Biomedical subjects

Arndt Weinmann

Publications and source records attributed to Arndt Weinmann.

9 recordsLinked to original sources

PubMed2006

Genome-wide analysis of factors regulating gene expression in liver.

In recent decades, multiple individual genes have been studied with respect to their level of expression in liver tissue and in many cases substantial progress has been made in identifying individual factors promoting gene expression in liver. However, the overall picture is still undefined and general rules or factors regulating gene expression in liver have not yet been established. Thus, a genome-wide screen for factors regulating gene expression in liver is of high interest, as it may reveal common regulatory mechanisms for most genes highly expressed in liver. These factors represent potential new targets in liver disease associated with differential gene expression. Using a novel bioinformatics approach, we have performed a genome-wide, bioinformatic screen to identify genetic factors regulating gene expression in liver. As the expression of an individual gene is generally driven by its promoter activity, we compared the level of expression to individual promoter sequences. Expression data of 15,704 individual genes in 12 tissues were obtained from a normal tissue microarray dataset. The genes were subsequently divided into two groups, according to whether or not their highest expression level was found in liver tissue. Scanning 1000 bp upstream of the transcription start of each individual gene and using the PromoterScan algorithm, we were able to identify a total of 7042 promoters containing a total of 241,984 transcription factors. To eliminate the possibility that currently unknown transcription factors may be crucial to liver expression regulation, we investigated all possible nucleotide combinations of 8 bp and 10 bp which we reasoned may serve as novel binding sites for transcription factors. In both screens we did not detect any significant, biologically relevant differences in numbers of transcription factors and binding sites between the two groups. Furthermore, we excluded possible differences in distribution of TATA-boxes or CpG islands as well as differences in nucleotide composition of RNA sequences or amino acid composition of transcribed protein sequences. We conclude that the existence of central, superordinated regulatory factors in liver gene expression is unlikely and that expression of individual genes in liver is more likely to be dependent on individual combinations of regulating factors for each gene.

Algorithms↗

PubMed2006

Suppression of Mcl-1 via RNA interference sensitizes human hepatocellular carcinoma cells towards apoptosis induction.

BACKGROUND: Hepatocelluar carcinoma (HCC) is one of the most common cancers worldwide and a major cause of cancer-related mortality. HCC is highly resistant to currently available chemotherapeutic drugs. Defects in apoptosis signaling contribute to this resistance. Myeloid cell leukemia-1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 protein family which interferes with mitochondrial activation. In a previous study we have shown that Mcl-1 is highly expressed in tissues of human HCC. In this study, we manipulated expression of the Mcl-1 protein in HCC cells by RNA interference and analyzed its impact on apoptosis sensitivity of HCC cells in vitro. METHODS: RNA interference was performed by transfecting siRNA to specifically knock down Mcl-1 expression in HCC cells. Mcl-1 expression was measured by quantitative real-time PCR and Western blot. Induction of apoptosis and caspase activity after treatment with chemotherapeutic drugs and different targeted therapies were measured by flow cytometry and fluorometric analysis, respectively. RESULTS: Here we demonstrate that Mcl-1 expressing HCC cell lines show low sensitivity towards treatment with a panel of chemotherapeutic drugs. However, treatment with the anthracycline derivative epirubicin resulted in comparatively high apoptosis rates in HCC cells. Inhibition of the kinase PI3K significantly increased apoptosis induction by chemotherapy. RNA interference efficiently downregulated Mcl-1 expression in HCC cells. Mcl-1 downregulation sensitized HCC cells to different chemotherapeutic agents. Sensitization was accompanied by profound activation of caspase-3 and -9. In addition, Mcl-1 downregulation also increased apoptosis rates after treatment with PI3K inhibitors and, to a lower extent, after treatment with mTOR, Raf I and VEGF/PDGF kinase inhibitors. TRAIL-induced apoptosis did not markedly respond to Mcl-1 knockdown. Additionally, knockdown of Mcl-1 efficiently enhanced apoptosis sensitivity towards combined treatment modalities: Mcl-1 knockdown significantly augmented apoptosis sensitivity of HCC cells towards chemotherapy combined with PI3K inhibition. CONCLUSION: Our data suggest that specific downregulation of Mcl-1 by RNA interference is a promising approach to sensitize HCC cells towards chemotherapy and molecularly targeted therapies.

Antineoplastic Agents↗

PubMed2006

Genetic association of autoimmune hepatitis and human leucocyte antigen in German patients.

