An autosomal genomic screen for dementia in an extended Amish family

Apolipoprotein E (APOE) is the only universally confirmed susceptibility gene for late-onset Alzheimer disease (LOAD), although many loci are believed to modulate LOAD risk. The genetic homogeneity of isolated populations, such as the Amish, potentially provide increased power to identify LOAD susceptibility genes. Population homogeneity in these special populations may reduce the total number of susceptibility genes contributing to the complex disorder, thereby increasing the ability to identify any one susceptibility gene. Dementia in the Amish is clinically indistinguishable from LOAD in the general population. Previous studies in the Amish demonstrated a significantly decreased frequency of the APOE-4 susceptibility allele, but significant familial clustering of dementia [M.A. Pericak-Vance, C.C. Johnson, J.B. Rimmler, A.M. Saunders, L.C. Robinson, E.G. D'Hondt, C.E. Jackson, J.L. Haines, Alzheimer's disease and apolipoprotein E-4 allele in an Amish population, Ann. Neurol. 39 (1996) 700-704]. These data suggested that a genetic etiology independent of APOE may underlie the dementia observed in this population. In the present analysis, we focused on a large, multiplex, inbred Amish family (24 sampled individuals; 10 of whom are affected). We completed a genomic screen to identify novel LOAD loci (n=316 genetic markers), using both model-dependent "affecteds-only" analysis (dominant and recessive) and model-independent affected relative pair analysis. Interesting results (lod>1.5 or p<0.01) were obtained for markers on eight chromosomes (2q, 5q, 6q, 7p, 8p, 8q, 11p, 18p, 18q, and 19q). The highest overall score was a multipoint lod score of 3.1 on chromosome 11p. Most regions we identified were not previously detected by genomic screens of outbred populations and may represent population-specific susceptibilities to LOAD. These loci are currently under further investigation in a study of LOAD including additional Amish families.

Analysis of the RELN gene as a genetic risk factor for autism

Several genome-wide screens have indicated the presence of an autism susceptibility locus within the distal long arm of chromosome 7 (7q). Mapping at 7q22 within this region is the candidate gene reelin (RELN). RELN encodes a signaling protein that plays a pivotal role in the migration of several neuronal cell types and in the development of neural connections. Given these neurodevelopmental functions, recent reports that RELN influences genetic risk for autism are of significant interest. The total data set consists of 218 Caucasian families collected by our group, 85 Caucasian families collected by AGRE, and 68 Caucasian families collected at Tufts University were tested for genetic association of RELN variants to autism. Markers included five single-nucleotide polymorphisms (SNPs) and a repeat in the 5'-untranslated region (5'-UTR). Tests for association in Duke and AGRE families were also performed on four additional SNPs in the genes PSMC2 and ORC5L, which flank RELN. Family-based association analyses (PDT, Geno-PDT, and FBAT) were used to test for association of single-locus markers and multilocus haplotypes with autism. The most significant association identified from this combined data set was for the 5'-UTR repeat (PDT P-value=0.002). These analyses show the potential of RELN as an important contributor to genetic risk in autism.

Role of thioredoxin in the response of normal and transformed cells to histone deacetylase inhibitors

This study examines the basis of resistance and sensitivity of normal and transformed cells to histone deacetylase inhibitor (HDACi)-induced cell death, specifically the role of caspases and thioredoxin (Trx). An important attribute of HDACis is that they induce cancer cell death at concentrations to which normal cells are relatively resistant, making them well suited for cancer therapy. The mechanism underlying this selectivity has not been understood. In this study we found that the HDACi suberoylanilide hydroxamic acid (SAHA) and MS-275, a benzamide, cause an accumulation of reactive oxygen species (ROS) and caspase activation in transformed but not normal cells. Inhibition of caspases does not block HDACi-induced cell death. These studies provide a possible mechanism that can explain why normal but not certain transformed cells are resistant to HDACi-induced cell death. The HDACi causes an increase in the level of Trx, a major reducing protein for many targets, in normal cells but not in transformed cells. The SAHA-induced increase in Trx activity in normal cells is associated with no increase in ROS accumulation. Transfection of transformed cells with Trx small interfering RNA caused a marked decrease in the level of Trx protein with an increase in ROS, a decrease in cell proliferation, and an increase in sensitivity to SAHA-induced cell death. Thus, Trx, independent of the caspase apoptotic pathway, is an important determinant of resistance of cells to HDACi-induced cell death.

