CDNA microarray gene expression analysis of B-cell chronic lymphocytic leukemia proposes potential new prognostic markers involved in lymphocyte trafficking.

Human cancer is characterized by complex molecular perturbations leading to variable clinical behavior, often even in single-disease entities. We performed a feasibility study systematically comparing large-scale gene expression profiles with clinical features in human B-cell chronic lymphocytic leukemia (B-CLL). cDNA microarrays were employed to determine the expression levels of 1,024 selected genes in 54 peripheral blood lymphocyte samples obtained from patients with B-CLL. Statistical analyses were applied to correlate the expression profiles with a number of clinical parameters including patient survival and disease staging. We were able to identify genes whose expression levels significantly correlated with patient survival and/or with clinical staging. Most of these genes code either for cell adhesion molecules (L-selectin, integrin-beta2) or for factors inducing cell adhesion molecules (IL-1beta, IL-8, EGR1), suggesting that prognosis of this disease may be related to a defect in lymphocyte trafficking. This report demonstrates the feasibility of a systematic integration of large-scale gene expression profiles with clinical data as a general approach for dissecting human diseases.

Correlation of clinical data with proteomics profiles in 24 patients with B-cell chronic lymphocytic leukemia.

The development of human cancer is caused by complex molecular perturbations leading to variable clinical behavior often even in single disease entities. To prove that expression profiling on the protein level can be correlated with clinical data we systematically compared in a pilot study the protein expression patterns obtained by 2-dimensional gel electrophoresis with clinical features in human B-cell chronic lymphocytic leukemia (B-CLL), a disease characterized by broad clinical variability. Statistical methods were devised to analyze the spot pattern from 24 patient samples. This analysis allowed the identification of proteins that clearly discriminated between the patient groups with defined chromosomal characteristics or whose expression levels did correlate with clinical parameters such as patient survival. This report demonstrates that the correlation of large-scale protein expression profiles with clinical data can be used to gain new insights into molecular aspects of a disease. The data described here show that B-CLL patient populations with shorter survival times exhibit changed levels of redox enzymes, heat shock protein 27 and protein disulfide isomerase. These molecules may be potentially involved in drug resistance.

Detection of chromosomal imbalances in leiomyosarcoma by comparative genomic hybridization and interphase cytogenetics.

Leiomyosarcomas comprise a group of malignant soft-tissue tumors with smooth-muscle differentiation. In this study, 14 cases of leiomyosarcoma were screened for changes in relative chromosome copy number by comparative genomic hybridization. A high number of imbalances (mean, 16.3; range, 6-26) was detected, with chromosomal gains occurring about twice as much as losses. The most frequent gains were found in 5p15, 8q24, 15q25-->q26, 17p, and Xp (43% to 50%), whereas the most frequent losses were found in 10q and 13q (50% and 78%, respectively). Twenty high-level amplifications affecting 15 different chromosomal subregions were detected in nine different tumors. In three leiomyosarcomas, sequences on chromosome arm 17p were found to be highly amplified, with a minimal overlapping region on subbands 17p12-->p11. We further discovered that the Smith-Magenis syndrome critical region on 17p11.2 is included in the 17p amplicons of two leiomyosarcoma cases. Using probes flanking this genetically unstable region, a mean of 14 and 22 signals per nucleus, respectively, was detected in both leiomyosarcomas by fluorescence in situ hybridization. In conclusion, this analysis identifies a number of characteristic chromosomal imbalances in leiomyosarcomas and provides evidence for the localization of potential oncogenes and tumor suppressor genes active in leiomyosarcoma genomes.

Mapping of the breakpoints on the short arm of chromosome 17 in neoplasms with an i(17q).

