Parameters and algorithms to evaluate cardiac mechanics by conductance catheter

This work is structured as follows: In Section 1 we discuss the clinical problem of heart failure. In particular, we present the phenomenon known as ventricular mechanical dyssynchrony: its impact on cardiac function, the therapy for its treatment and the methods for its quantification. Specifically, we describe the conductance catheter and its use for the measurement of dyssynchrony. At the end of the Section 1, we propose a new set of indexes to quantify the dyssynchrony that are studied and validated thereafter. In Section 2 we describe the studies carried out in this work: we report the experimental protocols, we present and discuss the results obtained. Finally, we report the overall conclusions drawn from this work and we try to envisage future works and possible clinical applications of our results. Ancillary studies that were carried out during this work mainly to investigate several aspects of cardiac resynchronization therapy (CRT) are mentioned in Appendix. -------- Ventricular mechanical dyssynchrony plays a regulating role already in normal physiology but is especially important in pathological conditions, such as hypertrophy, ischemia, infarction, or heart failure (Chapter 1,2.). Several prospective randomized controlled trials supported the clinical efficacy and safety of cardiac resynchronization therapy (CRT) in patients with moderate or severe heart failure and ventricular dyssynchrony. CRT resynchronizes ventricular contraction by simultaneous pacing of both left and right ventricle (biventricular pacing) (Chapter 1.). Currently, the conductance catheter method has been used extensively to assess global systolic and diastolic ventricular function and, more recently, the ability of this instrument to pick-up multiple segmental volume signals has been used to quantify mechanical ventricular dyssynchrony. Specifically, novel indexes based on volume signals acquired with the conductance catheter were introduced to quantify dyssynchrony (Chapter 3,4.). Present work was aimed to describe the characteristics of the conductancevolume signals, to investigate the performance of the indexes of ventricular dyssynchrony described in literature and to introduce and validate improved dyssynchrony indexes. Morevoer, using the conductance catheter method and the new indexes, the clinical problem of the ventricular pacing site optimization was addressed and the measurement protocol to adopt for hemodynamic tests on cardiac pacing was investigated. In accordance to the aims of the work, in addition to the classical time-domain parameters, a new set of indexes has been extracted, based on coherent averaging procedure and on spectral and cross-spectral analysis (Chapter 4.). Our analyses were carried out on patients with indications for electrophysiologic study or device implantation (Chapter 5.). For the first time, besides patients with heart failure, indexes of mechanical dyssynchrony based on conductance catheter were extracted and studied in a population of patients with preserved ventricular function, providing information on the normal range of such a kind of values. By performing a frequency domain analysis and by applying an optimized coherent averaging procedure (Chapter 6.a.), we were able to describe some characteristics of the conductance-volume signals (Chapter 6.b.). We unmasked the presence of considerable beat-to-beat variations in dyssynchrony that seemed more frequent in patients with ventricular dysfunction and to play a role in discriminating patients. These non-recurrent mechanical ventricular non-uniformities are probably the expression of the substantial beat-to-beat hemodynamic variations, often associated with heart failure and due to cardiopulmonary interaction and conduction disturbances. We investigated how the coherent averaging procedure may affect or refine the conductance based indexes; in addition, we proposed and tested a new set of indexes which quantify the non-periodic components of the volume signals. Using the new set of indexes we studied the acute effects of the CRT and the right ventricular pacing, in patients with heart failure and patients with preserved ventricular function. In the overall population we observed a correlation between the hemodynamic changes induced by the pacing and the indexes of dyssynchrony, and this may have practical implications for hemodynamic-guided device implantation. The optimal ventricular pacing site for patients with conventional indications for pacing remains controversial. The majority of them do not meet current clinical indications for CRT pacing. Thus, we carried out an analysis to compare the impact of several ventricular pacing sites on global and regional ventricular function and dyssynchrony (Chapter 6.c.). We observed that right ventricular pacing worsens cardiac function in patients with and without ventricular dysfunction unless the pacing site is optimized. CRT preserves left ventricular function in patients with normal ejection fraction and improves function in patients with poor ejection fraction despite no clinical indication for CRT. Moreover, the analysis of the results obtained using new indexes of regional dyssynchrony, suggests that pacing site may influence overall global ventricular function depending on its relative effects on regional function and synchrony. Another clinical problem that has been investigated in this work is the optimal right ventricular lead location for CRT (Chapter 6.d.). Similarly to the previous analysis, using novel parameters describing local synchrony and efficiency, we tested the hypothesis and we demonstrated that biventricular pacing with alternative right ventricular pacing sites produces acute improvement of ventricular systolic function and improves mechanical synchrony when compared to standard right ventricular pacing. Although no specific right ventricular location was shown to be superior during CRT, the right ventricular pacing site that produced the optimal acute hemodynamic response varied between patients. Acute hemodynamic effects of cardiac pacing are conventionally evaluated after stabilization episodes. The applied duration of stabilization periods in most cardiac pacing studies varied considerably. With an ad hoc protocol (Chapter 6.e.) and indexes of mechanical dyssynchrony derived by conductance catheter we demonstrated that the usage of stabilization periods during evaluation of cardiac pacing may mask early changes in systolic and diastolic intra-ventricular dyssynchrony. In fact, at the onset of ventricular pacing, the main dyssynchrony and ventricular performance changes occur within a 10s time span, initiated by the changes in ventricular mechanical dyssynchrony induced by aberrant conduction and followed by a partial or even complete recovery. It was already demonstrated in normal animals that ventricular mechanical dyssynchrony may act as a physiologic modulator of cardiac performance together with heart rate, contractile state, preload and afterload. The present observation, which shows the compensatory mechanism of mechanical dyssynchrony, suggests that ventricular dyssynchrony may be regarded as an intrinsic cardiac property, with baseline dyssynchrony at increased level in heart failure patients. To make available an independent system for cardiac output estimation, in order to confirm the results obtained with conductance volume method, we developed and validated a novel technique to apply the Modelflow method (a method that derives an aortic flow waveform from arterial pressure by simulation of a non-linear three-element aortic input impedance model, Wesseling et al. 1993) to the left ventricular pressure signal, instead of the arterial pressure used in the classical approach (Chapter 7.). The results confirmed that in patients without valve abnormalities, undergoing conductance catheter evaluations, the continuous monitoring of cardiac output using the intra-ventricular pressure signal is reliable. Thus, cardiac output can be monitored quantitatively and continuously with a simple and low-cost method. During this work, additional studies were carried out to investigate several areas of uncertainty of CRT. The results of these studies are briefly presented in Appendix: the long-term survival in patients treated with CRT in clinical practice, the effects of CRT in patients with mild symptoms of heart failure and in very old patients, the limited thoracotomy as a second choice alternative to transvenous implant for CRT delivery, the evolution and prognostic significance of diastolic filling pattern in CRT, the selection of candidates to CRT with echocardiographic criteria and the prediction of response to the therapy.