AIM: To report on our large German collective and updated data of 142 patients with autoimmune hepatitis (AIH) type 1. METHODS: Key investigations performed were liver biopsy, serum autoantibodies as well as serum markers such as IgG and elevated transaminases. Antinuclear antigen (ANA) and smooth muscle antigen (SMA) autoantibodies characterized type 1 AIH. Type 3 (AIH) was solely characterized by the occurrence of soluble liver antigen/liver-pancreas antigen (SLA/LP) autoantibodies either with or without ANA or SMA autoantibodies. RESULTS: Most prevalent HLAs were A2 (68 patients, 48%), B8 (63 patients, 44%), C7 (90 patients, 63%), DR3 (49 patients, 38%), DR4 (49 patients, 38%) and DQ2 (42 patients, 30%). Compared to the Italian and North American patients, we found fewer patients with a DQ2 subtype. Furthermore, the B8-DR3-DQ2 human leucocyte antigen (HLA) was also less prominent compared to the North American patients. However, prevalences of B8, DR3, DR4, DR7, DR11 and DR13 were comparable to the Italian and North American patients. Furthermore, we report on an additional subgroup of patients with SLA/LP positive AIH. Generally, in this subgroup of patients the same HLA subtypes were favoured as the AIH type 1. CONCLUSION: Although HLA subtypes were comparable between these three collectives, the German patients were distinct from the Italian and North American patients with respect to DQ2 and from the North American patients with respect to B8-DR3-DQ2 HLA. A clinical correlation, e.g. difference in severity or treatability of AIH type 1, has yet to be determined.

Autoantigens↗

PubMed2006

Actin binding LIM protein 3 (abLIM3).

LIM domain proteins were demonstrated to play key roles in various biological processes such as embryonic development, cell lineage determination, and cancer differentiation. Actin binding LIM protein 1 (abLIM1) was reported to be localized in a genomic region often deleted in human cancers and suggested to be involved in axon guidance. Recently, existence of a second family member was reported, actin binding LIM protein 2. By means of computational biology and comparative genomics, we now characterized an additional, third member of the actin binding LIM protein subgroup, actin binding LIM protein 3 (abLIM3). The human mRNA sequence was previously annotated as differentially regulated in hepatoblastoma compared to normal livers. Conservation of key structural features of abLIM1 and abLIM2, four LIM domains and a VHD domain, suggested comparable biological function of abLIM3 as a linker between actin cytoskeleton and cell signaling pathways. AbLIM3 was found to be conserved in vertebrates, as orthologous sequences were characterized for mouse, fish, and frog. In addition, we report the existence of abLIM2 orthologs in fish and frog, suggesting a similar degree of evolutionary conservation. The intracellular localization of the abLIM3 protein was predicted to be nuclear by means of Reinhardt's neural network and the k-nearest neighbor algorithm. The corresponding abLIM3 gene was localized to chromosome 5q32 and spanned 119 kb, organized in 24 exons. An RT-PCR based expression profile available from the human unidentified gene-encoded (HUGE) database demonstrated highest expression for abLIM3 in heart, lung, liver, and brain/cerebellum accompanied by lower expression in multiple other tissues. Furthermore, abLIM3 was expressed in fetal liver, CNS, and spinal cord.

Amino Acid Sequence↗

PubMed2006

Current bioinformatics tools in genomic biomedical research (Review).

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has rapidly developed into an essential aid for genomic data analysis and powerful bioinformatics tools have been developed, many of them publicly available through the World Wide Web. In this review, we summarize and describe the basic bioinformatics tools for genomic research such as: genomic databases, genome browsers, tools for sequence alignment, single nucleotide polymorphism (SNP) databases, tools for ab initio gene prediction, expression databases, and algorithms for promoter prediction.

Computational Biology↗

PubMed2005

Characterization of OEBT, a LIM protein.

LIM Proteins have been demonstrated to play key roles in pattern formation during embryonic development, cell lineage determination, and cancer differentiation. These proteins are characterized by their conserved LIM domain, which functions as a specific protein-binding site. Recently, two new members of the LIM protein family, PRICKLE1 and PRICKLE2, were characterized in silico and demonstrated to be human orthologues of the Drosophila prickle proteins. We report on an additional member of this protein family, overexpressed breast tumor protein (OEBT). The corresponding gene was mapped to human chromosome 6p22.31. Orthologues in mouse and rat with 72 and 54% identities on a protein level were identified and the corresponding genes were mapped to mouse chromosome 17 and rat chromosome 9. The protein displays two LIM domains, as well as a PET domain, and was predicted to be localized in the nucleus. Expression of human OEBT was analyzed in silico, and the corresponding RNA was annotated to be highly expressed in a broad range of tissues. ESTs from several malignant tissue differentiations point towards a possible role of OEBT in cancer differentiation.