Isochromosomes are monocentric or dicentric chromosomes with homologous arms that are attached in a reverse configuration as mirror images. With an incidence of 3-4%, the i(17q) represents the most frequent isochromosome in human cancer. It is found in a variety of tumors, particularly in blast crisis of chronic myeloid leukemia (CML-BC), acute myeloid leukemia (AML), non-Hodgkin's lymphoma (NHL), and medulloblastoma (MB), and indicates a poor prognosis. To determine the breakpoints on the molecular genetic level, we analyzed 18 neoplasms (six CML, four AML, one NHL, and seven MB) with an i(17q) and two MB with a pure del(17p) applying fluorescence in situ hybridization (FISH) with yeast artificial chromosome (YAC) clones, P1-artificial chromosome (PAC) clones, and cosmids from a well-characterized contig covering more than 6 Mb of genomic DNA. We identified four different breakpoint cluster regions. One is located close to or within the centromere of chromosome 17 and a second in the Charcot-Marie-Tooth (CMT1A) region at 17(p11.2). A third breakpoint was found telomeric to the CMT1A region. The fourth, most common breakpoint was detected in MB, AML, and in CML-BC specimens and was bordered by two adjacent cosmid clones (clones D14149 and M0140) within the Smith-Magenis syndrome (SMS) region. These results indicate that the low copy number repeat gene clusters which are present in the CMT and SMS regions may be one of the factors for the increased instability that may trigger the formation of an i(17q).

DNA chip technology ante portas.

The recent popularity of DNA chip technology has been fostered by the increasing demand for new diagnostic tools which allow the simultaneous analysis of large numbers of nucleic acid hybridization experiments in a timely fashion. The development of DNA chip-based assays has been strongly driven by modern approaches aiming at the comprehensive analysis of multiple gene mutations and expressed sequences. The broad range of current DNA chip applications include the detection of pathogens, the measurement of differences in the expression of genes between different cell populations, and the analysis of genomic alterations such as sequence and copy number alterations in disease-related genes and single nucleotide polymorphisms. We present an overview of the impact of DNA chip technology on the field of molecular medicine and discuss developments that can be expected in the near future.

Gene expression profiling in drug discovery and development.

Recent advances in technology, especially the merger between molecular biology, automation technology and computer science, are rapidly changing the manner in which pharmaceutical companies will discover new drug targets and develop new therapeutic drugs. One example of such a merger between different disciplines has been the development of technology platforms, such as cDNA microarrays and oligonucleotide arrays, allowing the generation of comprehensive gene expression profiles in a previously insurmountable throughput. Hereby, the major limitation is currently shifting from the efficient generation of biological information to the extraction of biological knowledge. However, given the foreseeable developments in data mining technologies and diverse computational biology tools, it can be anticipated that this information will foster the effectiveness to develop new and hopefully better drugs.

Mapping of chromosomal imbalances in gastric adenocarcinoma revealed amplified protooncogenes MYCN, MET, WNT2, and ERBB2.

Gastric adenocarcinoma is a malignant tumor with a high incidence and a low survival rate. In order to identify genetic alterations associated with this tumor, we screened 23 gastric adenocarcinomas for recurrent chromosomal imbalances by using comparative genomic hybridization (CGH). The most common gains of chromosomal material were found on chromosome arms 20q (10 cases), 16p (7 cases), and 1q (4 cases) and on chromosome 11 (4 cases). Losses were observed on chromosome arms 4q, 5q, 9p, and 21q (3 cases each). Four tumors exhibited high-level amplifications localized on chromosome regions 2p23-p24, 7q31-q32, 8p21-p22, 10q25-q26, 11q13, 17q11-q21, and 20q. Based on the position of these amplifications, candidate (onco)genes were selected and subsequently tested by Southern blot analysis of the respective tumors. Of the seven tested candidates, MYCN, MET, WNT2, and ERBB2 were found to participate in the amplicons of the respective tumor samples. Of these four presumably activated oncogenes, two, MYCN and WNT2, were previously not assumed to play a pathogenic role in stomach cancer. Among the other regions of imbalance, gain of 20q seems particularly interesting, because it is found in almost half of the analyzed cases and is highly amplified. Our data allowed us to narrow the relevant region down to the commonly gained bands 20q12-q13.1. This and other imbalanced regions provide a basis for searching new putative oncogenes and tumor suppressor genes involved in the development or progression of gastric adenocarcinoma.

DMBT1, a new member of the SRCR superfamily, on chromosome 10q25.3-26.1 is deleted in malignant brain tumours.

