Ultrasonography in the Assessment of Tumors of the Cheek: Water Mouth Distension Technique.

PURPOSE: To describe a new B-mode ultrasound examination technique to assess cheek tumors. MATERIALS AND METHODS: 30 cheek oral cavity lesions of different histological types (11 benign and 19 malignant) from 23 patients (11 women and 12 men, 7-82 years old, mean age of 49.5 years) were analyzed. Transcutaneous oral B-mode ultrasound (5-12 MHz transducer) was carried out in two stages. Initially it was performed conventionally with an empty mouth. Next, the patient was asked to keep their oral cavity filled with water (like when using a mouthwash) during imaging for the new test examination technique. The anatomical layers of this region and the characteristics of the tumors were evaluated. Lesions were classified as ill defined, partially defined, or defined. Conventional findings were compared to those of the new technique using the Wilcoxon signed-rank test. Ultrasound results were compared to histological findings analyzed by an independent team. RESULTS: The conventional empty mouth technique was able to confidently define lesion extension in only 6 of the 30 lesions, while the water-filled mouth technique was able to confidently define lesion extension in 29 of the 30 lesions (p<0.00001). CONCLUSION: We present a novel technique that dramatically improves ultrasound staging of cheek oral cavity tumors. In addition to the increase in ultrasound accuracy, this technique does not require any special equipment or extra cost, is very well tolerated by patients, and thus should be considered in the evaluation of every patient undergoing transcutaneous cheek ultrasound for oral cavity lesion characterization.

Synthetic polypeptide crotamine: characterization as a myotoxin and as a target of combinatorial peptides.

Crotamine is a rattlesnake-derived toxin that causes fast-twitch muscle paralysis. As a cell-penetrating polypeptide, crotamine has been investigated as an experimental anti-cancer and immunotherapeutic agent. We hypothesized that molecules targeting crotamine could be designed to study its function and intervene in its adverse activities. Here, we characterize synthetic crotamine and show that, like the venom-purified toxin, it induces hindlimb muscle paralysis by affecting muscle contraction and inhibits KCNA3 (Kv1.3) channels. Synthetic crotamine, labeled with a fluorophore, displayed cell penetration, subcellular myofiber distribution, ability to induce myonecrosis, and bind to DNA and heparin. Here, we used this functionally validated synthetic polypeptide to screen a combinatorial phage display library for crotamine-binding cyclic peptides. Selection for tryptophan-rich peptides was observed, binding of which to crotamine was confirmed by ELISA and gel shift assays. One of the peptides (CVWSFWGMYC), synthesized chemically, was shown to bind both synthetic and natural crotamine and to block crotamine-DNA binding. In summary, our study establishes a functional synthetic substitute to the venom-derived toxin and identifies peptides that could further be developed as probes to target crotamine. KEY MESSAGES: Synthetic crotamine was characterized as a functional substitute for venom-derived crotamine based on myotoxic effects. A combinatorial peptide library was screened for crotamine-binding peptides. Tryptophan-rich peptides were shown to bind to crotamine and interfere with its DNA binding. Crotamine myofiber distribution and affinity for tryptophan-rich peptides provide insights on its mechanism of action.

Toxin bioportides: exploring toxin biological activity and multifunctionality.

Toxins have been shown to have many biological functions and to constitute a rich source of drugs and biotechnological tools. We focus on toxins that not only have a specific activity, but also contain residues responsible for transmembrane penetration, which can be considered bioportides-a class of cell-penetrating peptides that are also intrinsically bioactive. Bioportides are potential tools in pharmacology and biotechnology as they help deliver substances and nanoparticles to intracellular targets. Bioportides characterized so far are peptides derived from human proteins, such as cytochrome c (CYCS), calcitonin receptor (camptide), and endothelial nitric oxide synthase (nosangiotide). However, toxins are usually disregarded as potential bioportides. In this review, we discuss the inclusion of some toxins and molecules derived thereof as a new class of bioportides based on structure activity relationship, minimization, and biological activity studies. The comparative analysis of the amino acid residue composition of toxin-derived bioportides and their short molecular variants is an innovative analytical strategy which allows us to understand natural toxin multifunctionality in vivo and plan novel pharmacological and biotechnological products. Furthermore, we discuss how many bioportide toxins have a rigid structure with amphiphilic properties important for both cell penetration and bioactivity.

