Clinical, epidemiological and molecular features of the HIV-1 subtype C and recombinant forms that are circulating in the city of São Paulo, Brazil

Abstract Background The city of Sao Paulo has the highest AIDS case rate, with nearly 60% in Brazil. Despite, several studies involving molecular epidemiology, lack of data regarding a large cohort study has not been published from this city. Objectives This study aimed to describe the HIV-1 subtypes, recombinant forms and drug resistance mutations, according to subtype, with emphasis on subtype C and BC recombinants in the city of São Paulo, Brazil. Study design RNA was extracted from the plasma samples of 302 HIV-1-seropositive subjects, of which 211 were drug-naive and 82 were exposed to ART. HIV-1 partial pol region sequences were used in phylogenetic analyses for subtyping and identification of drug resistance mutations. The envelope gene of subtype C and BC samples was also sequenced. Results From partial pol gene analyses, 239 samples (79.1%) were assigned as subtype B, 23 (7.6%) were F1, 16 (5.3%) were subtype C and 24 (8%) were mosaics (3 CRF28/CRF29-like). The subtype C and BC recombinants were mainly identified in drug-naïve patients (72.7%) and the heterosexual risk exposure category (86.3%), whereas for subtype B, these values were 69.9% and 57.3%, respectively (p = 0.97 and p = 0.015, respectively). An increasing trend of subtype C and BC recombinants was observed (p < 0.01). Conclusion The HIV-1 subtype C and CRFs seem to have emerged over the last few years in the city of São Paulo, principally among the heterosexual population. These findings may have an impact on preventive measures and vaccine development in Brazil.

HIV-1 tropism and CD4 T lymphocyte recovery in a prospective cohort of patients initiating HAART in Ribeirão Preto, Brazil

While human immunodeficiency virus (HIV)-1 chemokine co-receptors 5 tropism and the GWGR motif in the envelope third variable region (V3 loop) have been associated with a slower disease progression, their influence on antiretroviral response remains unclear. The impact of baseline V3 characteristics on treatment response was evaluated in a randomised, double blind, prospective cohort study with patients initiating highly active antiretroviral therapy with lopinavir or efavirenz plus azithothymidine/3TC (1:1) over 48 weeks. Similar virological and immunological responses were observed for both treatment regimens. The 43 individuals had a mean baseline CD4 T cell count of 119 cells/mm³ [standard deviation (SD) = 99] and a mean viral load of 5.09 log10 copies/mL (SD = 0.49). The GWGR motif was not associated with a CD4 T cell response, but predicted R5 tropism by the geno2pheno[clinical20%] algorithm correlated with higher CD4 T cell levels at all monitoring points (p < 0.05). Moreover, higher false-positive rates (FPR) values from this analysis revealed a strong correlation with CD4 T cell recovery (p < 0.0001). Transmitted drug resistance mutations, documented in 3/41 (7.3%) cases, were unrelated to the assigned antiretroviral regimen and had no impact on patient outcomes. In conclusion, naÏve HIV-1 R5 infected patients exhibited higher CD4 T cell counts at baseline; this difference was sustained throughout therapy. The geno2pheno[clinical] option FPR positively correlated with CD4 T cell gain and may be useful in predicting CD4 T cell recovery.

A study of multidrug-resistant tuberculosis in risk groups in the city of Santos, São Paulo, Brazil

Monitoring the extent of and trends in multidrug-resistant tuberculosis (MDR-TB) is a priority of the Brazilian National Tuberculosis Control Programme. The current study aimed to estimate the incidence of MDR-TB, describe the profile of TB drug resistance in risk groups and examine whether screening for MDR-TB adhered to the recommended guidelines. A descriptive study that examined diagnosed cases of pulmonary TB was conducted in the city of Santos, Brazil, between 2000-2004. Of the 2,176 pulmonary TB cases studied, 671 (30.8%) met the criteria for drug sensitivity testing and, of these cases, 31.7% (213/671) were tested. Among the tested cases, 9.4% were resistant to one anti-TB drug and 15% were MDR. MDR was observed in 11.6% of 86 new TB cases and 17.3% of 127 previously treated cases. The average annual incidence of MDR-TB was 1.9 per 100,000 inhabitants-years. The extent of known MDR-TB in the city of Santos is high, though likely to be underestimated. Our study therefore indicates an inadequate adherence to the guidelines for MDR-TB screening and suggests the necessity of alternative strategies of MDR-TB surveillance.