Adaptor Proteins, Signal Transducing↗

PubMed2005

In silico characterization of LZTS3, a potential tumor suppressor.

Members of the leucine zipper tumor suppressor (LZTS) protein family are thought to play roles in cell growth modulation. The two currently known members were identified by analyzing genomic and chromosomal alterations reported to be either involved or deleted in various types of cancer, suggesting a causative relationship. By means of computational biology, we have now identified a novel member of the LZTS protein family named LZTS3. The corresponding gene was localized to chromosome 20p13 and consisted of three exons. The novel LZTS3 protein demonstrated a high similarity to LAPSER1/LZTS2 and FEZ1/LZTS1, two members of the LZTS family. The conserved FEZ1 domain contains a leucine zipper motif similar to the cAMP-responsive activating transcription factor 5. As FEZ1 inhibits cancer cell growth through the regulation of mitosis and its alteration resulted in abnormal cell growth, the LZTS3 protein was expected to have similar functions during cancer differentiation. Furthermore, the protein was conserved in vertebrates, as orthologs could be identified in mouse, rat, and zebrafish. The intracellular localization of the LZTS3 protein was predicted to be nuclear by means of Reinhardt's neural network and the k-nearest neighbor algorithm. An RT-PCR-based expression profile available from the human unidentified gene-encoded (HUGE) database demonstrated the highest expression in the brain and kidney, accompanied by lower expression in multiple other tissues.

Amino Acid Sequence↗

PubMed2005

In silico characterization of an Iroquois family-related homeodomain protein.

Homeobox genes have been demonstrated to play important roles during cancer differentiation and embryonic development. The subset of Iroquois-related homeobox genes (IRXs) have furthermore been demonstrated to be involved in several embryonic developmental processes such as patterning of the anterior-posterior and dorso-ventral axis, as well as specific regions of the central nervous system, and differentiation of the otic vesicle, branchial epithelium, and limbs. We have characterized a novel homeodomain protein and corresponding gene by means of computational biology. Since the protein sequence displayed high similarity to the human IRX proteins, the newly identified homeodomain protein was named Iroquois family related homeodomain protein (IFRX). The IFRX protein sequence was found to be highly conserved in vertebrates. The corresponding IFRX gene was located on chromosome 10p12.1 and is organized in seven exons. The protein is predicted to be localized to the nucleus, supporting evidence for a functional role as a transcription factor, as suggested by the existence of a homeodomain. Preliminary expression profiling by biocomputational means predicted a rather broad expression profile with expression in the bone marrow, brain, heart, kidney, liver, lung, pancreas, prostate, skeletal muscle, spinal cord, spleen and thymus. However, expression in several tissues seemed to be low. In addition, approximately one third of all available EST sequences were obtained from embryonic tissues, suggesting that IFRX has a role in embryonic development.

Amino Acid Sequence↗

PubMed2005

LASS6, an additional member of the longevity assurance gene family.

Longevity assurance genes (LAGs) represent a subgroup of the homeobox gene family. Five mammalian homologs have been reported, and the corresponding proteins have previously been investigated with respect to their key role in ceramide synthesis. However, members of the LAG family have been shown to be involved in cell growth regulation and cancer differentiation. In an effort to characterize additional members of the LAG family, we have screened the latest releases of genomic databases and report on the bioinformatic characterization of yet another member, LAG1 longevity assurance homolog 6 (LASS6). Like other LAG family members, the LASS6 protein contained a homeodomain and LAG1 domain. In phylogenetic analyses, it displayed highest homology to LASS5. The corresponding gene was localized to human chromosome 2q24.3, spanning a rather large genomic region of 318 kb. Orthologous sequences in mouse and zebrafish suggested a conservation of LASS6 in vertebrates as the protein and corresponding genomic sequences were highly conserved. LASS6 expression was analyzed in silico, and the gene was shown to be broadly expressed in a wide range of tissues. Furthermore, available microarray data suggested a role in cancer differentiation and early embryonic development.

Amino Acid Sequence↗