Allogeneic Mesenchymal Stem Cell Transplantation in Dogs With Keratoconjunctivitis Sicca.

Keratoconjunctivitis sicca (KCS) is a dysfunction in tear production associated with clinical signs, which include conjunctival hyperemia, ocular discharge, discomfort, pain, and, eventually, corneal vascularization and pigmentation. Immunosuppressive drugs are routinely administrated for long periods to treat KCS but with side effects and limited results. Evaluation of the clinical benefits of intralacrimal transplantation of allogeneic mesenchymal stem cells (MSCs) in dogs with mild-moderate and severe KCS was done. A total of 24 eyes with KCS from 15 dogs of different breeds were enrolled in the present study. A single transplantation of MSCs (1 × 106) directly into lacrimal glands (dorsal and third eyelid) was performed. The Schirmer tear tests (STTs) and ocular surface improvements were used to assess short- and long-term effects of these cells. The STTs were carried out on day 0 (before MSCs transplantation) and on days 7, 14, 21, and 28, as well as 6 and 12 months after MSC transplantation. Our data demonstrate that allogeneic MSC transplantation in KCS dogs is safe since no adverse effects were observed immediately after transplantation and in short- and long-term follow-ups. A statistically significant increase in the STT and ocular surface improvements was found in all eyes studied. In all the eyes with mild-moderate KCS, STT values reverted to those of healthy eyes, while in eyes with severe KCS, although complete reversion was not found, there was improvement in tear production and in other clinical signs. Our study shows that a single dose of a low number of MSCs can be used to treat KCS in dogs. In contrast to immunosuppressive drug use, MSC transplantation has an effect over a long period (up to 12 months), even after a single administration, and does not require daily drug administration.

Cell-based technologies for Huntington's disease / Tecnologias celulares no doença de Huntington

ABSTRACT Huntington's disease (HD) is a fatal genetic disorder, which causes the progressive breakdown of neurons in the human brain. HD deteriorates human physical and mental abilities over time and has no cure. Stem cell-based technologies are promising novel treatments, and in HD, they aim to replace lost neurons and/or to prevent neural cell death. Herein we discuss the use of human fetal tissue (hFT), neural stem cells (NSCs) of hFT origin or embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs), in clinical and pre-clinical studies. The in vivo use of mesenchymal stem cells (MSCs), which are derived from non-neural tissues, will also be discussed. All these studies prove the potential of stem cells for transplantation therapy in HD, demonstrating cell grafting and the ability to differentiate into mature neurons, resulting in behavioral improvements. We claim that there are still many problems to overcome before these technologies become available for HD patient treatment, such as: a) safety regarding the use of NSCs and pluripotent stem cells, which are potentially teratogenic; b) safety regarding the transplantation procedure itself, which represents a risk and needs to be better studied; and finally c) technical and ethical issues regarding cells of fetal and embryonic origin.

RESUMO A doença de Huntington (DH) é uma desordem genética que provoca a destruição progressiva dos neurônios no cérebro humano. A DH deteriora progressivamente as habilidades físicas e mentais humanas, e é incurável. Tecnologias terapêuticas baseadas em células representam novas alternativas para diversas doenças neurodegenerativas, pois visam substituir neurônios e/ou prevenir a morte neuronal. Nesta revisão discutirmos o uso de tecido fetal humano, células tronco neurais (CTN) de origem fetal ou de células tronco embrionárias ou células tronco pluripotentes induzidas, em estudos pré-clínicos e clínicos. Além disso, o uso terapêutico de células derivadas de tecidos não-neurais, como células tronco mesenquimais, também será discutido. Todos estes estudos provam o potencial do transplante celular na DH, demonstrando a sua habilidade em enxertar no encéfalo e diferenciar em neurônios in vivo, resultando em melhorias comportamentais e motoras em modelos animais da DH. Nós também discutimos que há muitos problemas a serem resolvidos quanto à terapia celular na DH, tais como: a) questões associadas à segurança do uso de CTNs, as quais são consideradas potencialmente teratogênicas; b) segurança do procedimento de transplante intracerebral, que representa um risco ao paciente; c) e, finalmente, questões técnicas e éticas associadas ao uso de células de origem fetal e embrionária.