Infecções de corrente sanguínea por bactérias multirresistentes em UTI de tratamento de queimados: experiência de 4 anos

INTRODUÇÃO: O conhecimento do perfil de resistência aos antibióticos das bactérias de um nosocômio é essencial para orientar tratamento adequado dos pacientes. Isso é especialmente importante para os pacientes mais graves, já que o tratamento deve ser instituído antes do resultado das culturas. O objetivo deste estudo foi analisar o perfil das bactérias multirresistentes encontradas nas hemoculturas de pacientes admitidos na Unidade de Tratamento Intensivo (UTI) da Unidade de Queimados do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. MÉTODO: Foram analisados 178 pacientes internados na UTI para tratamento de queimados, no período de 2009 a 2011, sendo 131 do sexo masculino, com média de idade de 29,2 anos. RESULTADOS: Entre os pacientes analisados, 80 (44,9%) apresentaram hemocultura periférica positiva, sendo 66 (82,5%) casos com bactérias multirresistentes. Em 48 pacientes, foram isoladas Staphylococcus sp., que se apresentaram resistentes à oxacilina em 33 deles. Em 11 pacientes, foram isoladas Acinetobacter baumanii, que se apresentaram resistentes a imipenem em 8 casos. Em 19 pacientes, foram isoladas Pseudomonas sp., resistentes a imipenem em 16 casos. Em 10 pacientes foram isoladas Enterobacter sp., resistentes a amicacina e ciprofloxacina em 2 casos. A presença de bactérias multirresistentes não foi associada a maior ocorrência de óbitos, porém foi verificado maior tempo de internação (52,6 dias vs. 36,3 dias para os grupos com e sem bactérias multirresistentes, respectivamente; P = 0,0306). Não foi encontrada interação significante entre superfície corpórea queimada e presença de bactérias MR. CONCLUSÕES: A presença de bactérias multirresistentes é um problema grave, tanto pela prevalência como pela morbidade e mortalidade associadas.

RNA Interference and cyclooxygenase-2 (COX-2) regulation in colon cancer cells

Despite new methods and combined strategies, conventional cancer chemotherapy still lacks specificity and induces drug resistance. Gene therapy can offer the potential to obtain the success in the clinical treatment of cancer and this can be achieved by replacing mutated tumour suppressor genes, inhibiting gene transcription, introducing new genes encoding for therapeutic products, or specifically silencing any given target gene. Concerning gene silencing, attention has recently shifted onto the RNA interference (RNAi) phenomenon. Gene silencing mediated by RNAi machinery is based on short RNA molecules, small interfering RNAs (siRNAs) and microRNAs (miRNAs), that are fully o partially homologous to the mRNA of the genes being silenced, respectively. On one hand, synthetic siRNAs appear as an important research tool to understand the function of a gene and the prospect of using siRNAs as potent and specific inhibitors of any target gene provides a new therapeutical approach for many untreatable diseases, particularly cancer. On the other hand, the discovery of the gene regulatory pathways mediated by miRNAs, offered to the research community new important perspectives for the comprehension of the physiological and, above all, the pathological mechanisms underlying the gene regulation. Indeed, changes in miRNAs expression have been identified in several types of neoplasia and it has also been proposed that the overexpression of genes in cancer cells may be due to the disruption of a control network in which relevant miRNA are implicated. For these reasons, I focused my research on a possible link between RNAi and the enzyme cyclooxygenase-2 (COX-2) in the field of colorectal cancer (CRC), since it has been established that the transition adenoma-adenocarcinoma and the progression of CRC depend on aberrant constitutive expression of COX-2 gene. In fact, overexpressed COX-2 is involved in the block of apoptosis, the stimulation of tumor-angiogenesis and promotes cell invasion, tumour growth and metastatization. On the basis of data reported in the literature, the first aim of my research was to develop an innovative and effective tool, based on the RNAi mechanism, able to silence strongly and specifically COX-2 expression in human colorectal cancer cell lines. In this study, I firstly show that an siRNA sequence directed against COX-2 mRNA (siCOX-2), potently downregulated COX-2 gene expression in human umbilical vein endothelial cells (HUVEC) and inhibited PMA-induced angiogenesis