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.

Trasduzione del segnale inositide-dipendente nel carcinoma della mammella

Breast carcinoma, one of the most frequent malignancies in women, is a complex disease in which a number of different factors combine to drive pathogenesis. The biopathological characterization of these tumors is essential to determine their aggressiveness and to find the most appropriate therapy. As in others neoplasms, the deregulation of signal transduction pathways is frequently responsible for conferring selective biological advantages to the tumor. Phosphoinositides play an essential role in diverse cellular functions, their metabolism is highly active, and is tightly controlled. Among the enzymes implicated in this pathway, phospholipase C beta 1 (PLCβ1) is one of the key regulators, both at the cytoplasmic and the nuclear level. The PLCβ1 gene maps onto the short arm of chromosome 20, a region that has been shown to be altered in several solid tumors, including breast cancer. In the present study a FISH approach was used to investigate the genetic alterations of the PLCβ1 gene in various classes of breast cancer which differ in their invasiveness and proliferation status, according to their mitotic index. The overall aim was to find out whether this enzyme could be a suitable prognostic marker for this neoplasm. Our results show that 83% of cases had aneusomies at the 20p12 level, and the most frequent alteration is a gain in this specific locus. Indeed, we found that this amplification is not related to the invasion status since there were no differences in amplified tumor frequencies between in situ and invasive breast cancer. On the contrary, the gain of PLCβ1 was significantly related to the mitotic index (p = 0.001). To verify if the change in genetic dosage influences the expression of PLCβ1 we performed Real Time PCR and Immunohystochemical analysis. Our results confirmed that amplified tumors have higher levels of PLCβ1 mRNA, which is the sum of the two splicing isoforms 1a and 1b. On the other hand, even if protein levels were higher in the majority of cases compared to the nontumoral specimens, there were no significant associations between gain and overexpression. Finally, the significant association between the amplification of PLCβ1 and others important clinicopathological parameters, such as grading and hormonal receptors status, confirmed a correlation of this enzyme with the aggressiveness of breast cancer. This suggests that PLCβ1 has the potential to be a prognostic marker in these tumors. However, further work needs to be carried out to validate these preliminary findings.