Cell-based technologies for Huntington's disease.

Huntington's disease (HD) is a fatal genetic disorder, which causes the progressive breakdown of neurons in the human brain. HD deteriorates human physical and mental abilities over time and has no cure. Stem cell-based technologies are promising novel treatments, and in HD, they aim to replace lost neurons and/or to prevent neural cell death. Herein we discuss the use of human fetal tissue (hFT), neural stem cells (NSCs) of hFT origin or embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs), in clinical and pre-clinical studies. The in vivo use of mesenchymal stem cells (MSCs), which are derived from non-neural tissues, will also be discussed. All these studies prove the potential of stem cells for transplantation therapy in HD, demonstrating cell grafting and the ability to differentiate into mature neurons, resulting in behavioral improvements. We claim that there are still many problems to overcome before these technologies become available for HD patient treatment, such as: a) safety regarding the use of NSCs and pluripotent stem cells, which are potentially teratogenic;b) safety regarding the transplantation procedure itself, which represents a risk and needs to be better studied; and finallyc) technical and ethical issues regarding cells of fetal and embryonic origin.

A doença de Huntington (DH) é uma desordem genética que provoca a destruição progressiva dos neurônios no cérebro humano. A DH deteriora progressivamente as habilidades físicas e mentais humanas, e é incurável. Tecnologias terapêuticas baseadas em células representam novas alternativas para diversas doenças neurodegenerativas, pois visam substituir neurônios e/ou prevenir a morte neuronal. Nesta revisão discutirmos o uso de tecido fetal humano, células tronco neurais (CTN) de origem fetal ou de células tronco embrionárias ou células tronco pluripotentes induzidas, em estudos pré-clínicos e clínicos. Além disso, o uso terapêutico de células derivadas de tecidos não-neurais, como células tronco mesenquimais, também será discutido. Todos estes estudos provam o potencial do transplante celular na DH, demonstrando a sua habilidade em enxertar no encéfalo e diferenciar em neurônios in vivo, resultando em melhorias comportamentais e motoras em modelos animais da DH. Nós também discutimos que há muitos problemas a serem resolvidos quanto à terapia celular na DH, tais como:a) questões associadas à segurança do uso de CTNs, as quais são consideradas potencialmente teratogênicas;b) segurança do procedimento de transplante intracerebral, que representa um risco ao paciente;c) e, finalmente, questões técnicas e éticas associadas ao uso de células de origem fetal e embrionária.

Blood-based protein biomarker panel for the detection of colorectal cancer.

BACKGROUND: The majority of colorectal cancer (CRC) cases are preventable by early detection and removal of precancerous polyps. Even though CRC is the second most common internal cancer in Australia, only 30 per cent of the population considered to have risk factors participate in stool-based test screening programs. Evidence indicates a robust, blood-based, diagnostic assay would increase screening compliance. A number of potential diagnostic blood-based protein biomarkers for CRC have been reported, but all lack sensitivity or specificity for use as a stand-alone diagnostic. The aim of this study was to identify and validate a panel of protein-based biomarkers in independent cohorts that could be translated to a reliable, non-invasive blood-based screening test. PRINCIPAL FINDINGS: In two independent cohorts (n = 145 and n = 197), we evaluated seven single biomarkers in serum of CRC patients and age/gender matched controls that showed a significant difference between controls and CRC, but individually lack the sensitivity for diagnostic application. Using logistic regression strategies, we identified a panel of three biomarkers that discriminated between controls and CRC with 73% sensitivity at 95% specificity, when applied to either of the two cohorts. This panel comprised of Insulin like growth factor binding protein 2 (IGFBP2), Dickkopf-3 (DKK3), and Pyruvate kinase M2(PKM2). CONCLUSIONS: Due to the heterogeneous nature of CRC, a single biomarker is unlikely to have sufficient sensitivity or specificity for use as a stand-alone diagnostic screening test and a panel of markers may be more effective. We have identified a 3 biomarker panel that has higher sensitivity and specificity for early stage (Stage I and -II) disease than the faecal occult blood test, raising the possibility for its use as a non-invasive blood diagnostic or screening test.

