Tumor specimen cold ischemia time impacts molecular cancer drug target discovery.

Tumor tissue collections are used to uncover pathways associated with disease outcomes that can also serve as targets for cancer treatment, ideally by comparing the molecular properties of cancer tissues to matching normal tissues. The quality of such collections determines the value of the data and information generated from their analyses including expression and modifications of nucleic acids and proteins. These biomolecules are dysregulated upon ischemia and decompose once the living cells start to decay into inanimate matter. Therefore, ischemia time before final tissue preservation is the most important determinant of the quality of a tissue collection. Here we show the impact of ischemia time on tumor and matching adjacent normal tissue samples for mRNAs in 1664, proteins in 1818, and phosphosites in 1800 cases (tumor and matching normal samples) of four solid tumor types (CRC, HCC, LUAD, and LUSC NSCLC subtypes). In CRC, ischemia times exceeding 15 min impacted 12.5% (mRNA), 25% (protein), and 50% (phosphosites) of differentially expressed molecules in tumor versus normal tissues. This hypoxia- and decay-induced dysregulation increased with longer ischemia times and was observed across tumor types. Interestingly, the proteomics analysis revealed that specimen ischemia time above 15 min is mostly associated with a dysregulation of proteins in the immune-response pathway and less so with metabolic processes. We conclude that ischemia time is a crucial quality parameter for tissue collections used for target discovery and validation in cancer research.

Role for LAMP-2 in endosomal cholesterol transport.

The mechanisms of endosomal and lysosomal cholesterol traffic are still poorly understood. We showed previously that unesterified cholesterol accumulates in the late endosomes and lysosomes of fibroblasts deficient in both lysosome associated membrane protein-2 (LAMP-2) and LAMP-1, two abundant membrane proteins of late endosomes and lysosomes. In this study we show that in cells deficient in both LAMP-1 and LAMP-2 (LAMP(-/-)), low-density lipoprotein (LDL) receptor levels and LDL uptake are increased as compared to wild-type cells. However, there is a defect in esterification of both endogenous and LDL cholesterol. These results suggest that LAMP(-/-) cells have a defect in cholesterol transport to the site of esterification in the endoplasmic reticulum, likely due to defective export of cholesterol out of late endosomes or lysosomes. We also show that cholesterol accumulates in LAMP-2 deficient liver and that overexpression of LAMP-2 retards the lysosomal cholesterol accumulation induced by U18666A. These results point to a critical role for LAMP-2 in endosomal/lysosomal cholesterol export. Moreover, the late endosomal/lysosomal cholesterol accumulation in LAMP(-/-) cells was diminished by overexpression of any of the three isoforms of LAMP-2, but not by LAMP-1. The LAMP-2 luminal domain, the membrane-proximal half in particular, was necessary and sufficient for the rescue effect. Taken together, our results suggest that LAMP-2, its luminal domain in particular, plays a critical role in endosomal cholesterol transport and that this is distinct from the chaperone-mediated autophagy function of LAMP-2.

The human SUMF1 gene, required for posttranslational sulfatase modification, defines a new gene family which is conserved from pro- to eukaryotes.

Recently, the human C(alpha)-formylglycine (FGly)-generating enzyme (FGE), whose deficiency causes the autosomal-recessively transmitted lysosomal storage disease multiple sulfatase deficiency (MSD), has been identified. In sulfatases, FGE posttranslationally converts a cysteine residue to FGly, which is part of the catalytic site and is essential for sulfatase activity. FGE is encoded by the sulfatase modifying factor 1 (SUMF1) gene, which defines a new gene family comprising orthologs from prokaryotes to higher eukaryotes. The genomes of E. coli, S. cerevisiae and C. elegans lack SUMF1, indicating a phylogenetic gap and the existence of an alternative FGly-generating system. The genomes of vertebrates including mouse, man and pufferfish contain a sulfatase modifying factor 2 (SUMF2) gene encoding an FGE paralog of unknown function. SUMF2 evolved from a single exon SUMF1 gene as found in diptera prior to divergent intron acquisition. In several prokaryotic genomes, the SUMF1 gene is cotranscribed with genes encoding sulfatases which require FGly modification. The FGE protein contains a single domain that is made up of three highly conserved subdomains spaced by nonconserved sequences of variable lengths. The similarity among the eukaryotic FGE orthologs varies between 72% and 100% for the three subdomains and is highest for the C-terminal subdomain, which is a hotspot for mutations in MSD patients.