RAS oncogene mutations and outcome of therapy for childhood acute lymphoblastic leukemia

Activating mutations in the RAS oncogenes are among the most common genetic alterations in human cancers, including patients with acute lymphoblastic leukemia (ALL). We sought to define the frequency and spectrum, and possible prognostic importance, of N- and K-RAS mutations in children with ALL treated with contemporary therapy. Leukemic blast DNA from 870 children was analyzed for the presence of activating mutations in the N- or K-RAS oncogenes using a sensitive mutation detection algorithm. RAS mutations were present in the blasts of 131 (15.1%) pediatric ALL patients. The spectrum of mutations included 81 (9.3%) mutations of codons 12/13 of N-RAS, 12 (1.4%) mutations of codon 61 of N-RAS, 39 (4.5%) mutations of codons 12/13 of K-RAS, and 2 (0.2%) mutations of codon 61 of K-RAS. The presence of N- or K-RAS mutations was not associated with white blood cell count at diagnosis, sex, race, extramedullary testicular involvement, central nervous system disease, or NCI/CTEP ALL Risk Group. Patients with an exon 1 K-RAS mutation (codons 12/13) were significantly younger at diagnosis (P=0.001) and less frequently B-lineage phenotype (P=0.01). RAS mutation status did not predict overall survival, event-free survival and disease-free survival. While N- and K-RAS mutations can be identified in 15% of children with newly diagnosed ALL, they do not represent a significant risk factor for outcome using contemporary chemotherapy regimens.

No association between the APOE gene and autism

Autism is a neurodevelopmental disorder characterized by stereotypic and repetitive behavior and interests, together with social and communicative deficiencies. The results of several genomic screens suggest the presence of an autism susceptibility locus on chromosome 19p13.2-q13.4. The apolipoprotein E (APOE) gene on chromosome 19 encodes for a protein, apoE, whose different isoforms (E2, E3, E4) influence neuronal growth. APOE participates in lipid transport and metabolism, repair, growth, and maintenance of axons and myelin during neuronal development. The APOE protein competes with the Reelin protein for VLDL/APOER2 receptor binding. Several studies have reported evidence for an association between autism and the Reelin gene. Based on these data we tested for association between APOE and autism using family-based association methods in a data set of 322 autism families. Three promoter, one intronic, and one 3' UTR single nucleotide polymorphisms (SNPs) in the APOE gene (-491a/t, -427c/t, -219g/t, 113c/g, and 5361c/t) as well as the APOE functional polymorphism (E2, E3, E4) were examined and failed to reveal significant evidence that autism is associated with APOE.

Rodent osteoblastic cells express voltage-sensitive calcium channels lacking a gamma subunit

Voltage-sensitive calcium channels (VSCC) open in response to external stimuli, including calcitropic hormones, that alter plasma membrane calcium (Ca2+) permeability. Ca2+ that enters the cell through these channels serves a second messenger function, eliciting cellular responses that include secretion and changes in gene expression. In osteoblasts, VSCCs serve as key regulators of Ca2+ permeability and are a major class of calcitropic hormone-sensitive Ca2+ channels present in the plasma membrane. The members of the VSCC family exist as a complex of polypeptide subunits that are comprised of a pore-forming alpha1 subunit, an intracellular beta subunit, a dimer of disulfide-linked alpha2 and delta subunits, and in some tissues, a gamma subunit. Previous studies in our laboratory have shown that the major functional alpha1 subunit present in osteoblasts is the alpha1C (CaV1.2). To determine the complement of auxiliary subunits present in rodent osteoblastic cells, we employed RT-PCR using a battery of subunit specific primers and appropriate tissue controls. Immunohistochemistry also was performed, using available subunit specific antibodies, to measure protein expression and localization. Cell types examined included MC3T3-E1 at various stages of differentiation, ROS 17/2.8 osteosarcoma, and primary cultures of rat calvarial osteoblasts. The results indicate that all cells expressed multiple beta subunit classes and alpha2delta dimers, but no gamma subunits, regardless of differentiation state. We propose a structure for the functional osteoblast VSCC that consists of alpha1, beta, alpha2delta subunits and is devoid of a gamma subunit.

Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder

Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain, acting via the GABAA receptors. The GABAA receptors are comprised of several different homologous subunits, forming a group of receptors that are both structurally and functionally diverse. Three of the GABAA receptor subunit genes (GABRB3, GABRA5 and GABRG3) form a cluster on chromosome 15q11-q13, in a region that has been genetically associated with autistic disorder (AutD). Based on these data, we examined 16 single nucleotide polymorphisms (SNPs) located within GABRB3, GABRA5 and GABRG3 for linkage disequilibrium (LD) in 226 AutD families (AutD patients and parents). Genotyping was performed using either OLA (oligonucleotide ligation assay), or SSCP (single strand conformation polymorphism) followed by DNA sequencing. We tested for LD using the Pedigree Disequilibrium Test (PDT). PDT results gave significant evidence that AutD is associated with two SNPs located within the GABRG3 gene (exon5_539T/C, p=0.02 and intron5_687T/C, p=0.03), suggesting that the GABRG3 gene or a gene nearby contributes to genetic risk in AutD.