Colorectal cancer biomarkers: to be or not to be? Cautionary tales from a road well travelled.

Colorectal cancer (CRC) is the second most common cause of cancer-related death worldwide and places a major economic burden on the global health care system. The time frame for development from premalignant to malignant disease typically spans 10-15 years, and this latent period provides an ideal opportunity for early detection and intervention to improve patient outcomes. Currently, early diagnosis of CRC is hampered by a lack of suitable non-invasive biomarkers that are clinically or economically acceptable for population-based screening. New blood-based protein biomarkers for early detection of CRC are therefore urgently required. The success of clinical biomarker discovery and validation studies is critically dependent on understanding and adjusting for potential experimental, analytical, and biological factors that can interfere with the robust interpretation of results. In this review we outline some important considerations for research groups undertaking biomarker research with exemplars from our studies. Implementation of experimental strategies to minimise the potential effects of these problems will facilitate the identification of panels of biomarkers with the sensitivity and specificity required for the development of successful tests for the early detection and surveillance of CRC.

Increasing trends of sleep complaints in the city of Sao Paulo, Brazil.

OBJECTIVE: The aim of this study was to compare the prevalence of sleep habits and complaints and to estimate the secular trends through three population-based surveys carried out in 1987, 1995, and 2007 in the general adult population of the city of Sao Paulo, Brazil. METHODS: Surveys were performed using the same three-stage cluster-sampling technique in three consecutive decades to obtain representative samples of the inhabitants of Sao Paulo with respect to gender, age (20-80 years), and socio-economic status. Sample sizes were 1000 volunteers in 1987 and 1995 surveys and 1101 in a 2007 survey. In each survey, the UNIFESP Sleep Questionnaire was administered face-to-face in each household selected. RESULTS: For 1987, 1995, and 2007, respectively, difficulty initiating sleep (weighted frequency %; 95% CI) [(13.9; 11.9-16.2), (19.15; 16.8-21.6), and (25.0; 22.5-27.8)], difficulty maintaining sleep [(15.8; 13.7-18.2), (27.6; 24.9-30.4), and (36.5; 33.5-39.5)], and early morning awakening [(10.6; 8.8-12.7), (14.2; 12.2-16.5), and (26.7; 24-29.6)] increased in the general population over time, mostly in women. Habitual snoring was the most commonly reported complaint across decades and was more prevalent in men. There was no statistically significant difference in snoring complaints between 1987 (21.5; 19.1-24.2) and 1995 (19.0; 16.7-21.6), but a significant increase was noted in 2007 (41.7; 38.6-44.8). Nightmares, bruxism, leg cramps, and somnambulism complaints were significantly higher in 2007 compared to 1987 and 1995. All were more frequent in women. CONCLUSIONS: This is the first study comparing sleep complaints in probabilistic population-based samples from the same metropolitan area, using the same methodology across three consecutive decades. Clear trends of increasing sleep complaints were observed, which increased faster between 1995 and 2007 than from 1987 to 1995. These secular trends should be considered a relevant public health issue and support the need for development of health care and educational strategies to supply the population's increased need for information on sleep disorders and their consequences.

Epigenetic silencing of manganese superoxide dismutase (SOD-2) in KAS 6/1 human multiple myeloma cells increases cell proliferation.