in vitro in a specific, non-toxic manner. Moreover, I found that the insertion of a specific cassette carrying anti-COX-2 shRNA sequence (shCOX-2, the precursor of siCOX-2 previously tested) into a viral vector (pSUPER.retro) greatly increased silencing potency in a colon cancer cell line (HT-29) without activating any interferon response. Phenotypically, COX-2 deficient HT-29 cells showed a significant impairment of their in vitro malignant behaviour. Thus, results reported here indicate an easy-to-use, powerful and high selective virus-based method to knockdown COX-2 gene in a stable and long-lasting manner, in colon cancer cells. Furthermore, they open up the possibility of an in vivo application of this anti-COX-2 retroviral vector, as therapeutic agent for human cancers overexpressing COX-2. In order to improve the tumour selectivity, pSUPER.retro vector was modified for the shCOX-2 expression cassette. The aim was to obtain a strong, specific transcription of shCOX-2 followed by COX-2 silencing mediated by siCOX-2 only in cancer cells. For this reason, H1 promoter in basic pSUPER.retro vector [pS(H1)] was substituted with the human Cox-2 promoter [pS(COX2)] and with a promoter containing repeated copies of the TCF binding element (TBE) [pS(TBE)]. These promoters were choosen because they are partculary activated in colon cancer cells. COX-2 was effectively silenced in HT-29 and HCA-7 colon cancer cells by using enhanced pS(COX2) and pS(TBE) vectors. In particular, an higher siCOX-2 production followed by a stronger inhibition of Cox-2 gene were achieved by using pS(TBE) vector, that represents not only the most effective, but also the most specific system to downregulate COX-2 in colon cancer cells. Because of the many limits that a retroviral therapy could have in a possible in vivo treatment of CRC, the next goal was to render the enhanced RNAi-mediate COX-2 silencing more suitable for this kind of application. Xiang and et al. (2006) demonstrated that it is possible to induce RNAi in mammalian cells after infection with engineered E. Coli strains expressing Inv and HlyA genes, which encode for two bacterial factors needed for successful transfer of shRNA in mammalian cells. This system, called “trans-kingdom” RNAi (tkRNAi) could represent an optimal approach for the treatment of colorectal cancer, since E. Coli in normally resident in human intestinal flora and could easily vehicled to the tumor tissue. For this reason, I tested the improved COX-2 silencing mediated by pS(COX2) and pS(TBE) vectors by using tkRNAi system. Results obtained in HT-29 and HCA-7 cell lines were in high agreement with data previously collected after the transfection of pS(COX2) and pS(TBE) vectors in the same cell lines. These findings suggest that tkRNAi system for COX-2 silencing, in particular mediated by pS(TBE) vector, could represent a promising tool for the treatment of colorectal cancer. Flanking the studies addressed to the setting-up of a RNAi-mediated therapeutical strategy, I proposed to get ahead with the comprehension of new molecular basis of human colorectal cancer. In particular, it is known that components of the miRNA/RNAi pathway may be altered during the progressive development of colorectal cancer (CRC), and it has been already demonstrated that some miRNAs work as tumor suppressors or oncomiRs in colon cancer. Thus, my hypothesis was that overexpressed COX-2 protein in colon cancer could be the result of decreased levels of one or more tumor suppressor miRNAs. In this thesis, I clearly show an inverse correlation between COX-2 expression and the human miR- 101(1) levels in colon cancer cell lines, tissues and metastases. I also demonstrate that the in vitro modulating of miR-101(1) expression in colon cancer cell lines leads to significant variations in COX-2 expression, and this phenomenon is based on a direct interaction between miR-101(1) and COX-2 mRNA. Moreover, I started to investigate miR-101(1) regulation in the hypoxic environment since adaptation to hypoxia is critical for tumor cell growth and survival and it is known that COX-2 can be induced directly by hypoxia-inducible factor 1 (HIF-1). Surprisingly, I observed that COX-2 overexpression induced by hypoxia is always coupled to a significant decrease of miR-101(1) levels in colon cancer cell lines, suggesting that miR-101(1) regulation could be involved in the adaption of cancer cells to the hypoxic environment that strongly characterize CRC tissues.