Analisi genetico-molecolare dei linfomi a cellule T periferiche

Molecular profiling of Peripheral T-cell lymphomas not otherwise specified Peripheral T-cell lymphomas (PTCLs) are a heterogeneous group of tumors that the WHO classification basically subdivides into specified and not otherwise specified (NOS). In Western countries, they represent around 12% of all non-Hodgkin's lymphomas. In particular, PTCL/NOS is the commonest subtype, corresponding to about 60-70% of all T-cell lymphomas. However, it remains a complex entity showing great variety regarding either morphology, immunophenotype or clinical behavior. Specially, the molecular pathology of these tumors is still poorly known. In fact, many alteration were found, but no single genes were demonstrated to have a pathogenetic role. Recently, gene expression profiling (GEP) allowed the identification of PTCL/NOS-associated molecular signatures, leading to better understanding of their histogenesis, pathogenesis and prognostication. Interestingly, proliferation pathways are commonly altered in PTCLs, being highly proliferative cases characterized by poorer prognosis. In this study, we aimed to investigate the possible role in PTCL/NOS pathogenesis of selected molecules, known to be relevant for proliferation control. In particular, we analyzed the cell cycle regulators PTEN and CDKN1B/p27, the NF-kB pathway, and the tyrosin kinase PDGFR. First, we found that PTEN and p27 seem to be regulated in PTCL/NOS as in normal T-lymphocytes, as to what expression and cellular localization are concerned, and do not present structural abnormalities in the vast majority of PTCL/NOS. Secondly, NF-kB pathway appeared to be variably activated in PTCL/NOS. In particular, according to NF-kB gene expression levels, the tumors could be divided into two clusters (C1 and C2). Specially, C1 corresponded to cases presenting with a global down-regulation of the entire pathway, while C2 showed over-expression of genes involved in TNF signaling. Notably, by immunohistochemistry, we showed that either the canonical or the alternative NK-kB pathway were activated in around 40% of cases. Finally, we found PGDFRA to be consistently over-expressed (at mRNA and protein level) and activated in almost all PTCLs/NOS. Noteworthy, when investigating possible causes for PDGFRA deregulation, we had evidences that PDGFR over-expression is due to the absence of miR-152, which appeared to be responsible for PDGFRA silencing in normal T-cells. Furthermore, we could demonstrate that its aberrant activation is sustained by an autocrine loop. Importantly, this is the first case, to the best of our knowledge, of hematological tumor in which tyrosin kinase aberrant activity is determined by deregulated miRNA expression and autocrine loop activation. Taken together, our results provide novel insight in PTCL/NOS pathogenesis by opening new intriguing scenarios for innovative therapeutic interventions.