Loss of sequences from human chromosome 10q has been associated with the progression of human cancer. Medulloblastoma and glioblastoma multiforme are the most common malignant brain tumours in children and adults, respectively. In glioblastoma multiforme, the most aggressive form, 80% of the tumours show loss of 10q. We have used representational difference analysis to identify a homozygous deletion at 10q25.3-26.1 in a medulloblastoma cell line and have cloned a novel gene, DMBT1, spanning this deletion. DMBT1 shows homology to the scavenger receptor cysteine-rich (SRCR) superfamily. Intragenic homozygous deletions has been detected in 2/20 medulloblastomas and in 9/39 glioblastomas multiformes. Lack of DMBT1 expression has been demonstrated in 4/5 brain-tumour cell lines. We suggest that DMBT1 is a putative tumour-suppressor gene implicated in the carcinogenesis of medulloblastoma and glibolastoma multiforme.

Molecular characterization of a genetically unstable region containing the SMS critical area and a breakpoint cluster for human PNETs.

Recently we demonstrated the clustering of deletion breakpoints in the pericentromeric region of human chromosome 17p in human primitive neuroectodermal tumors (PNETs). Chromosomal disruption was shown to occur between the two markers D17S805 and D17S953, a region previously shown to be deleted in the Smith-Magenis syndrome. To characterize the molecular basis of this genomic instability, we established clone contigs covering this region. An initial physical map of chromosome 17p has been constructed with overlapping sets of YACs. YAC clones were transformed into five clone contigs according to their content of 30 previously known and 16 newly established sequence-tagged sites (STSs). To circumvent the complications inherent in YAC technologies, such as internal deletions, chimerism, and complex rearrangements, we then converted the YAC contigs to PAC and cosmid contigs. Thirty-nine individual PAC/cosmid clones were identified and were used to construct six different PAC/cosmid contigs ranging from 130 to 1200 kb in size and covering approximately 2.5 Mb of genomic DNA. The composite YAC/PAC/cosmid map covers a region of > 6 Mb of genomic DNA consisting of four different clone contigs of up to 2.9 Mb in size. We have demonstrated that three STSs (D17S58, PS1, and D17S842) are duplicated, suggesting the occurrence of low abundant repetitive sequences in this region. By integration of publicly available information we further mapped 10 genes and ESTs to their precise chromosomal positions and thus could exclude or identify them as candidate genes for PNET and/or the Smith-Magenis syndrome.

High-resolution deletion mapping of chromosome arm 17p in childhood primitive neuroectodermal tumors reveals a common chromosomal disruption within the Smith-Magenis region, an unstable region in chromosome band 17p11.2.

Loss of heterozygosity (LOH) on chromosome arm 17p is the most common genetic aberration in childhood primitive neuroectodermal tumors (PNETs). To determine the frequency and extent of 17p deletions, 29 loci on 17p were investigated in 24 tumors by using restriction fragment length polymorphism (RFLP) and microsatellite analysis. LOH on 17p was found in 9 of 24 tumors. In all tumors with LOH, a continuous stretch from the telomere to chromosome band 17p11.2 was completely deleted, and no interstitial or terminal small-scale deletions were detected in the remaining 15 tumors. In four tumors with LOH on 17p, the chromosomal breakpoint was located between D17S953 and D17S805. To identify this deletion breakpoint on the cytogenetic map of chromosome 17 and to exclude uniparental disomy, we verified our data by using fluorescence in situ hybridization (FISH) analyses. By using two yeast artificial chromosome (YAC) clones that were positive for D17S689 and D17S953, the same breakpoint was confirmed in two specimens of cerebrospinal fluid (CSF) metastases by using FISH on interphase preparations. We demonstrate that, in most childhood PNETs with LOH on 17p, the breakpoint is close to, but not within, the centromere. It varies, and it occurs predominantly between the two markers D17S689 and D17S953, which is an unstable chromosomal region that is deleted or duplicated in the Smith-Magenis syndrome. Because LOH of 17p is associated with the formation of isochromosome 17q in the majority of PNETs, this study provides entry points to determine the molecular nature of this phenomenon.

Ordering of 66 STSs along the entire short arm of human chromosome 17 and chromosome assignment of a transcribed sequence (FMR1L2) homologous to FMR1.

Sixty-four PCR-markers previously assigned to the short arm of chromosome 17 and two newly established STSs were localized on a hybrid cell-YAC clone panel. The 66 STSs fell into 23 unique retention patterns, providing a map converting the entire short arm of human chromosome 17 with an average resolution of approximately 1.2 Mb. The combination of radiation-reduced hybrids, somatic cell hybrids and selected YAC clones enabled the precise localization of break-points in two cell hybrids. Since polymorphic STSs from the CEPH as well as the UTAH genetic map were used in this study, a physical link has been generated between these two high resolution genetic maps. FMR1L2, a second FMR1 autosomal homologue has been identified and assigned to a genomic interval between D17S796 and D17S799.