Mitochondrial dysfunction in a cell model of thyroid oncocytoma

The role of mitochondrial dysfunction in cancer has long been a subject of great interest. In this study, such dysfunction has been examined with regards to thyroid oncocytoma, a rare form of cancer, accounting for less than 5% of all thyroid cancers. A peculiar characteristic of thyroid oncocytic cells is the presence of an abnormally large number of mitochondria in the cytoplasm. Such mitochondrial hyperplasia has also been observed in cells derived from patients suffering from mitochondrial encephalomyopathies, where mutations in the mitochondrial DNA(mtDNA) encoding the respiratory complexes result in oxidative phosphorylation dysfunction. An increase in the number of mitochondria occurs in the latter in order to compensate for the respiratory deficiency. This fact spurred the investigation into the presence of analogous mutations in thyroid oncocytic cells. In this study, the only available cell model of thyroid oncocytoma was utilised, the XTC-1 cell line, established from an oncocytic thyroid metastasis to the breast. In order to assess the energetic efficiency of these cells, they were incubated in a medium lacking glucose and supplemented instead with galactose. When subjected to such conditions, glycolysis is effectively inhibited and the cells are forced to use the mitochondria for energy production. Cell viability experiments revealed that XTC-1 cells were unable to survive in galactose medium. This was in marked contrast to the TPC-1 control cell line, a thyroid tumour cell line which does not display the oncocytic phenotype. In agreement with these findings, subsequent experiments assessing the levels of cellular ATP over incubation time in galactose medium, showed a drastic and continual decrease in ATP levels only in the XTC-1 cell line. Furthermore, experiments on digitonin-permeabilised cells revealed that the respiratory dysfunction in the latter was due to a defect in complex I of the respiratory chain. Subsequent experiments using cybrids demonstrated that this defect could be attributed to the mitochondrially-encoded subunits of complex I as opposed to the nuclearencoded subunits. Confirmation came with mtDNA sequencing, which detected the presence of a novel mutation in the ND1 subunit of complex I. In addition, a mutation in the cytochrome b subunit of complex III of the respiratory chain was detected. The fact that XTC-1 cells are unable to survive when incubated in galactose medium is consistent with the fact that many cancers are largely dependent on glycolysis for energy production. Indeed, numerous studies have shown that glycolytic inhibitors are able to induce apoptosis in various cancer cell lines. Subsequent experiments were therefore performed in order to identify the mode of XTC-1 cell death when subjected to the metabolic stress imposed by the forced use of the mitochondria for energy production. Cell shrinkage and mitochondrial fragmentation were observed in the dying cells, which would indicate an apoptotic type of cell death. Analysis of additional parameters however revealed a lack of both DNA fragmentation and caspase activation, thus excluding a classical apoptotic type of cell death. Interestingly, cleavage of the actin component of the cytoskeleton was observed, implicating the action of proteases in this mode of cell demise. However, experiments employing protease inhibitors failed to identify the specific protease involved. It has been reported in the literature that overexpression of Bcl-2 is able to rescue cells presenting a respiratory deficiency. As the XTC-1 cell line is not only respiration-deficient but also exhibits a marked decrease in Bcl-2 expression, it is a perfect model with which to study the relationship between Bcl-2 and oxidative phosphorylation in respiratory-deficient cells. Contrary to the reported literature studies on various cell lines harbouring defects in the respiratory chain, Bcl-2 overexpression was not shown to increase cell survival or rescue the energetic dysfunction in XTC-1 cells. Interestingly however, it had a noticeable impact on cell adhesion and morphology. Whereas XTC-1 cells shrank and detached from the growth surface under conditions of metabolic stress, Bcl-2-overexpressing XTC-1 cells appeared much healthier and were up to 45% more adherent. The target of Bcl-2 in this setting appeared to be the actin cytoskeleton, as the cleavage observed in XTC-1 cells expressing only endogenous levels of Bcl-2, was inhibited in Bcl-2-overexpressing cells. Thus, although unable to rescue XTC-1 cells in terms of cell viability, Bcl-2 is somehow able to stabilise the cytoskeleton, resulting in modifications in cell morphology and adhesion. The mitochondrial respiratory deficiency observed in cancer cells is thought not only to cause an increased dependency on glycolysis but it is also thought to blunt cellular responses to anticancer agents. The effects of several therapeutic agents were thus assessed for their death-inducing ability in XTC-1 cells. Cell viability experiments clearly showed that the cells were more resistant to stimuli which generate reactive oxygen species (tert-butylhydroperoxide) and to mitochondrial calcium-mediated apoptotic stimuli (C6-ceramide), as opposed to stimuli inflicting DNA damage (cisplatin) and damage to protein kinases(staurosporine). Various studies in the literature have reported that the peroxisome proliferator-activated receptor-coactivator 1(PGC-1α), which plays a fundamental role in mitochondrial biogenesis, is also involved in protecting cells against apoptosis caused by the former two types of stimuli. In accordance with these observations, real-time PCR experiments showed that XTC-1 cells express higher mRNA levels of this coactivator than do the control cells, implicating its importance in drug resistance. In conclusion, this study has revealed that XTC-1 cells, like many cancer cell lines, are characterised by a reduced energetic efficiency due to mitochondrial dysfunction. Said dysfunction has been attributed to mutations in respiratory genes encoded by the mitochondrial genome. Although the mechanism of cell demise in conditions of metabolic stress is unclear, the potential of targeting thyroid oncocytic cancers using glycolytic inhibitors has been illustrated. In addition, the discovery of mtDNA mutations in XTC-1 cells has enabled the use of this cell line as a model with which to study the relationship between Bcl-2 overexpression and oxidative phosphorylation in cells harbouring mtDNA mutations and also to investigate the significance of such mutations in establishing resistance to apoptotic stimuli.