Bonded structures for enhanced damage tolerant pressurized fuselages

Adhesive bonding provides solutions to realize cost effective and low weight aircraft fuselage structures, in particular where the Damage Tolerance (DT) is the design criterion. Bonded structures that combine Metal Laminates (MLs) and eventually Selective Reinforcements can guarantee slow crack propagation, crack arrest and large damage capability. To optimize the design exploiting the benefit of bonded structures incorporating selective reinforcement requires reliable analysis tools. The effect of bonded doublers / selective reinforcements is very difficult to be predicted numerically or analytically due to the complexity of the underlying mechanisms and failures modes acting. Reliable predictions of crack growth and residual strength can only be based on sound empirical and phenomenological considerations strictly related to the specific structural concept. Large flat stiffened panels that combine MLs and selective reinforcements have been tested with the purpose of investigating solutions applicable to pressurized fuselages. The large test campaign (for a total of 35 stiffened panels) has quantitatively investigated the role of the different metallic skin concepts (monolithic vs. MLs) of the aluminum, titanium and glass-fiber reinforcements, of the stringers material and cross sections and of the geometry and location of doublers / selective reinforcements. Bonded doublers and selective reinforcements confirmed to be outstanding tools to improve the DT properties of structural elements with a minor weight increase. However the choice of proper materials for the skin and the stringers must be not underestimated since they play an important role as well. A fuselage structural concept has been developed to exploit the benefit of a metal laminate design concept in terms of high Fatigue and Damage Tolerance (F&DT) performances. The structure used laminated skin (0.8mm thick), bonded stringers, two different splicing solutions and selective reinforcements (glass prepreg embedded in the laminate) under the circumferential frames. To validate the design concept a curved panel was manufactured and tested under loading conditions representative of a single aisle fuselage: cyclic internal pressurization plus longitudinal loads. The geometry of the panel, design and loading conditions were tailored for the requirements of the upper front fuselage. The curved panel has been fatigue tested for 60 000 cycles before the introduction of artificial damages (cracks in longitudinal and circumferential directions). The crack growth of the artificial damages has been investigated for about 85 000 cycles. At the end a residual strength test has been performed with a “2 bay over broken frame” longitudinal crack. The reparability of this innovative concept has been taken into account during design and demonstrated with the use of an external riveted repair. The F&DT curved panel test has confirmed that a long fatigue life and high damage tolerance can be achieved with a hybrid metal laminate low weight configuration. The superior fatigue life from metal laminates and the high damage tolerance characteristics provided by integrated selective reinforcements are the key concepts that provided the excellent performances. The weight comparison between the innovative bonded concept and a conventional monolithic riveted design solution showed a significant potential weight saving but the weight advantages shall be traded off with the additional costs.

Mitochondrial Genomics: structure, inheritance and phylogenetic utility of the Mitochondrial genome in Bivalvia and Insecta

This PhD Thesis is the result of my research activity in the last three years. My main research interest was centered on the evolution of mitochondrial genome (mtDNA), and on its usefulness as a phylogeographic and phylogenetic marker at different taxonomic levels in different taxa of Metazoa. From a methodological standpoint, my main effort was dedicated to the sequencing of complete mitochondrial genomes, and the approach to whole-genome sequencing was based on the application of Long-PCR and shotgun sequences. Moreover, this research project is a part of a bigger sequencing project of mtDNAs in many different Metazoans’ taxa, and I mostly dedicated myself to sequence and analyze mtDNAs in selected taxa of bivalves and hexapods (Insecta). Sequences of bivalve mtDNAs are particularly limited, and my study contributed to extend the sampling. Moreover, I used the bivalve Musculista senhousia as model taxon to investigate the molecular mechanisms and the evolutionary significance of their aberrant mode of mitochondrial inheritance (Doubly Uniparental Inheritance, see below). In Insects, I focused my attention on the Genus Bacillus (Insecta Phasmida). A detailed phylogenetic analysis was performed in order to assess phylogenetic relationships within the genus, and to investigate the placement of Phasmida in the phylogenetic tree of Insecta. The main goal of this part of my study was to add to the taxonomic coverage of sequenced mtDNAs in basal insects, which were only partially analyzed.

