O controle epigenético da expressão gênica na carcinogênese mamária: investigação de genes candidatos a supressores tumorais mapeados em 3p21.3

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Efeitos da clonagem na inativação do cromossomo X e da regulação nutricional do metabolismo da metionina na qualidade ovocitária em bovinos

Pós-graduação em Medicina Veterinária - FMVZ

Single CpG island methylation is not sufficient to maintain the silenced expression of CASPASE-8 apoptosis-related gene among women with epithelial ovarian cancer

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Avaliação do padrão de metilação dos genes ESR1, ESR2 e PGR nas linhagens celulares derivadas do câncer de mama

Breast cancer has received an increasing attention because it is one of the most common cancer type and a leading cause of morbity and mortality among women worldwide. This disease has been considered as a heterogeneous condition, demonstrating a large spectrum of clinical and histopathological variability. In the last two decades, several studies have been conducted to identify new molecular markers of cancer cells, including the alterations of DNA methylation, which is the major epigenetic mechanism associated with the control of gene expression. The hypermethylation of promoter-associated CpG islands contributes to the loss of function of several cancer-related genes, including those encoding to the estrogen receptor (ESR) and progesterone receptor (PGR). This study aimed to determine the methylation patterns of CpG islands of the genes encoding the estrogen receptor α (ESR1 gene, promoters A and B), estrogen receptor β (ESR2 gene) and progesterone receptor (PGR gene, promoter A and B) in 15 cell lines derived from breast cancer. The DNA methylation analysis was based on the “Methylation Specific-Polymerase Chain Reaction” (MSP), which provides a qualitative assessment of the methylation status of a specific CpG island. The results revealed heterogeneous data: the promoter region of ESR1A showed complete methylation in one cell line (BT549) and only two cell lines showed partial methylation (MDA-MB-231 and MDA-MB-453), while the others lineages presented unmethylated alleles. The promoter region of isoform ESR1B was unmethylated in the cell lines BT549, SKBR3 and T47D; partial methylation were observed in the cell lines MDA-MB- 231, MCF-7 and ZR-75-30, while the others cell lines presented complete methylation. All lineages showed complete or partial methylation of the ESR2 gene. The methylation pattern of the promoter A of the PGR ...(Complete abstract click electronic access below)

Análise de metilação do gene FOXE1 em carcinoma de células escamosas em cães: padronização metodológica

It is believed that epigenetic mechanisms such as DNA methylation are important for the tumorigenesis and maintenance of the altered state of tumor cells. DNA methylation occurs by the addition of a methyl group to carbon 5 of cytosine, catalyzed by the enzyme DNA methyl-transferase, which can change the expression of a gene, including the tumor suppressor genes. In human squamous cell carcinoma, several features have shown the etiological role of genes in tumor development. Among them, FOXE1 gene (forkhead box E1 - thyroid transcription factor) is presented with an important role in susceptibility to disease. Similarly the FOXE1 methylation pattern could alter the expression of this gene in dogs and predisposed to tumor on. Therefore, this study aims to investigate in dogs, the validity of the strategy employed in humans to analyze the FOXE1 methylation status. DNA extraction from fresh frozen tumoral samples was performed by Wizard Genomic® DNA Purification Kit. The methylation status was determined by MSP-PCR (methylation-specific polymerase chain reaction), using 2.0 ng of DNA treated with sodium bisulphate. One hundred micrograms of bisulphite-modified DNA was amplified using primers specific for either methylated or unmethylated DNA (primers sequences are available at http://pathology2.jhu.edu/pancreas/primer.pdf). The analysis of fragments was loaded on to 7% polyacrylamide gels and silver nitrate staining. In this stage of technical approach, 60% were FOXE1 hypermethylated. In conclusion, it was observed that the standard technique for assessing the methylation pattern of gene FOXE1 in humans can be used for the same evaluation in dogs. The correlation of these molecular data with clinical and histopathological parameters may have diagnostic and prognostic value and still be used as a tumor marker for therapeutic decision and surgical approach