The generation of reactive oxygen species (ROS) by mitochondrial electron transport chain (ETC) and oxidative phosphorylation activity, has been linked to modifications of multiple molecular processes, including lipid peroxidation, signaling pathway and transcription factor modulation, and oxidative damage to DNA. Oxidative damage by endogenous ROS has been associated with the etiology of various pathological states. There are numerous reports that levels of manganese superoxide dismutase enzyme (MnSOD), an antioxidant enzyme responsible for the attenuation of ROS, are lowered in cancer cells, but the reasons for this reduction are poorly defined. Epigenetic silencing of genes involved in tumor suppression and DNA repair is known to occur in a variety of malignant cell types. Here we report that in the human multiple myeloma cell line KAS 6/1, the SOD-2 gene, encoding manganese superoxide dismutase, is epigenetically silenced as a result of promoter hypermethylation. The DNA methyltransferase inhibitor Zebularine reverses SOD-2 promoter methylation, increasing gene expression and enzyme levels. Infection of KAS 6/1 cells with a recombinant adenovirus carrying the MnSOD cDNA reduced the cell proliferation rate by approximately one-half, confirming the detrimental effects of epigenetic silencing of SOD-2 expression.

Comparative toxicity of oleic acid and linoleic acid on Raji cells.

OBJECTIVE: Parenteral diets are often administered to critically ill patients. To study one of the effects of commercially available parenteral lipid diets, rich in triacylglycerol esters of omega-6 polyunsaturated fatty acids or omega-9 monounsaturated fatty acids, on the immune system of such patients, we evaluated the cytotoxicity of oleic and linoleic acids on Raji cells that had been derived from human B-lymphocytes. METHODS: Cell death intensity and type were investigated by flow cytometry by quantitation of cell volume, granularity, DNA fragmentation, mitochondrial depolarization, and lipid accumulation. Fluorescence microscopy was used to determine chromatin condensation and type of cell death (acridine orange/ethidium bromide assay). Gene expression of BCL-XL, BCL-XS, C-MYC, and P53 was studied by reverse transcriptase polymerase chain reaction. RESULTS: Oleic acid was less toxic than linoleic acid to Raji cells. Both fatty acids promote apoptosis and necrosis of these cells. The mechanism of cell death induced by these fatty acids seemed to involve mitochondrial depolarization, lipid accumulation, and overexpression of C-MYC and P53. CONCLUSION: Oleic acid may offer a less harmful alternative to linoleic acid in parenteral diets with respect to patient B-lymphocyte-mediated immunologic activity.

Differential expression of genes within the cochlea as defined by a custom mouse inner ear microarray.

Microarray analyses have contributed greatly to the rapid understanding of functional genomics through the identification of gene networks as well as gene discovery. To facilitate functional genomics of the inner ear, we have developed a mouse inner-ear-pertinent custom microarray chip (CMA-IE1). Nonredundant cDNA clones were obtained from two cDNA library resources: the RIKEN subtracted inner ear set and the NIH organ of Corti library. At least 2000 cDNAs unique to the inner ear were present on the chip. Comparisons were performed to examine the relative expression levels of these unique cDNAs within the organ of Corti, lateral wall, and spiral ganglion. Total RNA samples were obtained from the three cochlear-dissected fractions from adult CF-1 mice. The total RNA was linearly amplified, and a dendrimer-based system was utilized to enhance the hybridization signal. Differentially expressed genes were verified by comparison to known gene expression patterns in the cochlea or by correlation with genes and gene families deduced to be present in the three tissue types. Approximately 22-25% of the genes on the array had significant levels of expression. A number of differentially expressed genes were detected in each tissue fraction. These included genes with known functional roles, hypothetical genes, and various unknown or uncharacterized genes. Four of the differentially expressed genes found in the organ of Corti are linked to deafness loci. None of these are hypothetical or unknown genes.

Epigenetic silencing of the human nucleotide excision repair gene, hHR23B, in interleukin-6-responsive multiple myeloma KAS-6/1 cells.