Untersuchung des murinen, nukleären pSS- und SLE-Autoantigens La/SS-B unter physiologischen und pathophysiologischen Bedingungen

Zusammenfassung der Dissertation von Christian Schörner 'Untersuchung des murinen, nukleären pSS- und SLE-Autoantigens La/SS-B unter physiologischen und pathophysiologischen Bedingungen' am Fachbereich Biologie der Johannes Gutenberg-Universität Mainz Seren von Patienten mit Kollagenosen, wie SLE und pSS, enthalten Antikörper gegen das Autoantigen La/SS-B. Im murinen Tiermodell musste die Expression des La/SS-B verstanden werden. Das murine Strukturgen codierte für 13 Exons, das Start-AUG befand sich im Exon 2. Die alternativen mRNAs unterschieden sich nur in ihrer 5'-UTR. Das Exon 1b war im Vergleich zum Exon 1a am 3'-Ende um 27 Nukleotide verlängert. Die alternativen mRNAs entstanden durch einen Promotorwechsel in Kombination mit einem alternativen Spleißvorgang. Die Polyadenylierung erfolgte an zwei alternativen Polyadenylierungssequenzen. Die mRNAs waren vollständig gesplissen, zytoplasmatisch und funktionell. Die Exon 1a- und die Exon 1c-mRNA wurden ubiquitär exprimiert, die Exon 1b-mRNA dagegen nur in proliferierenden Zellen. Im C-Terminus fand sich eine Nager-spezifische Insertion sowie eine -deletion. Das Protein besaß mit 16 isoelektrischen Proteinformen eine hohe Ladungsheterogenität. NO steigerte die Proteinexpression um das 5fache und bewirkte eine Translokation des Proteins vom Zellkern in das Zytoplasma. Das humane La/SS-B-Neoepitop induzierte in Versuchstieren die Bildung von Antikörper gegen das Neoepitop und natives La/SS-B.

Studies of OPA1 pathogenic mechanisms in Dominant Optic Atrophy and novel protein function in mitochondrial DNA stability