Investigação do perfil de metilação de genes candidatos a biomarcadores na endometriose

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

PHF21B as a candidate tumor suppressor gene in head and neck squamous cell carcinomas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comprehensive genome methylation and whole genome expression analysis in penile carcinoma: Uncovering new molecular markers

Background: Penile carcinoma (PeCa) is frequently associated with high morbidity rates. Unlikely of the vast majority of tumors, there is no molecular markers described that are able to assist in diagnosis and prognosis or with potential to be therapeutic targets in PeCa. Patients and methods: DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies) and large-scale expression analysis (4x44K Whole Human Genome Microarray, Agilent Technologies) were performed in 35 and 37 PeCa, respectively. Quantitative bisulfite pyrosequencing (qBP) and RT-qPCR were used to validate the findings in 93 samples. HPV status was assessed using the Linear Array HPV Genotyping kit (Roche Molecular Diagnostics, CA, USA). Results: Methylome analysis revealed 171 hypermethylated and 449 hypomethylated CpGs sites and the transcriptome profiling showed 2986 down- and 2817 over-expressed genes. HPV positivity was found in 32.7% of the cases, mainly the HPV16. The integrative analysis in 32 PeCa revealed a panel of 96 genes with inverse correlation between methylation and gene expression levels. The CpG hypermetlylation and gene downexpression, was confirmed for TWIST1, RSOP2, SOX3, SOX17, CD133, OTX2, HOXA3 and MEIS. In addition, BIRC5, DNMT1 and DNMT3B presented low levels of methylation and overexpression. The comparison of the results with clinical findings revealed that LIN28A, NKX2.2, NKX2.3, LHX5, BDNF, FOXA1 and CDX2 were associated with poor prognosis features. Conclusion: Putative prognostic markers were detected revealing that DNA methylation modulates the expression of several genes in PeCa. These data may prove instrumental for biomarker discovery in clinics and molecular epidemiology of PeCa.

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Background: Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results: Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions: Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

Treatment of Nuclear-Donor Cells or Cloned Zygotes with Chromatin-Modifying Agents Increases Histone Acetylation But Does Not Improve Full-Term Development of Cloned Cattle

Although somatic cell nuclear transfer (SCNT) is a promising tool, its potential use is hampered by the high mortality rates during the development to term of cloned offspring. Abnormal epigenetic reprogramming of donor nuclei after SCNT is thought to be the main cause of this low efficiency. We hypothesized that chromatin-modifying agents (CMAs) targeting chromatin acetylation and DNA methylation could alter the chromatin configuration and turn them more amenable to reprogramming. Thus, bovine fibroblasts were treated with 5-aza-2'-deoxycytidine (AZA) plus trichostatin (TSA) or hydralazine (HH) plus valproic acid (VPA) whereas, in another trial, cloned bovine zygotes were treated with TSA. The treatment of fibroblasts with either AZA + TSA or HH + VPA increased histone acetylation, but did not affect the level of DNA methylation. However, treatment with HH + VPA decreased cellular viability and proliferation. The use of these cells as nuclear donors showed no positive effect on pre- and postimplantation development. Regarding the treatment of cloned zygotes with TSA, treated one-cell embryos showed an increase in the acetylation patterns, but not in the level of DNA methylation. Moreover, this treatment revealed no positive effect on pre- and postimplantation development. This work provides evidence the treatment of either nuclear donor cells or cloned zygotes with CMAs has no positive effect on pre- and postimplantation development of cloned cattle.