Myc-mediated control of gene transcription in cancer cells

The Myc oncoproteins belong to a family of transcription factors composed by Myc, N-Myc and L-Myc. The most studied components of this family are Myc and N-Myc because their expressions are frequently deregulated in a wide range of cancers. These oncoproteins can act both as activators or repressors of gene transcription. As activators, they heterodimerize with Max (Myc associated X-factor) and the heterodimer recognizes and binds a specific sequence elements (E-Box) onto gene promoters recruiting histone acetylase and inducing transcriptional activation. Myc-mediated transcriptional repression is a quite debated issue. One of the first mechanisms defined for the Myc-mediated transcriptional repression consisted in the interaction of Myc-Max complex Sp1 and/or Miz1 transcription factors already bound to gene promoters. This interaction may interfere with their activation functions by recruiting co-repressors such as Dnmt3 or HDACs. Moreover, in the absence of , Myc may interfere with the Sp1 activation function by direct interaction and subsequent recruitment of HDACs. More recently the Myc/Max complex was also shown to mediate transcriptional repression by direct binding to peculiar E-box. In this study we analyzed the role of Myc overexpression in Osteosarcoma and Neuroblastoma oncogenesis and the mechanisms underling to Myc function. Myc overexpression is known to correlate with chemoresistance in Osteosarcoma cells. We extended this study by demonstrating that c-Myc induces transcription of a panel of ABC drug transporter genes. ABCs are a large family trans-membrane transporter deeply involved in multi drug resistance. Furthermore expression levels of Myc, ABCC1, ABCC4 and ABCF1 were proved to be important prognostic tool to predict conventional therapy failure. N-Myc amplification/overexpression is the most important prognostic factor for Neuroblastoma. Cyclin G2 and Clusterin are two genes often down regulated in neuroblastoma cells. Cyclin G2 is an atypical member of Cyclin family and its expression is associated with terminal differentiation and apoptosis. Moreover it blocks cell cycle progression and induces cell growth arrest. Instead, CLU is a multifunctional protein involved in many physiological and pathological processes. Several lines of evidences support the view that CLU may act as a tumour suppressor in Neuroblastoma. In this thesis I showed that N-Myc represses CCNG2 and CLU transcription by different mechanisms. • N-Myc represses CCNG2 transcription by directly interacting with Sp1 bound in CCNG2 promoter and recruiting HDAC2. Importantly, reactivation of CCNG2 expression through epigenetic drugs partially reduces N-Myc and HDAC2 mediated cell proliferation. • N-Myc/Max complex represses CLU expression by direct binding to a peculiar E-box element on CLU promoter and by recruitment of HDACs and Polycomb Complexes, to the CLU promoter. Overall our findings strongly support the model in which Myc overexpression/amplification may contribute to some aspects of oncogenesis by a dual action: i) transcription activation of genes that confer a multidrug resistant phenotype to cancer cells; ii), transcription repression of genes involved in cell cycle inhibition and cellular differentiation.

L'associazione Tipifarnib-Bortezomib nel trattamento delle leucemie acute mieloidi: risultati di uno studio multicentrico di fase I/II e validazione di un profilo genico predittivo di risposta

Background. Outcome of elderly acute myeloid leukemia (AML) patients is dismal. Targeted-therapies might improve current results by overcoming drug-resistance and reducing toxicity. Aim. We conduced a phase II study aiming to assess efficacy and toxicity of Tipifarnib (Zarnestra®) and Bortezomib (Velcade®) association in AML patients >18 years, unfit for conventional therapy, or >60 years, in relapse. Furthermore, we aimed to evaluated the predictive value of the RASGRP1/APTX ratio, which was previously found to be associated to treatment sensitivity in patients receiving Zarnestra alone. Methods. Velcade (1.0 mg/m2) was administered as weekly infusion for 3 weeks (days 1, 8, 15). Zarnestra was administered at dose of 300-600 mg BID for 21 consecutive days. Real-time quantitative-PCR (q-PCR) was used for RASGRP1/APTX quantification. Results. 50 patients were enrolled. Median age was 71 years (56-89). 3 patients achieved complete remission (CR) and 1 partial response (PR). 2 patients obtained an hematological improvement (HI), and 3 died during marrow aplasia. 10 had progressive disease (PD) and the remaining showed stable disease (SD). RASGRP1/APTX was evaluated before treatment initiation on bone marrow (BM) and/or peripheral blood (PB). The median RASGRP/APTX value on BM was higher in responder (R) patients than in non responders (NR) ones, respectively (p=0.006). Interestingly, no marrow responses were recorded in patients with BM RASGRP1/APTX ratio <12, while the response rate was 50% in patients with ratio >12. Toxicity was overall mild, the most common being febrile neutropenia. Conclusion. We conclude that the clinical efficacy of the combination Zarnestra-Velcade was similar to what reported for Zarnestra alone. However we could confirm that the RASGPR1/APTX level is an effective predictor of response. Though higher RASGRP1/APTX is relatively rare (~10% of cases), Zarnestra (±Velcade) may represent an important option in a subset of high risk/frail AML patients.

Farmacogenomica della Clofarabina nel trattamento delle Leucemie Acute pediatriche: identificazione di nuovi bersagli molecolari e del profilo genomico associato all’efficacia terapeutica del farmaco antitumorale