The mitochondrion is an essential cytoplasmic organelle that provides most of the energy necessary for eukaryotic cell physiology. Mitochondrial structure and functions are maintained by proteins of both mitochondrial and nuclear origin. These organelles are organized in an extended network that dynamically fuses and divides. Mitochondrial morphology results from the equilibrium between fusion and fission processes, controlled by a family of “mitochondria-shaping” proteins. It is becoming clear that defects in mitochondrial dynamics can impair mitochondrial respiration, morphology and motility, leading to apoptotic cell death in vitro and more or less severe neurodegenerative disorders in vivo in humans. Mutations in OPA1, a nuclear encoded mitochondrial protein, cause autosomal Dominant Optic Atrophy (DOA), a heterogeneous blinding disease characterized by retinal ganglion cell degeneration leading to optic neuropathy (Delettre et al., 2000; Alexander et al., 2000). OPA1 is a mitochondrial dynamin-related guanosine triphosphatase (GTPase) protein involved in mitochondrial network dynamics, cytochrome c storage and apoptosis. This protein is anchored or associated on the inner mitochondrial membrane facing the intermembrane space. Eight OPA1 isoforms resulting from alternative splicing combinations of exon 4, 4b and 5b have been described (Delettre et al., 2001). These variants greatly vary among diverse organs and the presence of specific isoforms has been associated with various mitochondrial functions. The different spliced exons encode domains included in the amino-terminal region and contribute to determine OPA1 functions (Olichon et al., 2006). It has been shown that exon 4, that is conserved throughout evolution, confers functions to OPA1 involved in maintenance of the mitochondrial membrane potential and in the fusion of the network. Conversely, exon 4b and exon 5b, which are vertebrate specific, are involved in regulation of cytochrome c release from mitochondria, and activation of apoptosis, a process restricted to vertebrates (Olichon et al., 2007). While Mgm1p has been identified thanks to its role in mtDNA maintenance, it is only recently that OPA1 has been linked to mtDNA stability. Missense mutations in OPA1 cause accumulation of multiple deletions in skeletal muscle. The syndrome associated to these mutations (DOA-1 plus) is complex, consisting of a combination of dominant optic atrophy, progressive external ophtalmoplegia, peripheral neuropathy, ataxia and deafness (Amati- Bonneau et al., 2008; Hudson et al., 2008). OPA1 is the fifth gene associated with mtDNA “breakage syndrome” together with ANT1, PolG1-2 and TYMP (Spinazzola et al., 2009). In this thesis we show for the first time that specific OPA1 isoforms associated to exon 4b are important for mtDNA stability, by anchoring the nucleoids to the inner mitochondrial membrane. Our results clearly demonstrate that OPA1 isoforms including exon 4b are intimately associated to the maintenance of the mitochondrial genome, as their silencing leads to mtDNA depletion. The mechanism leading to mtDNA loss is associated with replication inhibition in cells where exon 4b containing isoforms were down-regulated. Furthermore silencing of exon 4b associated isoforms is responsible for alteration in mtDNA-nucleoids distribution in the mitochondrial network. In this study it was evidenced that OPA1 exon 4b isoform is cleaved to provide a 10kd peptide embedded in the inner membrane by a second transmembrane domain, that seems to be crucial for mitochondrial genome maintenance and does correspond to the second transmembrane domain of the yeasts orthologue encoded by MGM1 or Msp1, which is also mandatory for this process (Diot et al., 2009; Herlan et al., 2003). Furthermore in this thesis we show that the NT-OPA1-exon 4b peptide co-immuno-precipitates with mtDNA and specifically interacts with two major components of the mitochondrial nucleoids: the polymerase gamma and Tfam. Thus, from these experiments the conclusion is that NT-OPA1- exon 4b peptide contributes to the nucleoid anchoring in the inner mitochondrial membrane, a process that is required for the initiation of mtDNA replication and for the distribution of nucleoids along the network. These data provide new crucial insights in understanding the mechanism involved in maintenance of mtDNA integrity, because they clearly demonstrate that, besides genes implicated in mtDNA replications (i.e. polymerase gamma, Tfam, twinkle and genes involved in the nucleotide pool metabolism), OPA1 and mitochondrial membrane dynamics play also an important role. Noticeably, the effect on mtDNA is different depending on the specific OPA1 isoforms down-regulated, suggesting the involvement of two different combined mechanisms. Over two hundred OPA1 mutations, spread throughout the coding region of the gene, have been described to date, including substitutions, deletions or insertions. Some mutations are predicted to generate a truncated protein inducing haploinsufficiency, whereas the missense nucleotide substitutions result in aminoacidic changes which affect conserved positions of the OPA1 protein. So far, the functional consequences of OPA1 mutations in cells from DOA patients are poorly understood. Phosphorus MR spectroscopy in patients with the c.2708delTTAG deletion revealed a defect in oxidative phosphorylation in muscles (Lodi et al., 2004). An energetic impairment has been also show in fibroblasts with the severe OPA1 R445H mutation (Amati-Bonneau et al., 2005). It has been previously reported by our group that OPA1 mutations leading to haploinsufficiency are associated in fibroblasts to an oxidative phosphorylation dysfunction, mainly involving the respiratory complex I (Zanna et al., 2008). In this study we have evaluated the energetic efficiency of a panel of skin fibroblasts derived from DOA patients, five fibroblast cell lines with OPA1 mutations causing haploinsufficiency (DOA-H) and two cell lines bearing mis-sense aminoacidic substitutions (DOA-AA), and compared with control fibroblasts. Although both types of DOA fibroblasts maintained a similar ATP content when incubated in a glucose-free medium, i.e. when forced to utilize the oxidative phosphorylation only to produce ATP, the mitochondrial ATP synthesis through complex I, measured in digitonin-permeabilized cells, was significantly reduced in cells with OPA1 haploinsufficiency only, whereas it was similar to controls in cells with the missense substitutions. Furthermore, evaluation of the mitochondrial membrane potential (DYm) in the two fibroblast lines DOA-AA and in two DOA-H fibroblasts, namely those bearing the c.2819-2A>C mutation and the c.2708delTTAG microdeletion, revealed an anomalous depolarizing response to oligomycin in DOA-H cell lines only. This finding clearly supports the hypothesis that these mutations cause a significant alteration in the respiratory chain function, which can be unmasked only when the operation of the ATP synthase is prevented. Noticeably, oligomycin-induced depolarization in these cells was almost completely prevented by preincubation with cyclosporin A, a well known inhibitor of the permeability transition pore (PTP). This results is very important because it suggests for the first time that the voltage threshold for PTP opening is altered in DOA-H fibroblasts. Although this issue has not yet been addressed in the present study, several are the mechanisms that have been proposed to lead to PTP deregulation, including in particular increased reactive oxygen species production and alteration of Ca2+ homeostasis, whose role in DOA fibroblasts PTP opening is currently under investigation. Identification of the mechanisms leading to altered threshold for PTP regulation will help our understanding of the pathophysiology of DOA, but also provide a strategy for therapeutic intervention.