Xenopus Dead end mRNA is a localized maternal determinant that serves a conserved function in germ cell development.

Germ plasm formation is considered to define the first step in germ cell development. Xenopus Dead end represents a germ plasm specific transcript that is homologous to the previously characterized zebrafish dead end, which is required for germ cell migration and survival. XDead end mRNA localizes to the vegetal pole of Xenopus oocytes; in contrast to all other known germ plasm associated transcripts in Xenopus, XDead end is transported via the late transport pathway, suggesting a different mode of germ plasm restriction. Vegetal localization in the oocyte is achieved via a localization element mapping to a 251 nucleotide element in the 3'-UTR. This RNA sequence binds to a set of proteins characteristic for the late localization pathway and to one additional protein of 38 kDa. Inhibition of XDead end translation in Xenopus embryos results in a loss of primordial germ cells at tadpole stages of development. Early specification events do not seem to be affected, but the primordial germ cells fail to migrate dorsally and eventually disappear. This phenotype is very similar to what has been observed in the zebrafish, indicating that the role of XDead end in germ cell development has been conserved in evolution.

LAMP-2 deficient mice show depressed cardiac contractile function without significant changes in calcium handling.

OBJECTIVE: Mutations in the highly glycosylated lysosome associated membrane protein-2 (LAMP-2) cause, as recently shown, familial Danon disease with mental retardation, mild myopathy and fatal cardiomyopathy. Extent and basis of the contractile dysfunction is not completely understood. METHODS: In LAMP-2 deficient mice, we investigated cardiac function in vivo using Doppler-echocardiography and contractile function in vitro in isolated myocardial trabeculae. RESULTS: LAMP-2 deficient mice displayed reduced ejection fraction (EF) (58.9+/-3.4 vs. 80.7+/-5.1%, P<0.05) and reduced cardiac output (8.3+/-3.1 vs. 14.7+/-3.6 ml/min, P<0.05) as compared to wild-type controls. Isolated multicellular muscle preparations from LAMP-2 deficient mice confirmed depressed force development (3.2+/-0.6 vs. 8.4+/-0.9 mN/mm2, P<0.01). All groups showed similar force-frequency behaviour when normalised to baseline force. Post-rest potentiation was significantly depressed at intervals>15 s in LAMP-2 deficient mice (P<0.05). Although attenuated in absolute force development, the normalised inotropic response to increased calcium and beta-adrenoreceptor stimulation was unaltered. Electron microscopic analysis revealed autophagic vacuoles in LAMP-2 deficient cardiomyocytes. Protein analysis showed unaltered levels of SERCA2a, calsequestrin and phospholamban. CONCLUSIONS: Cardiac contractile function in LAMP-2 deficient mice as a model for Danon disease is significantly attenuated. The occurrence of autophagic vacuoles in LAMP-2 deficient myocytes is likely to be causal for the depressed contractile function resulting in an attenuated cardiac pump reserve.

Chlamydia trachomatis modulates expression of tumor suppressor gene caveolin-1 and oncogene C-myc in the transformation zone of non-neoplastic cervical tissue.

OBJECTIVES: The obligate intracellular bacterium Chlamydia trachomatis is frequently found in association with benign proliferative, pre-neoplastic and malignant changes in cervical epithelium. The present study addresses the possible role of C. trachomatis infection of the uterine cervix in modulating human cancer gene expression. METHODS: RNA was extracted from both C. trachomatis infected and non-infected human fibroblast cultures treated with ITFgamma. The extracted RNA was used for cDNA microarrays carrying 33,000 human genes to detect abnormal gene expression induced by Chlamydia. Forty specimens of cervix dissected from the transformation zone had previously tested negative for HPV and positive for C. trachomatis by standard DNA PCR (20). These samples were subjected to RT-PCR to detect the expression of the abnormal genes induced by Chlamydia infection. RESULTS: The ITFgamma-induced, non-replicative Chlamydia-infected fibroblast cultures showed significant modulation of gene expression. The cultures showed a 2-fold decrease in the expression of the gene coding for the tumor suppressor caveolin-1, and increased expression of the oncogene C-myc, a promoter of cervical carcinogenesis. In tissues from the Chlamydia-infected cervical transformation zone, real-time RT-PCR demonstrated a highly significant average 4.7-fold reduction of caveolin-1 mRNA (P < or = 0.0001) and an average 2.1-fold increase in C-myc (P < 0.05). CONCLUSIONS: Human ITFgamma-treated fibroblasts as well as non-neoplastic cervical tissues responded to C. trachomatis with a strong down-regulation of caveolin-1 mRNA and a light up-regulation of C-myc mRNA. These changes were independent of the HPV high-risk types. This study reveals possible mechanisms by which C. trachomatis infection may contribute to neoplastic changes in the transformation of uterine cervix. These possible mechanisms require further evaluation.