Inactivation of the putative suppressor gene DOK1 by promoter hypermethylation in primary human cancers

The DOK1 gene is a putative tumour suppressor gene located on the human chromosome 2p13 which is frequently rearranged in leukaemia and other human tumours. We previously reported that the DOK1 gene can be mutated and its expression down-regulated in human malignancies. However, the mechanism underlying DOK1 silencing remains largely unknown. We show here that unscheduled silencing of DOK1 expression through aberrant hypermethylation is a frequent event in a variety of human malignancies. DOK1 was found to be silenced in nine head and neck cancer (HNC) cell lines studied and DOK1 CpG hypermethylation correlated with loss of gene expression in these cells. DOK1 expression could be restored via demethylating treatment using 5-aza-2'deoxycytidine. In addition, transduction of cancer cell lines with DOK1 impaired their proliferation, consistent with the critical role of epigenetic silencing of DOK1 in the development and maintenance of malignant cells. We further observed that DOK1 hypermethylation occurs frequently in a variety of primary human neoplasm including solid tumours (93% in HNC, 81% in lung cancer) and haematopoietic malignancy (64% in Burkitt's lymphoma). Control blood samples and exfoliated mouth epithelial cells from healthy individuals showed a low level of DOK1 methylation, suggesting that DOK1 hypermethylation is a tumour specific event. Finally, an inverse correlation was observed between the level of DOK1 gene methylation and its expression in tumour and adjacent non tumour tissues. Thus, hypermethylation of DOK1 is a potentially critical event in human carcinogenesis, and may be a potential cancer biomarker and an attractive target for epigenetic-based therapy.

Mechanismen der Caveolin-Genregulation in neuralen Zellsystemen

Caveolae sind vesikuläre Invaginationen der eukaryontischen Zellmembran, die bei einer Vielzahl zellbiologischer Prozesse eine bedeutende Rolle spielen. Die strukturellen und funktionellen Hauptbestandteile der Caveolae sind die Caveolin-Proteine, welche von drei homologen Genen (Caveolin-1,-2,-3) kodiert werden. Die Caveoline stellen die Struktur-Organisatoren der Caveolae dar, und regulieren direkt die Aktivität von zahlreichen Caveolae-assoziierten Rezeptorproteinen und Signalmolekülen. Oftmals werden die pleiotropen Effekte der Caveoline über eine Veränderung der Caveolin-Genexpressionsstärke moduliert. In der vorliegenden Arbeit wurden drei unterschiedliche biologische Steuerfaktoren identifiziert, unter deren Kontrolle die Caveolin-Genexpression in neuralen Zellsystemen steht. Bei diesen Faktoren handelt es sich um das Steroidhormon Oestrogen und seine Rezeptoren, den Wachstumsfaktor TGFa und den sekundären Botenstoff zyklisches AMP (cAMP). Oestrogen wirkt über die Aktivierung von Oestrogen-Rezeptoren (ERs) im zentralen Nervensystem in der Regel als neurotropher Faktor. In der vorliegenden Arbeit konnte erstmalig gezeigt werden, daß in humanen Neuroblastom-Zellen (SK-N-MC) die stabile, rekombinante Expression des ERa-Subtyps zu einer drastischen Reduktion der Caveolin-1/-2-Transkription führt, und daß in der Folge die zelluläre Caveolin-Biosynthese eingestellt wird. Eine Analyse des Caveolin-1-Gens ergab, daß einhergehend mit der Inaktivierung der Caveolin-1-Transkription eine Vielzahl der im Promoter enthaltenen CpG-Dinukleotide methyliert vorliegen. Durch pharmakologische Inhibition der nukleären DNA-Methyltransferasen sowie der Histon-Deacetylasen konnte die Caveolin-1-Transkription teilweise wiederhergestellt werden. Diese Befunde lassen auf die Existenz eines DNA-Methylierungs-abhängigen Stilllegungsmechanismus der Caveolin-Genexpression durch ERa schließen. Dagegen führte die Überexpression des ERb-Subtyps in SK-N-MC-Zellen zu keiner Veränderung der Caveolin-1/-2-Expression. Interessanterweise wurde die supprimierende Wirkung des ERa durch die gleichzeitige Überexpression des ERb vollständig aufgehoben. Der mitogene Wachstumsfaktor TGFa wurde als zweites extrazelluläres Signalmolekül identifiziert, welches eine Reduktion der Caveolin-1/-2-Genexpression bewirkt. In primären kortikalen Astrozyten konnte gezeigt werden, daß TGFa seine supprimierende Wirkung auf die Caveolin-1-Expression partiell über die Aktivierung des PI3-Kinase-abhängigen Signalweges vermittelt. Zudem wurde die supprimierende Wirkung von TGFa durch einen Inhibitior der Histon-Deacetylasen relativiert. Daher scheinen sowohl für den ERa als auch für TGFa epigenetische Prozesse bei der Suppression der Caveolin-1-Genexpression eine entscheidende Rolle zu spielen. Intrazellulär wirkte neben der PI3-Kinase auch der Botenstoff cAMP in kortikalen Astrozyten als Suppressor der Caveolin-Genexpression. Es wäre denkbar, daß die Caveolin-Suppression funktioneller Bestandteil des seit langem etablierten Effekts der cAMP-induzierten Astrozyten-Differenzierung ist. Desweiteren wiesen der cAMP- und TGFa-abhängige Signalweg ein überlappendes, Gehirnregion-spezifisches Regulationsprofil der Caveolin-Expression in Astrozyten auf: während in Kortex und Striatum eine Regulation durch cAMP und TGFa erfolgte, blieb diese in Klein- und Zwischenhirn aus. Somit bewirken drei zentrale regulatorische Faktoren der Proliferation und Differenzierung neuraler Zellen eine Reduktion in der Konzentration der pleiotrop funktionellen Caveoline. Zukünftige Studien müssen zeigen, inwieweit die reduzierte Caveolin-Expression für die morphologischen und biochemischen Primärwirkungen dieser Faktoren während der Entwicklung und im Zuge der Tumorgenese mitverantwortlich ist. Außerdem könnten über die Beobachtungen der zellbiologischen Auswirkungen reduzierter Caveolin-Spiegel neue Erkenntnisse über die Funktion dieser Proteine gewonnen werden.