Transcriptional functions of DNA Topoisomerases at a genome-wide scale and a single gene levels

The DNA topology is an important modifier of DNA functions. Torsional stress is generated when right handed DNA is either over- or underwound, producing structural deformations which drive or are driven by processes such as replication, transcription, recombination and repair. DNA topoisomerases are molecular machines that regulate the topological state of the DNA in the cell. These enzymes accomplish this task by either passing one strand of the DNA through a break in the opposing strand or by passing a region of the duplex from the same or a different molecule through a double-stranded cut generated in the DNA. Because of their ability to cut one or two strands of DNA they are also target for some of the most successful anticancer drugs used in standard combination therapies of human cancers. An effective anticancer drug is Camptothecin (CPT) that specifically targets DNA topoisomerase 1 (TOP 1). The research project of the present thesis has been focused on the role of human TOP 1 during transcription and on the transcriptional consequences associated with TOP 1 inhibition by CPT in human cell lines. Previous findings demonstrate that TOP 1 inhibition by CPT perturbs RNA polymerase (RNAP II) density at promoters and along transcribed genes suggesting an involvement of TOP 1 in RNAP II promoter proximal pausing site. Within the transcription cycle, promoter pausing is a fundamental step the importance of which has been well established as a means of coupling elongation to RNA maturation. By measuring nascent RNA transcripts bound to chromatin, we demonstrated that TOP 1 inhibition by CPT can enhance RNAP II escape from promoter proximal pausing site of the human Hypoxia Inducible Factor 1 (HIF-1) and c-MYC genes in a dose dependent manner. This effect is dependent from Cdk7/Cdk9 activities since it can be reversed by the kinases inhibitor DRB. Since CPT affects RNAP II by promoting the hyperphosphorylation of its Rpb1 subunit the findings suggest that TOP 1inhibition by CPT may increase the activity of Cdks which in turn phosphorylate the Rpb1 subunit of RNAP II enhancing its escape from pausing. Interestingly, the transcriptional consequences of CPT induced topological stress are wider than expected. CPT increased co-transcriptional splicing of exon1 and 2 and markedly affected alternative splicing at exon 11. Surprisingly despite its well-established transcription inhibitory activity, CPT can trigger the production of a novel long RNA (5’aHIF-1) antisense to the human HIF-1 mRNA and a known antisense RNA at the 3’ end of the gene, while decreasing mRNA levels. The effects require TOP 1 and are independent from CPT induced DNA damage. Thus, when the supercoiling imbalance promoted by CPT occurs at promoter, it may trigger deregulation of the RNAP II pausing, increased chromatin accessibility and activation/derepression of antisense transcripts in a Cdks dependent manner. A changed balance of antisense transcripts and mRNAs may regulate the activity of HIF-1 and contribute to the control of tumor progression After focusing our TOP 1 investigations at a single gene level, we have extended the study to the whole genome by developing the “Topo-Seq” approach which generates a map of genome-wide distribution of sites of TOP 1 activity sites in human cells. The preliminary data revealed that TOP 1 preferentially localizes at intragenic regions and in particular at 5’ and 3’ ends of genes. Surprisingly upon TOP 1 downregulation, which impairs protein expression by 80%, TOP 1 molecules are mostly localized around 3’ ends of genes, thus suggesting that its activity is essential at these regions and can be compensate at 5’ ends. The developed procedure is a pioneer tool for the detection of TOP 1 cleavage sites across the genome and can open the way to further investigations of the enzyme roles in different nuclear processes.