In quest’ultimi decenni si è assistito ad un notevole miglioramento nella terapia delle Leucemie Acute (LA) pediatriche, nonostante tutto si assiste oggi ad una fase di plateau della curva di sopravvivenza e le leucemie continuano a costituire la principale causa di morte pediatrica per malattia. Ulteriori progressi nel trattamento delle LA potrebbero essere ottenuti mediante studi di farmacogenomica che, identificando le componenti genetiche associate alla risposta individuale ai trattamenti farmacologici, consentono il disegno di terapie personalizzate e tumore-specifiche, ad alta efficacia e bassa tossicità per ciascun paziente. Il lavoro svolto è stato, dunque, finalizzato allo studio della farmacogenomica del farmaco antitumorale Clofarabina (CLO) nel trattamento delle LA pediatriche al fine di identificare marcatori genetici predittivi di risposta delle cellule leucemiche al farmaco, delucidare i meccanismi di resistenza cellulare ed individuare nuovi bersagli verso cui indirizzare terapie più mirate ed efficaci. L’analisi in vitro della sensibilità alla CLO di blasti provenienti da pazienti pediatrici affetti da Leucemia Acuta Linfoblastica (LAL) e Mieloide (LAM) ha consentito l’identificazione di due sottopopolazioni di cellule LAL ad immunofenotipo T a diversa sensibilità alla CLO. Mediante DNA-microarrays, si è identificata la “signature” genetica specificamente associata alla diversa risposta delle cellule LAL-T al farmaco. Successivamente, la caratterizzazione funzionale dei geni differenziali e l’analisi dei pathways hanno consentito l’identificazione specifica di potenziali biomarcatori di risposta terapeutica aprendo nuove prospettive per la comprensione dei meccanismi di resistenza cellulare alla CLO e suggerendo un nuovo bersaglio terapeutico per le forme LAL-T a bassa sensibilità al farmaco. In conclusione, nel lavoro svolto si sono identificati set di geni e pathways di rilievo biologico per la risposta delle cellule LAL-T alla CLO suggerendo marcatori genetici in grado di identificare i soggetti eleggibili per il trattamento o verso cui disegnare terapie innovative. Il lavoro è paradigma per l’applicazione della farmacogenomica in altre neoplasie.

Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

The search for Multiple Myeloma Stem cells: molecular characterization and self-renewal mechanisms involved in the disease persistence

The existence of Multiple Myeloma Stem cells (MMSCs)is supposed to be one of the major causes of MM drug-resistance. However, very little is known about the molecular characteristics of MMSCs, even if some studies suggested that these cells resembles the memory B cells. In order to molecularly characterize MMSCs, we isolated the 138+138- population. For each cell fraction we performed a VDJ rearrangement analysis. The complete set of aberrations were performed by SNP Array 6.0 and HG-U133 Plus 2.0 microarray analyses (Affymetrix). The VDJ rearrangement analyses confirmed the clonal relationship between the 138+ clone and the immature clone. Both BM and PBL 138+ clones showed exactly the same genomic macroalterations. In the BM and PBL 138-19+27+ cell fractions several micro-alterations (range: 1-350 Kb) unique of the memory B cells clone were highlighted. Any micro-alterations detected were located out of any genomic variants region and are presumably associated to the MM pathogenesis, as confirmed by the presence of KRAS, WWOX and XIAP genes among the amplified regions. To get insight into the biology of the clonotypic B cell population, we compared the gene expression profile of 8 MM B cells samples 5 donor B cells vs, thus showing a differential expression of 11480 probes (p-value: <0,05). Among the self-renewal mechanisms, we observed the down-regulation of Hedgehog pathway and the iperactivation of Notch and Wnt signaling. Moreover, these immature cells showed a particular phenotype correlated to resistance to proteasome inhibitors (IRE1α-XBP1: -18.0; -19.96. P<0,05). Data suggested that the MM 138+ clone might resume the end of the complex process of myelomagenesis, whereas the memory B cells have some intriguing micro-alterations and a specific transcriptional program, supporting the idea that these post germinal center cells might be involved in the transforming event that originate and sustain the neoplastic clone.

Valutazione del coinvolgimento dell'oncogene c-myc e dei trasportatori abc nella farmacoresistenza dell'osteosarcoma ad alto grado

L’insorgenza di fenomeni coinvolti nello sviluppo della farmacoresistenza costituisce al momento la principale causa di mancata risposta al trattamento chemioterapico nell’osteosarcoma. Questo è in parte dovuto ad una sovraespressione di diversi trasportatori ABC nelle cellule tumorali che causano un aumento dell’efflusso extracellulare del chemioterapico e pertanto una ridotta risposta al trattamento farmacologico. L'oncogene C-MYC è coinvolto nella resistenza al metothrexate, alla doxorubicina e al cisplatino ed è un fattore prognostico avverso, se sovraespresso al momento della diagnosi, in pazienti affetti da osteosarcoma. C-MYC è in grado di regolare l'espressione di diversi trasportatori ABC, probabilmente coinvolti nella resistenza ai farmaci nell’osteosarcoma, e questo potrebbe spiegare l’impatto prognostico avverso dell’oncogene in questo tumore. L’espressione genica di C-MYC e di 16 trasportatori ABC, regolati da C-MYC e / o responsabili dell'efflusso di diversi chemioterapici, è stata valutata su due diverse casistiche cliniche e su un pannello di linee cellulari di osteosarcoma umano mediante real-time PCR. L'espressione della proteina è stata valutata per i 9 trasportatori ABC risultati più rilevanti.Infine l'efficacia in vitro di un inibitore, specifico per ABCB1 e ABCC1, è stata valutata su linee cellulari di osteosarcoma. ABCB1 e ABCC1 sono i trasportatori più espressi nelle linee cellulari di osteosarcoma. ABCB1 è sovraespresso al momento della diagnosi in circa il 40-45% dei pazienti affetti da osteosarcoma e si conferma essere un fattore prognostico avverso se sovraespresso al momento della diagnosi. Pertanto ABCB1 diventa il bersaglio di elezione per lo sviluppo di strategie terapeutiche alternative, nel trattamento dell’osteosarcoma, atte al superamento della farmacoresistenza. L’inibizione dell'attività di tale trasportatore causa un aumento della sensibilità al trattamento chemioterapico nelle linee cellulari di osteosarcoma farmacoresistenti, indicando questo approccio come una possibile strategia per superare il problema della mancata risposta al trattamento farmacologico nei pazienti con osteosarcoma che sovraesprimono ABCB1.