Alkylantien induzierte Zytotoxizität, DNA-schadensinduzierte Reparaturkapazität und Apoptoseinduktion von Immunzellen

Monozyten und Monozyten-abgeleitete Dendritische Zellen (DCs) spielen eine bedeutende Rolle im Immunsystem. Da DCs bei der Tumorabwehr mitwirken, ist es wichtig, dass Monozyten als auch DCs sich gegenüber zytotoxischen Agenzien aus der Chemotherapie wehren können. Chemotherapeutika reagieren mit der DNA, jedoch die DNA-Reparaturkapazität von Monozyten und DCs wurde noch nicht untersucht. Dazu wurde die Sensitivität in Monozyten und DCs gegenüber verschiedene genotoxische Agenzien untersucht. Dabei wurde herausgefunden, dass Monozyten sensitiv auf methylierende Agenzien (MNNG, MMS und Temozolomid) reagieren und ein verstärktes Zellsterben und Apoptoseinduktion zeigen. Im Vergleich zu weiteren Zytostatika wie Fotemustin, Mafosfamid und Cisplatin reagierten Monozyten und DCs gleich sensitiv. Diese Ergebnisse weisen auf einen Defekt in der Reparatur von DNA-Methylierungsschäden in Monozyten hin. Da die Expression des Reparaturproteins O6-Methylguanin-DNA Methyltransferase (MGMT) in Monozyten höher war als in DCs und deren Inhibierung durch O6-Benzylguanin keinen Effekt auf die Sensitivität von Monozyten hatte, wurde der Reparaturweg der Basenexzisionsreparatur untersucht. Im Vergleich zu DCs waren die Monozyten unfähig die BER durchzuführen, welche durch Einzelzellgelelektrophorese gemessen wurde. Expressionsuntersuchungen ergaben, dass in Monozyten XRCC1 und Ligase IIIα fehlen im Vergleich zu DCs, Makrophagen, hämatopoetische Stammzellen und Lymphozyten, welche diese Proteine exprimieren. Diese Ergebnisse zeigen einen spezifischen DNA-Reparaturdefekt in einer bestimmten Blutzellpopulation. Durch den BER Defekt in Monozyten kann es durch methylierende Tumorwirkstoffe während einer Chemotherapie zur Depletion und zu einer abgeschwächten Immunantwort kommen.