Life after the screen: making sense of many P-values

A multiple analytic approach may be useful for analyzing complex traits since different methods extract both similar and distinct, but complementary pieces of information from genome screen data on extended pedigrees. We examined the usefulness of combining p-values both across methods and across adjacent markers, taking into account the observed correlation structure among these p-values. To this end, we employed the recently proposed truncated product method [Zaykin et al., Genet Epidemiol, in press]. It appears that this approach is helpful for visualizing priority regions for follow-up analysis and reducing the number of false-positive linkage signals.

[A new lymph-node staging system for gastric cancer]

OBJECTIVE

To evaluate the predictive effects of the new lymph node staging system based on the ratio of the number of metastatic lymph nodes to the total number of dissected lymph nodes comparing with N-staging of the 5th TNM (UICC, 1997).

METHODS

Lymph nodes harvested from operative specimens in 78 patients with gastric cancer were examined histologically. pN staging was carried out according to the two staging systems respectively. In our system, pN0, pN1, pN2, pN3 were defined as lymph node ratio(LNR) 0, <10%, <25% and >25%, respectively. All the patients were followed up and the data were analyzed statistically.

RESULTS

A total of 5388 lymph nodes were found with a mean of 69 per case (range 30-157). Lymph node metastases were detected in 59 patients (75.64%). The 3-year survival rates of pN0, pN1, pN2, pN3 of the new staging system were 100%, 68.42%, 7.58% and 6.78%, respectively.

CONCLUSION

The lymph node ratio is a relative variable, which reflects the degree of metastasis of lymph node, and is more predictable than the UICC 1997 5th N-staging system defined as the numbers of metastatic lymph node.

Crystallization and preliminary X-ray crystallographic analysis of native and selenomethionyl recombinant tabtoxin-resistance protein complexed with acetyl-coenzyme A

Tabtoxin-resistance protein (TTR), an acetyltransferase from Pseudomonas syringae pv. tabaci, was overexpressed in Eschericha coli M15 and the TTR fusion protein complexed with acetyl-coenzyme A (AcCoA) was purified and crystallized. Diffraction data were collected to 3.0 A resolution in-house and the crystal was found to belong to space group P2(1), with unit-cell parameters a = 47.6, b = 66.6, c = 53.5 A, beta = 104.3 degrees. Furthermore, a selenomethionine (SeMet) TTR fusion protein derivative was overexpressed in the same expression system and its complex with AcCoA was purified in a reductive environment. The SeMet TTR derivative crystallized in two forms: the first was identical to that observed for native crystals and the second belonged to space group C2, with unit-cell parameters a = 101.7, b = 45.6, c = 84.2 A, beta = 105.8 degrees. Data from the P2(1) crystal form were collected in-house to 2.3 A resolution. Subsequently, three different wavelength data sets of the C2 crystal form to 1.55 A resolution were collected at the Advanced Photon Source at Argonne National Laboratory.

Fabrication of nanometer-sized electrodes and tips for scanning electrochemical microscopy

A novel method for fabrication of nanometer-sized electrodes and tips suitable for scanning electrochemical microscopy (SECM) is reported. A fine etched Pt wire is coated with polyimide, which was produced by polymerization on the Pt surface initiated by heat. This method can prepare electrodes with effective radii varying from a few to hundreds of nanometers. Scanning electron microscopy, cyclic voltammetry, and SECM were used to characterize these electrodes. Well-defined steady-state voltammograms could be obtained in aqueous or in 1,2-dichloroethane solutions. This method produced the nanoelectrodes with exposed Pt on the apex, and they can also be employed as the nanotips for SECM investigations. Different sizes of Pt nanotips made by this method were employed to evaluate the kinetics of the redox reaction of Ru(NH3)6(3+) on the surface of a large Pt electrode by SECM, and the standard rate constant kappa0 of this system was calculated from the best fit of the SECM approach curve. This result is similar to the values obtained by analysis of the obtained voltammetric data.

Determination of lomefloxacin, an antibacterial drug, in pharmaceutical preparations based on its polarographic catalytic wave in the presence of 2-iodoacetamide

In a 0.125 mol/L phosphate (pH 6.6)/2.5 x 10(-4) mol/L 2-iodoacetamide solution, lomefloxacin yields a response of a polarographic catalytic current. The second-order derivative peak current of the catalytic wave of lomefloxacin is proportional to its concentration in the range of 1.0 x 10(-8)-1.0 x 10(-6) mol/L (r = 0.998). The sensitivity of the catalytic wave is 25-times higher than that of the corresponding reduction wave for 5.0 x 10(-7) mol/L lomefloxacin. The proposed method was applied to the determination of lomefloxacin in pharmaceutical preparations. The polarographic reduction wave is ascribed to a one-electron reduction of the C=C bond of lomefloxacin zwitterion accompanied by an acid-base equilibrium. The catalytic wave should be caused by regeneration of the lomefloxacin molecule at electrode surface due to the one-electron reduction product being further oxidized by electroreductive intermediate products of 2-iodoacetamide.