Acute lethal necrotising pancreatitis in childhood systemic lupus erythematosus--possible toxicity of immunosuppressive therapy.

We report on a 16 year old girl with a three-year history of systemic lupus erythematosus who developed a case of acute lethal haemorrhagic pancreatitis. She presented with high grade fever, skin rash, malaise, and arthralgias. Laboratory lupus activity parameters were markedly elevated. In the absence of renal, pulmonary, cardiac or cerebral involvement, our patient developed pancreatitis leading to pancreatogenic shock. Until 14 days before the onset of pancreatitis, the patient's medications included prednisolone, azathioprine and methotrexate. At autopsy, no autoimmune vasculitis was found in the affected pancreatic tissue. Therefore, an etiologic role of combination therapy had to be considered. Whereas methotrexate has never been reported to be linked to pancreatitis, a few publications describing prednisolone and azathioprine in connection with pancreatitis do exist. Thus, if pancreatitis is not just termed idiopathic, it must be attributed to a combination regimen of drugs including methotrexate. A review of the literature shows that pancreatitis in SLE is rare and has never been associated with methotrexate therapy before.

Two fetuses with Fryns syndrome without diaphragmatic defects.

We report two fetuses with Fryns syndrome including the typical facial appearance and distal limb and lung hypoplasia, but no diaphragmatic hernias. The parents were consanguineous. Characteristic in both cases were the distal limb defects with brachytelephalangism and aplasia of the distal phalanges of the first toe. Since one of the two sibs had severe lung hypoplasia without macroscopic or microscopic defects of the diaphragm, we show that lung hypoplasia can occur independently from diaphragmatic defects in Fryns syndrome.

Structure and localization on the X chromosome of the gene coding for the human filopodial protein moesin (MSN).

Moesin is a member of a recently discovered family of closely related proteins that includes ezrin, radixin, and merlin. It is widely expressed in different tissues and cells and has been localized to filopodia and other membranous protrusions that are important for cell-cell recognition and signaling and cell movement. Here, we have localized the coding gene (MSN) to Xq11.2-q12 by Southern and Western blot analyses of Chinese hamster x human somatic cell hybrids and by fluorescence chromosomal in situ hybridization. Moesin-like sequences were identified on chromosomes 5 and 6. The murine Msn locus was mapped to the X chromosome as well by studying a rodent x mouse hybrid panel. The structure of the human moesin gene has been determined. The 12 exons are distributed over > 30 kb, and the exon/intron junctions demarcate individual highly conserved domains. Primer extension analysis revealed two major start transcription sites, 184 and 133 bp upstream of the initiation codon. The 5'-flanking region is GC-rich, lacks a TATA box, and contains four SP1 and one AP1 binding sites.

Molecular cloning, cDNA sequence, and chromosomal assignment of the human radixin gene and two dispersed pseudogenes.

Radixin is a cytoskeletal protein that may be important in linking actin to the plasma membrane. Recent cloning of the murine and porcine radixin cDNAs revealed a protein highly homologous to ezrin and moesin. We have cloned and sequenced the human radixin cDNA and found the predicted amino acid sequence for the human protein to be nearly identical to those predicted for radixin in the two other species. By Southern analyses of Chinese hamster x human somatic cell hybrid DNA and of PCR products derived from hybrids, the coding gene (RDX) was mapped to 11q. Fluorescence chromosomal in situ hybridization with a cDNA plasmid further localized this gene to band 11q23. However, PCR amplification with "radixin-specific" primers on the hybrid DNA panel yielded an additional, very similar DNA sequence that was further characterized by direct sequencing of PCR products. This sequence represents a truncated version and the respective locus (RDXP2) was assigned to Xp21.3. Furthermore, by employing a different set of primers, a third sequence was found that was 90% identical to the radixin sequence but contained termination codons and seemed to lack introns. This pseudogene (RDXP1) was mapped to 11p by Southern and PCR analyses.