Mannose 6-phosphate receptors, Niemann-Pick C2 protein, and lysosomal cholesterol accumulation.

Niemann-Pick disease type C (NPC), caused by mutations in the NPC1 gene or the NPC2 gene, is characterized by the accumulation of unesterified cholesterol and other lipids in endo/lysosomal compartments. NPC2 is a small, soluble, lysosomal protein that is targeted to this compartment via a mannose 6-phosphate-inhibitable pathway. To obtain insight into the roles of mannose 6-phosphate receptors (MPRs) in NPC2 targeting, we here examine the trafficking and function of NPC2 in fibroblast lines deficient in one or both of the two MPRs, MPR46 and MPR300. We demonstrate that either MPR alone is sufficient to transport NPC2 to the endo/lysosomal compartment, although MPR300 seems to be more efficient than MPR46. In the absence of both MPRs, NPC2 is secreted into the culture medium, and only a small amount of intracellular NPC2 can be detected, mainly in the endoplasmic reticulum. This leads to massive accumulation of unesterified cholesterol in the endo/lysosomal compartment of the MPR46/300-deficient fibroblasts, a phenotype similar to that of the NPC patient fibroblasts. In addition, we observed an upregulation of NPC1 protein and mRNA in the MPR-double-deficient cells. Taken together, our results suggest that the lysosomal targeting of NPC2 is strictly dependent on MPRs in fibroblasts.

Efficient two-sample designs for microarray experiments with biological replications.

In the last years, biostatistical research has begun to apply linear models and design theory to develop efficient experimental designs and analysis tools for gene expression microarray data. With two-colour microarrays, direct comparisons of RNA-targets are possible and lead to incomplete block designs. In this setting, efficient designs for simple and factorial microarray experiments have mainly been proposed for technical replicates. But for biological replicates, which are crucial to obtain inference that can be generalised to a biological population, this question has only been discussed recently and is not fully solved yet. In this paper, we propose efficient designs for independent two-sample experiments using two-colour microarrays enabling biologists to measure their biological random samples in an efficient manner to draw generalisable conclusions. We give advice for experimental situations with differing group sizes and show the impact of different designs on the variance and degrees of freedom of the test statistics. The designs proposed in this paper can be evaluated using SAS PROC MIXED or S+/R lme.

Permutation-validated principal components analysis of microarray data.

BACKGROUND: In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the assessment of the reliability of gene-selection procedures. Here we describe a method to assess reliability in multivariate microarray data analysis using permutation-validated principal components analysis (PCA). The approach is designed for microarray data with a group structure. RESULTS: We used PCA to detect the major sources of variance underlying the hybridization conditions followed by gene selection based on PCA-derived and permutation-based test statistics. We validated our method by applying it to well characterized yeast cell-cycle data and to two datasets from our laboratory. We could describe the major sources of variance, select informative genes and visualize the relationship of genes and arrays. We observed differences in the level of the explained variance and the interpretability of the selected genes. CONCLUSIONS: Combining data visualization and permutation-based gene selection, permutation-validated PCA enables one to illustrate gene-expression variance between several conditions and to select genes by taking into account the relationship of between-group to within-group variance of genes. The method can be used to extract the leading sources of variance from microarray data, to visualize relationships between genes and hybridizations and to select informative genes in a statistically reliable manner. This selection accounts for the level of reproducibility of replicates or group structure as well as gene-specific scatter. Visualization of the data can support a straightforward biological interpretation.