During tumorigenesis, selective proliferative advantage in certain cell subsets is associated with accumulation of multiple genetic alterations. For instance, multiple myeloma is characterized by frequent karyotypic instability at the earliest stage, progressing to extreme genetic abnormalities as the disease progresses. These successive genetic alterations can be attributed, in part, to defects in DNA repair pathways, perhaps based on epigenetic gene silencing of proteins involved in DNA damage repair. Here we report epigenetic hypermethylation of the hHR23B gene, a key component of the nucleotide excision repair in response to DNA damage, in interleukin-6 (IL-6)-responsive myeloma KAS-6/1 cells. This hypermethylation was significantly abated by Zebularine, a potent demethylating agent, with a consequent increase in the hHR23B mRNA level. Subsequent removal of this drug and supplementation with IL-6 in the culture medium re-established DNA hypermethylation of the hHR23B gene and silencing of mRNA expression levels. The inclination of DNA to be remethylated, at least within the hHR23B gene promoter region, reflects an epigenetic driving force by the cytogenetic/tumorigenic status of KAS-6/1 myeloma. The IL-6 response of KAS-6/1 myeloma also raises a question of whether the proneoplastic growth factor, such as IL-6, supports the epigenetic silencing of important DNA repair genes via promoter hypermethylation during the development of multiple myeloma.

Comparative toxicity of oleic acid and linoleic acid on Jurkat cells.

BACKGROUND: Lipid emulsions for parenteral nutrition commercially available are mainly composed of long-chain triacylglycerol containing a high proportion of alpha-6 polyunsaturated fatty acids or alpha-9 monounsaturated fatty acids. The immunological impact of such therapy is particularly important because parenteral and enteral diets are often administered to critical ill patients. The comparative toxicity of oleic acid and linoleic acid on Jurkat cells, a human T lymphocyte cell line, and the type of cell death induced by these fatty acids were determined. METHODS: Cell death was investigated by cytometry: decrease in cell volume, increase of granularity, DNA fragmentation, phosphatidylserine externalization, mitochondrial depolarization, lipid accumulation; by fluorescence microscopy: chromatin condensation and acridine orange/ethidium bromide assay; and by RT-PCR: mRNA expression of apoptotic genes. RESULTS: Evidence is presented herein that oleic acid is much less toxic to Jurkat cells than linoleic acid. Both fatty acids promote apoptosis and necrosis of these cells. The mechanism of cell death induced by these fatty acids seem to involve with mitochondrial depolarization, lipid accumulation and the levels of C-MYC and P53 mRNA expression. CONCLUSION: Therefore, oleic acid may offer an immunological less harmful alternative to linoleic acid for parenteral and enteral diets preparation.

Ciglitizone and 15d PGJ2 induce apoptosis in Jurkat and Raji cells.

Several studies have shown that PPARgamma agonists play a role in the regulation of lymphocytes function and apoptosis. However, the molecular mechanism(s) underlying the immunomodulatory effects of PPARgamma agonists are not defined yet. In this study, the effects of PPARgamma (15d PGJ2 and ciglitizone) ligands on proliferation, cytokine production and apoptosis of Jurkat and Raji cells (human T and B lymphocytes, respectively) were examined. Ciglitizone and 15d PGJ2 presented antiproliferative and cytotoxic effects on Jurkat and Raji cells as shown by [14C]-thymidine incorporation and cell viability assay. In addition, 15d PGJ2 inhibited cytokine production (IL-2 in Jurkat cells and IL-10 in Raji cells). The mechanism whereby PPARgamma agonists induced cytotoxicity is via apoptosis as shown by DNA fragmentation, nuclear condensation and phosphatidylserine externalization. The induction of apoptosis by ciglitizone and 15d PGJ2 on Jurkat and Raji cells may explain the suppression of cytokine production and the decrease in proliferation observed in both cell types. The apoptotic process was associated with a decrease in mitochondrial membrane potential and a marked down-regulation of the c-myc expression. These findings might play a key role in the apoptosis of T and B lymphocytes induced by PPARgamma agonists.

Gene expression profile of the mouse organ of Corti at the onset of hearing.