[Eye changes in acanthosis nigricans maligna--possible effect of growth factors in the etiopathogenesis of this paraneoplastic disease picture]. / Augenveränderungen bei Acanthosis nigricans maligna--möglicher Einfluss von Wachstumsfaktoren in der Atiopathogenese dieses paraneoplastischen Krankheitsbildes.

A 64-year-old white male presented to our hospital with hyperplastic tarsal and to a lesser degree bulbar conjunctivae. Approximately one month later the full clinical picture of acanthosis nigricans maligna developed. In addition to ectropia of the lower eyelids he showed madarosis; neither the linea grisea nor the lacrimal points were discerneable. On gastroscopy a diffusely growing gastric adenocarcinoma adjacent to the cardia was found and later confirmed histopathologically. The computertomography of the abdomen demonstrated one solitary metastasis to one parapancreatic lymphnode. It is generally assumed that in the course of paraneoplastic syndroms products secreted by the tumor induce changes in the target organs, e.g. the conjunctiva and the skin. In the presented case (1) southern blot analysis of the tumor tissue proved an increase of Epidermal Growth Factor-receptors, (2) immunohistochemistry showed prominent staining for Transforming Growth Factor-alpha. In conclusion, this case is suggestive of a possible link between growth factors and acanthosis nigricans maligna.

Expression of Cx26, Cx32 and Cx43 gap junction proteins in normal and neoplastic human tissues.

This report concerns the expression of the gap-junction proteins Connexin (Cx)26, 32 and 43 in different malignant and non-malignant human tissues. Affinity-purified polyclonal antibodies against Cx26, 32 and 43 were used for immunohistochemical as well as immunoblot analysis. Cx32, the major gap-junction protein in rat and mouse liver, was detected in human liver and kidney. By contrast, Cx43 was expressed in epithelial and mesenchymal tissues and Cx26 was detected in different epithelia. Whereas all of the benign tumors studied, and some malignant ones, showed stable expression of gap-junction proteins, breast cancer, renal-cell cancer and sarcomas showed a significant decrease in gap-junction proteins as opposed to normal tissue. Cx43, not detected in human normal liver, was found in human hepatocellular carcinoma and Cx26, not detected in human adult skin, was observed in tissue samples of basal-cell carcinoma. In immunoblot analysis, Cx32 antibodies recognized a 27-kDa protein in human liver and hepatocellular carcinoma. A 43-kDa polypeptide was detected in human kidney, renal-cell carcinoma, normal breast, connective tissue of invasive-duct carcinoma of the breast and hepatocellular carcinoma.

[EBV in malignant lymphomas]. / EBV bei malignen Lymphomen.

PCR and in-situ-Hybridization were used to detect EBV-DNA within Hodgkin- and Non-Hodgkin-Lymphomas. By the use of primers for the Bam H1 W fragment we could show EBV-DNA to be associated with 45% Hodgkin- and 25% T-Lymphomas, whereas we could not find EBV-DNA within B-Lymphomas. In about one third of the PCR-positive cases we could localize EBV-DNA mostly in the tumor cell nuclei by in-situ-hybridization.

Further evidence that acanthosis nigricans maligna is linked to enhanced secretion by the tumour of transforming growth factor alpha.

The pathogenesis of cutaneous paraneoplastic syndromes is still under discussion. Since many of these syndromes, including acanthosis nigricans, are proliferative skin disorders it is believed that products secreted by the tumour stimulate the keratinocytes to proliferate. Growth factors like transforming growth factor alpha (TGF-alpha) are known to be highly mitogenic for keratinocytes in vitro. Here we report on a patient with a poorly differentiated gastric cancer and a full clinical picture of acanthosis nigricans characterized by diffuse hyperkeratosis and multiple papillomatous lesions of the skin with involvement of the conjunctivae. In Southern blot analysis of the tumour tissue from this patient amplification of the epidermal growth factor (EGF) receptor, the common ligand for TGF-alpha and EGF, was shown. Immunohistochemically, prominent staining was found throughout the tumour using anti-TGF-alpha antibodies. In a series of 25 investigated gastric tumour biopsies, four tumours showed amplification of the EGF receptor and one additional biopsy was positive for TGF-alpha. Since there is no other report describing the link between TGF-alpha and acanthosis nigricans, except that of Ellis et al. 1987, we present a new case suggesting a possible link between growth factors and acanthosis nigricans maligna.