoplasy free and copious source of molecular evolutionary markers with precisely defined character polarity. Used as molecular cladistic markers in presence/absence analyses, they represent a powerful complement to phylogenetic reconstructions that are based on sequence comparisons on the level of nucleotide substitutions. Recent sequence comparisons of large data sets incorporating a broad eutherian taxonomic sample have led to considerations of the different primate infraorders to constitute a paraphyletic group. Statistically significant support against the monophyly of primates has been obtained by clustering the flying lemur-also termed colugo-(Cynocephalus, Dermoptera) amidst the primates as the sister group to anthropoid primates (New World monkeys, Old World monkeys, and hominoids). We discovered retrotransposed markers that clearly favor the monophyly of primates, with the markers specific to all extant primates but definitively absent at the orthologous loci in the flying lemur and other non-primates. By screening the colugo genome for phylogenetic informative SINEs, we also recovered a novel family of dermopteran specific SINE elements that we call CYN. This element is probably derived from the isoleucine tRNA and appears in monomeric, dimeric, and trimeric forms. It has no long tRNA unrelated region and no poly(A) linker between the monomeric subunits. The characteristics of the novel CYN-SINE family indicate a relatively recent history. Therefore, this SINE family is not suitable to solve the phylogenetic affiliation between dermopterans and primates. Nevertheless it is a valuable device to reconstruct the evolutionary steps from a functional tRNA to an interspersed SINE element.

Animals↗

PubMed2003

Memory B cells specific for the NC16A domain of the 180 kDa bullous pemphigoid autoantigen can be detected in peripheral blood of bullous pemphigoid patients and induced in vitro to synthesize autoantibodies.

Bullous pemphigoid is a subepidermal blistering disease characterized by the synthesis of autoantibodies against the 180 kDa and the 230 kDa bullous pemphigoid antigens. Whether autoimmunity is also reflected by the presence of circulating autoantigen-specific memory B cells is still a matter of debate. We used a new assay combining two-step immunomagnetic enrichment with multiparameter flow cytometry to detect and characterize bullous pemphigoid 180 kDa-specific IgG+ B cells in blood of bullous pemphigoid patients. In a first magnetic separation, B cells were isolated from peripheral blood mononuclear cells using releasable microbeads conjugated to a CD19 antibody. From pre-enriched B cells, bullous pemphigoid 180 kDa-specific cells were then positively selected using microbeads directly conjugated with a recombinant N-terminal fragment of the bullous pemphigoid 180 kDa ectodomain, containing the noncollagenous 16A domain, which was recently shown to harbor major epitopes of autoantibodies in bullous pemphigoid sera. Noncollagenous 16A domain-specific IgG+ B cells were detectable in blood of most, if not all patients with serum autoantibodies against the noncollagenous 16A domain. The specificity of the cells was confirmed by in vitro differentiation into antibody-forming cells and analysis of the culture supernatant for the presence of noncollagenous 16A domain-specific IgG antibodies. All noncollagenous 16A domain-specific IgG+ B cells showed a clear memory immunophenotype. Noncollagenous 16A domain-specific IgG+ memory B cells may be crucial for continuous noncollagenous 16A domain-specific autoantibody production and/or play a part as antigen-presenting cells for priming and restimulation of bullous pemphigoid 180 kDa-specific T helper cells.

Antibody Formation↗

PubMed2002

Frequent detection of thyroid peroxidase-specific IgG+ memory B cells in blood of patients with autoimmune thyroid disease.

Centrocytes in germinal centers on selection differentiate into plasma cells and/or memory B cells. Cells that have acquired autoreactivity by somatic mutation generally fail to undergo positive selection and die by apoptosis. Presence of isotype-switched high-affinity autoantibodies in serum of autoimmune patients suggests that autoreactive plasma cells eventually emerge from a germinal center reaction. Currently, it is still unclear to which extent the same is true for autoreactive memory B cells. To address this question, we have analyzed whether IgG-bearing memory B cells with specificity for thyroid peroxidase (TPO) can be found in blood of patients with autoimmune thyroid disease and in normal blood donors. Autoreactive TPO-specific IgG+ memory B cells were identified using a previously described assay combining two-step immunomagnetic enrichment with flow cytometric detection. Autoreactive IgG+ memory B cells were found in 65% of the patients with autoimmune thyroid disease and in 17% of normal blood donors; 40% of the latter had no detectable TPO-specific IgG in the serum. The specificity of enriched TPO-specific IgG+ memory B cells was confirmed by in vitro proliferation and differentiation into antibody-secreting cells at limiting dilution and analysis of the supernatants for the presence of TPO-specific IgG. Detection of TPO-specific IgG+ memory B cells in most patients with clinically manifested autoimmune thyroid disease and few normal blood donors may argue for a role of circulating memory B cells in onset of disease.

Adolescent↗

PubMed2002

Plasmacytoid dendritic cells: from specific surface markers to specific cellular functions.

We have recently described a panel of monoclonal antibodies (mAb), that recognize two novel leukocyte surface antigens, BDCA-2 and BDCA-4. BDCA-2 is a novel type II C-type lectin specifically expressed by plasmacytoid dendritic cells (PDCs) that can internalize antigen for presentation to T cells. Furthermore, signaling via BDCA-2 may play a role in switching from interferon (IFN)-alpha/beta-controlled to interleukin (IL)-12-controlled immune response pathways, as triggering of BDCA-2 potently inhibits secretion of IFN-alpha/beta by PDCs and thereby promotes IL-12 p70 production in PDCs and other cells. Viruses may exploit this switch to escape innate antiviral immunity, but it may be beneficial for patients with systemic lupus erythematosus (SLE) if induced, for instance by anti BDCA-2 mAb treatment. BDCA-4 is shown here to be identical to neuropilin-1 (NP-1), a neuronal receptor for the axon guidance factors belonging to the class-3 semaphorin subfamily, and a receptor on endothelial and tumor cells for vascular endothelial growth factor (VEGF-A). In blood and bone marrow, BDCA-4/NP-1 is exclusively expressed on PDCs, but in tonsils also on a few other cells, primarily follicular B helper memory T cells (T(FH)).

Antigens, Differentiation↗