[Combined high dose chemotherapy with autologous stem cell transplantation and total body radiotherapy for 32 malignant lymphoma patients]

OBJECTIVE

To evaluate the effect of high dose chemotherapy with or without total body irradiation (TBI) supported by autologous hematopoietic stem cell transplantation (AHSCT) for malignant lymphoma.

METHODS

From June 1991 to April 2000, 32 malignant lymphoma (ML) patients were treated with AHSCT. Their ages ranged from 19 to 52 years (median 37). There were 23 non-Hodgkin's lymphoma (NHL) and 9 Hodgkin's lymphom (HD). Twelve patients received autologous bone marrow transplantation (ABMT) and 20 patients received autologous peripheral blood stem cell transplantation (APBSCT). In the latter, the mobilization plan was carboplatin and etoposide (CE) or CHOP (CTX, ADM, VCR, PDN) plus G/GM-CSF 10 micrograms/kg/d in high dose chemotherapy. BEAM (BCNU, Vp-16, AraC, MEL) or MEL 140 mg/m2 + Vp-16 200 mg + total body irradiation (TBI) 8 Gy.

RESULTS

Up to May 2000, hematopoietic reconstitution was reestabished in 100% (32/32) patients after AHSCT, with median follow-up of 1,020 days (40-3,240). The 1- and 2-year disease-free survivals (DFS) were 78.1%(25/32) and 46.9% (15/32) with the longest survival of 8 years. Even though eight patients have developed relapse, there is no transplantation-related death.

CONCLUSION

High dose chemotherapy and radiotherapy supported by autologous hematopoietic stem cell transplantation (AHSCT) for high risk, relapsed or sensitive ML, being highly efficient, should be the first indication. It is better than the standard conventional treatment. The hematopoietic reconstitution of autologous peripheral blood stem cell transplantation (APBSCT) is quicker than autologous bone marrow transplantation (ABMT). No significant difference between chemotherapy alone and chemotherapy plus total body irradiation is observed.

Ultraviolet irradiation increases matrix metalloproteinase-8 protein in human skin in vivo

Humans express three distinct collagenases, MMP-1, MMP-8, and MMP-13, that initiate degradation of fibrillar type I collagen. We have previously reported that ultraviolet irradiation causes increased expression of MMP-1, but not MMP-13, in keratinocytes and fibroblasts in human skin in vivo. We report here that ultraviolet irradiation increases expression of MMP-8 in human skin in vivo. Western analysis revealed that levels of the full-length, 85 kDa proenzyme form of MMP-8 increased significantly within 8 h post ultraviolet irradiation (2 minimal erythema doses). Increased full-length MMP-8 protein was associated with infiltration into the skin of neutrophils, which are the major cell type that expresses MMP-8. Immunofluorescence revealed coexpression of MMP-8 and neutrophil elastase, a marker for neutrophils. Immunohistology demonstrated MMP-8 expression in neutrophils in the papillary dermis between 4 and 8 h post ultraviolet irradiation, and in the epidermis at 24 h post radiation. MMP-8 mRNA expression was not detected in nonirradiated or ultraviolet-irradiated human skin, indicating that increased MMP-8 following ultraviolet irradiation resulted from preexisting MMP-8 protein in infiltrating neutrophils. Pretreatment of skin with the glucocorticoid clobetasol, but not all-trans retinoic acid, significantly blocked ultraviolet-induced increases in MMP-8 protein levels, and neutrophil infiltration. In contrast, all-trans retinoic acid and clobetasol were equally effective in blocking ultraviolet induction of MMP-1 and degradation of collagen in human skin in vivo. Taken together, these data demonstrate that ultraviolet irradiation increases MMP-8 protein, which exists predominantly in a latent form within neutrophils, in human skin in vivo. Although ultraviolet irradiation induces both MMP-1 and MMP-8, ultraviolet-induced collagen degradation is initiated primarily by MMP-1, with little, if any, contribution by MMP-8.

Sequence-selective peptide detection by small synthetic chemosensors selected from an encoded combinatorial chemosensor library

Synthetic chemosensors hold great potential in many diagnostic applications. In this study, we describe the design and preparation of the first encoded combinatorial library of chemosensors for tripeptides. Subsequent screening of the library resulted in the discovery of novel chemosensors able to distinguish between random tripeptides.