Profili di espressione genetica ed epigenetica ad impatto prognostico e predittivo nel carcinoma squamoso e nelle lesioni potenzialmente maligne del cavo orale

Il carcinoma squamoso orale (CSO) è spesso preceduto da lesioni definite potenzialmente maligne tra cui la leucoplachia e il lichen ma una diagnosi precoce avviene ancora oggi in meno della metà dei casi. Inoltre spesso un paziente trattato per CSO svilupperà secondi tumori. Scopo del lavoro di ricerca è stato: 1) Studiare, mediante metodica di next generation sequencing, lo stato di metilazione di un gruppo di geni a partire da prelievi brushing del cavo orale al fine di identificare CSO o lesioni ad alto rischio di trasformazione maligna. 2) Valurare la relazione esistente tra sovraespressione di p16INK4A e presenza di HPV in 35 pazienti affetti da lichen 3) Valutare la presenza di marker istopatologici predittivi di comparsa di seconde manifestazioni tumorali 4) valutare la relazione clonale tra tumore primitivo e metastasi linfonodale in 8 pazienti mediante 2 metodiche di clonalità differenti: l’analisi di mtDNA e delle mutazioni del gene TP53. I risultati hanno mostrato: 1) i geni ZAP70 e GP1BB hanno presentato un alterato stato di metilazione rispettivamente nel 100% e nel 90,9% di CSO e lesioni ad alto rischio, mentre non sono risultati metilati nei controlli sani; ipotizzando un ruolo come potenziali marcatori per la diagnosi precoce nel CSO. 2)Una sovraespressione di p16INK4A è risultata in 26/35 pazienti affetti da lichen ma HPV-DNA è stato identificato in soli 4 campioni. Nessuna relazione sembra essere tra sovraespressione di p16INK4A e virus HPV. 3)L’invasione perineurale è risultato un marker predittivo della comparsa di recidiva locale e metastasi linfonodale, mentre lo stato dei margini chirurgici si è rilevato un fattore predittivo per la comparsa di secondi tumori primitivi 4) Un totale accordo nei risultati c’è stato tra analisi di mtDNA e analisi di TP53 e le due metodiche hanno identificato la presenza di 4 metastasi linfonodali non clonalmente correlate al tumore primitivo.

Evolutionary epigenetics of modern human populations

Epigenetic variability is a new mechanism for the study of human microevolution, because it creates both phenotypic diversity within an individual and within population. This mechanism constitutes an important reservoir for adaptation in response to new stimuli and recent studies have demonstrated that selective pressures shape not only the genetic code but also DNA methylation profiles. The aim of this thesis is the study of the role of DNA methylation changes in human adaptive processes, considering the Italian peninsula and macro-geographical areas. A whole-genome analysis of DNA methylation profile across the Italian penisula identified some genes whose methylation levels differ between individuals of different Italian districts (South, Centre and North of Italy). These genes are involved in nitrogen compound metabolism and genes involved in pathogens response. Considering individuals with different macro-geographical origins (individuals of Asians, European and African ancestry) more significant DMRs (differentially methylated regions) were identified and are located in genes involved in glucoronidation, in immune response as well as in cell comunication processes. A "profile" of each ancestry (African, Asian and European) was described. Moreover a deepen analysis of three candidate genes (KRTCAP3, MAD1L and BRSK2) in a cohort of individuals of different countries (Morocco, Nigeria, China and Philippines) living in Bologna, was performed in order to explore genetic and epigenetic diversity. Moreover this thesis have paved the way for the application of DNA methylation for the study of hystorical remains and in particular for the age-estimation of individuals starting from biological samples (such as teeth or blood). Noteworthy, a mathematical model that considered methylation values of DNA extracted from cementum and pulp of living individuals can estimate chronological age with high accuracy (median absolute difference between age estimated from DNA methylation and chronological age was 1.2 years).