In-vivo-Tumorbiologie mittels 68 Ga-PET: Beurteilung der p-Glykoprotein-Aktivität in Weichgewebe-Tumoren sowie Diagnose und Therapie von Knochenmetastasen

Krebs ist eine der häufigsten Krankheiten und stellt eine der wichtigsten medizinischen Herausforderungen des 21. Jahrhunderts dar. Eine frühzeitige Diagnose ist dabei essentiell für eine individuell angepasste Therapie zur Verbesserung der Lebensqualität und -erwartung der Patienten. Hierbei kommen der 68Ge/68Ga-Generator und das daraus resultierende PET-Nuklid 68Ga immer stärker in den Fokus von Wissenschaft und Medizin. rnrnFür eine erfolgreiche Therapie stellt die Chemoresistenz (Multi-Drug-Resistance) zahlreicher Tumore eine schwerwiegende Komplikation dar. Für das Therapieversagen ist die Aktivierung des Transportproteins p-Glykoprotein (pGP) maßgeblich mit verantwortlich. Mit Hilfe der Schiff’schen Base [68Ga]MFL6.MZ konnte die Aktivitätsänderung von pGP unter verschiedener Beeinflussung erstmals in vivo beobachtet werden. So zeigte sich, dass sich unter azidotischen Bedingungen in Tumoren die Aktivität des pGP erhöht und somit vermehrt auch Zytostatika, die pGP-Substrate sind, aus den Tumoren transportiert werden. Durch Aufklärung der Abhängigkeit der pGP-Aktivität von dessen Signalkaskade konnte gezeigt werden, dass durch eine Blockade der MAP-Kinase p38 eine Erniedrigung der pGP-Aktivität zu verzeichnen ist. Die ebenfalls in der Signalkaskade eingebundene MAP-Kinase ERK1/2 hingegen spielt hier nur eine untergeordnete Rolle.rnrnNeben dem Versagen der Chemotherapie stellt auch die Metastasierung eines Malignoms massive Einschnitte in die Lebensqualität von Erkrankten dar. Befallen die Metastasen das Skelett eines Menschen, wird dies zumeist erst spät registriert. 68Ga-markierte Bisphosphonate bieten nun die Möglichkeit, Patienten quantitativ auf Knochenmetastasen hin untersuchen zu können. So konnten zu Beginn einfache Phosphonate wie EDTMP und DOTP nicht die nötige in vivo Stabilität bzw. hohe radiochemische Ausbeuten liefern und sind damit für die Anwendung am Menschen uninteressant. Jedoch die DOTA-basierten Bisphosphonate allen voran der Ligand BPAMD zeigen ein großes Potential. In vivo-Versuche an Ratten mit Knochenmetastasen zeigten, dass sich [68Ga]BPAMD an den Metastasen anreichert und einen sehr guten Kontrast zum gesunden Knochen darstellt. Der Tracer konnte erstmals am Menschen angewendet werden und zeigte in ausgewählten Regionen eine höhere Anreicherung als eine zuvor durchgeführte PET-Aufnahme mit [18F]Fluorid. Der Ligand BPAMD bietet außerdem den Vorteil, neben 68Ga auch andere dreiwertige Radionuklide wie das therapeutische 177Lu komplexieren zu können. Durch Studien zur Komplexbildung und Stabilität konnte auch [177Lu]BPAMD in der klinischen Anwendung erprobt werden und zeigte eine Anreicherung an den Knochenmetastasen. So ist es nun möglich, Knochenmetastasen mittels 68Ga-PET zu diagnostizieren, eine entsprechende Dosisberechnung anzustellen und anschließend mit dem gleichen Liganden eine Therapie mit [177Lu]BPAMD durchzuführen.