We describe the generation of an expressed sequence tag (EST) database of the mouse organ of Corti (OC). Over 20,000 independent clones were isolated, analyzed, and grouped into 8690 unique gene clusters. A large pool of novel genes unique to the OC was identified. Sequence alignments frequently revealed alternatively spliced forms of known genes potentially relevant in the OC function. We have also electronically mapped a subset of OC mouse ESTs to several syntenic regions associated with human autosomal and recessive deafness, which may prove useful for the identification of new positional candidates for these human diseases. The EST dataset is available as an interactive Web-based public database at. This resource provides both a view of the profile of gene expression in the OC at the onset of hearing and a tool to identify novel genes of importance in hearing.

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.

A small-scale full-length library construction approach was developed to facilitate production of a mouse full-length cDNA encyclopedia representing approximately 250 enriched, normalized, and/or subtracted cDNA libraries. One library produced using this approach was a subtracted adult mouse inner ear cDNA library (sIEa). The average size of the inserts was approximately 2.5 kb, with the majority ranging from 0.5 to 7.0 kb. From this library 22,574 sequence reads were obtained from 15,958 independent clones. Sequencing and chromosomal localization established 5240 clusters, with 1302 clusters being unique and 359 representing new ESTs. Our sIEa library contributed 56.1% of the 7773 nonredundant Unigene clusters associated with the four mouse inner ear libraries in the NCBI dbEST. Based on homologous chromosomal regions between human and mouse, we identified 1018 UniGene clusters associated with the deafness locus critical regions. Of these, 59 clusters were found only in our sIEa library and represented approximately 50% of the identified critical regions.

Microarray analysis of epigenetic silencing of gene expression in the KAS-6/1 multiple myeloma cell line.

The epigenetic control of gene transcription in cancer has been the theme of many recent studies and therapeutic approaches. Carcinogenesis is frequently associated with hypermethylation and consequent down-regulation of genes that prevent cancer, e.g., those that control cell proliferation and apoptosis. We used the demethylating drug zebularine to induce changes in DNA methylation, then examined patterns of gene expression using cDNA array analysis and Restriction Landmark Genomic Scanning followed by RNase protection assay and reverse transcription-PCR to confirm the results. Microarray studies revealed that many genes were epigenetically regulated by methylation. We concluded that methylation decreased the expression of, or silenced, several genes, contributing to the growth and survival of multiple myeloma cells. For example, a number of genes (BAD, BAK, BIK, and BAX) involved in apoptosis were found to be suppressed by methylation. Sequenced methylation-regulated DNA fragments identified by Restriction Landmark Genomic Scanning were found to contain CpG islands, and some corresponded to promoters of genes that were regulated by methylation. We also observed that after the removal of the demethylating drug, the addition of interleukin 6 restored CpG methylation and re-established previously silenced gene patterns, thus implicating a novel role of interleukin 6 in processes regulating epigenetic gene repression and carcinogenesis.

Epigenetic Up-regulation of Gene Expression in KAS 6/1 Human Multiple Myeloma Cells.

Cytosine methylation, an epigenetic form of regulating gene transcription, has gained importance upon the discovery that genes involved in the carcinogenic process may be regulated by this mechanism and, moreover, that certain cancers respond to treatment with demethylation-promoting drugs. Typically, the use of DNA methyltransferase inhibitor drugs results in the up-regulation of important tumor suppressor genes, previously down-regulated by the existence of abnormal cytosine methylation within their promoters. Here, we show microarray and RT-PCR results indicating that many genes are down-regulated upon treatment of KAS 6/1 multiple myeloma cells with Zebularine, a demethylating agent. Our findings suggest that, in addition to the typical methylation inhibitor-induced up-regulation of genes, removal of methylation in some genes may have a profound down-regulating effect upon their expression. The analysis of gene function showed that, of the down-regulated genes, 38 are associated with cell proliferation and/or cancer. Our analysis of the promoters of the subset of selected genes containing CpG islands showed that the distribution of cis elements differs between genes up- and down-regulated by methylation. Finally, we propose a model which shows how genes containing methylation sites within their basic promoters and/or enhancer sequences are susceptible to down-regulation, whereas genes methylated within silencer regions are up-regulated, thus providing a model as to how DNA methylation could induce such opposing effects on transcription.