Biochemische Charakterisierung der Zyklin-abhängigen Kinase 2,Aktivator-Komplexe des Parasiten Eimeria tenella sowie deren Nutzung in der Wirkstoffforschung

Der Stamm der Apicomplexa ist eine artenreiche Gruppe, der einzellige, meist obligat intrazelluläre Parasiten angehören, darunter auch erstzunehmende Krankheitserreger wie Plasmodium sp. sowie tierpathogene Vertreter wie Eimeria sp. und Theileria sp. Eimeria sp. verursacht die Kokzidiose beim Huhn. Diese Krankheit bedingt weltweite Verluste in der Geflügelindustrie von etwa 3 Milliarden US$ pro Jahr [DALLOUL & LILLEHOJ, 2006; SHIRLEY et al., 2007; LUCIUS & LOOS-FRANK, 2008]. Die Parasiten weisen eine hohe Resistenzbildungsrate gegen vorhandene Wirkstoffe auf. Zudem ist der Einsatz von Vakzinen mit Nebenwirkungen verbunden und für hohe Produktionskosten verantwortlich. Daher ist die Entwicklung von neuen, kostengünstigen und effektiven Kokzidiostatika eine dringend notwendige Herausforderung [KINNAIRD et al., 2004]. rnAuf Grund ihrer essentiellen, regulatorischen Funktion im eukaryotischen Zellzyklus sind Zyklin-abhängige Kinasen (CDKs) validierte Zielproteine [LEHNINGER et al., 2005]. Auch Eimeria tenella CDC2-related kinase 2 (EtCRK2) wurde bereits mittels des bekannten CDK-Inhibitors Flavopiridol als Zielprotein chemisch validiert [ENGELS et al., 2010]. Wie bei allen CDKs ist die Aktivität von EtCRK2 abhängig von der Bindung eines Aktivators, der zur Zyklin-Proteinfamilie gehört. Dieser natürliche EtCRK2-Aktivator war jedoch bislang nicht bekannt. Deshalb war ein Teil dieser Arbeit die Identifizierung des natürlichen EtCRK2-Aktivators. Bioinformatische Analysen identifizierten vier E. tenella Zyklin-ähnliche Proteine (EtCYC1, EtCYC3a, EtCYC3b und EtCYC4), die nah verwandt zu den Plasmodium falciparum-Zyklinen sind [ENGELS et al., 2010; SUÁREZ FERNÁNDEZ et al., bislang unveröffentlichte Daten]. Im Rahmen dieser Arbeit konnten zwei neue Aktivatoren identifiziert und biochemisch charakterisiert werden: der bekannte CDK-Aktivator XlRINGO und das neue E. tenella-Zyklin EtCYC3a. Nachdem der nicht-radioaktive TR-FRET-Assay für die EtCRK2 etabliert und optimiert wurde, konnte die EtCRK2-Aktivität im Komplex mit beiden Aktivatoren und weitere wichtige kinetische Parameter bestimmt werden.rnZusätzlich wurde dieser Assay zum in vitro Screening einer kommerziellen Chemikalienbibliothek auf die EtCRK2 eingesetzt, um potentielle Inhibitoren für EtCRK2 zu identifizieren. Dieses in vitro Screening gefolgt von einer in silico Hit-Anreicherung identifizierte 19 aktive Verbindungen für die durch EtCYC3a und XlRINGO aktivierte EtCRK2. Zudem wurden drei Struktur-Cluster definiert: Naphthoquinone, 8-Hydroxyquinoline und 2-Pyrimidinyl-aminopiperidin-propan-2-ole. rnDie aktivsten Vertreter von jedem Cluster wurden als Leitstrukturen ausgewählt und auf EtCRK2 und HsCDK2 getestet. Aufgrund ihrer inhibierenden Wirkung auf EtCRK2 stellen diese Verbindungen viel versprechende Leitstrukturen für die Entwicklung eines neuen Antikokzidiums dar. Hiermit konnte auch gezeigt werden, dass BES124764, der Vertreter des 2-Pyrimidinyl-aminopiperidin-propan-2-ol-Clusters, in der Lage ist, die EtCRK2 selektiv zu inhibieren. rnDaher wird BES124764 sowie einige Derivate in den Leitstruktur-Optimierungsprozess für die Auffindung eines neuen Arzneimittelkandidaten gegen Kokzidiose eingehen.rn

Shikonin directly targets mitochondria and causes mitochondrial dysfunction in cancer cells

Chemotherapy is a mainstay of cancer treatment. Due to increased drug resistance and the severe side effects of currently used therapeutics, new candidate compounds are required for improvement of therapy success. Shikonin, a natural naphthoquinone, was used in traditional Chinese medicine for the treatment of different inflammatory diseases and recent studies revealed the anticancer activities of shikonin. We found that shikonin has strong cytotoxic effects on 15 cancer cell lines, including multidrug-resistant cell lines. Transcriptome-wide mRNA expression studies showed that shikonin induced genetic pathways regulating cell cycle, mitochondrial function, levels of reactive oxygen species, and cytoskeletal formation. Taking advantage of the inherent fluorescence of shikonin, we analyzed its uptake and distribution in live cells with high spatial and temporal resolution using flow cytometry and confocal microscopy. Shikonin was specifically accumulated in the mitochondria, and this accumulation was associated with a shikonin-dependent deregulation of cellular Ca(2+) and ROS levels. This deregulation led to a breakdown of the mitochondrial membrane potential, dysfunction of microtubules, cell-cycle arrest, and ultimately induction of apoptosis. Seeing as both the metabolism and the structure of mitochondria show marked differences between cancer cells and normal cells, shikonin is a promising candidate for the next generation of chemotherapy.