The study of a novel zinc finger gene cluster TZF and a genomic region flanking the histone H 4 replacement gene H 4 r of Drosophila melanogaster

Part I : A zinc finger gene Tzf1 was cloned in the earlier work of the lab by screening a ë-DASH2 cDNA expression library with an anti-Rat SC antibody. A ë-DASH2 genomic DNA library and cosmid lawrist 4 genomic DNA library were screened with the cDNA fragment of Tzf1 to determine the genomic organization of Tzf1. Another putative zinc finger gene Tzf2 was found about 700 bp upstream of Tzf1.RACE experiment was carried out for both genes to establish the whole length cDNA. The cDNA sequences of Tzf and Tzf2 were used to search the Flybase (Version Nov, 2000). They correspond to two genes found in the Flybase, CG4413 and CG4936. The CG4413 transcript seems to be a splicing variant of Tzf transcripts. Another two zinc finger genes Tzf3 and Tzf4 were discovered in silico. They are located 300 bp away from Tzf and Tzf2, and a non-tandem cluster was formed by the four genes. All four genes encode proteins with a very similar modular structure, since they all have five C2H2 type zinc fingers at their c-terminal ends. This is the most compact zinc finger protein gene cluster found in Drosophila melanogaster.Part II: 34,056 bp insert of the cosmid 19G11

Identifikation des Gruppe I Introns CDISt1 in offenen Leserastern des Clostridium difficile Genoms und dessen Charakterisierung als chimäres genetisches Element

Im tcdA-Gen des Clostridium difficile Stammes C34 wurde eine Insertion mit einer Größe von 1975 bp lokalisiert. Der als CdISt1 bezeichneten Insertion konnten charakteristische Merkmale von Gruppe I Introns und von Insertionselementen zugewiesen werden. Dem im 5’ Bereich gelegenen Anteil ließen sich die Intron-spezifischen Eigenschaften zuordnen, im 3’ Anteil wurden zwei offene Leseraster gefunden, die hohe Homologien zu Transposasen der IS605 Familie hatten. Funktionelle Analysen belegten die Spleißaktivität des chimären Ribozymes. CdISt1 konnte in mehren Kopien in allen untersuchten C. difficile Stämmen nachgewiesen werden. In anderen clostridialen Spezies konnte das Gruppe I Intron bislang nicht vorgefunden werden. Der Integrationsort in C. difficile war in allen untersuchten Fällen immer ein offenes Leseraster. Bislang waren Gruppe I Introns noch nie in bakteriellen offenen Leserastern beschrieben worden. Es kann angenommen werden, dass der chimäre Aufbau des Ribozymes die Integration in bakterielle offene Leseraster ermöglicht. Dabei wäre für die Spleißaktivität der Gruppe I Intron Anteil maßgeblich, die Mobilität würde über den IS Element Anteil vermittelt. Im Rahmen der Dissertationsarbeit konnten erste experimentelle Hinweise erbracht werden, dass das chimäre Ribozym an der evolution clostridialer Proteine beteiligt sein kann, wovon seinen Wirt C. difficile entsprechend profitieren würde.An insertion of 1975 bp is situated in the tcdA-gene of Clostridium difficile strain C34. The insertion was designated as CdISt1 and it had characteristics of group I introns and insertion elements. The group I characteristcs could be found in the 5’ area of the genetic element, in the 3’ area two open reading frames were located with high homologies to transposases of the IS605 family. Functional studies could proof the splicing activity of the ribozyme. CdISt1 could be found in several copies in all C. difficile strains examined so far. It was absent in other examined clostridial species. In all cases, the integration site in C. difficile was an open reading frame. Up to now, group I introns never were discovered in bacterial open reading frames. It can be assumed that the chimeric characteristics of the ribozyme permit an integration in bacterial open reading frames. The group I intron part would be responsible of the splicing activity, the IS element part could mediate the mobility of the genetic element. First experimental evidences point to a possible involvement of the chimeric ribozyme in the evolution of clostridial proteins, so the host C. difficile could benefit from its presence.

Charakterisierung von Tumorantigenen des kutanen T-Zell Lymphoms

Immuntherapien stellen basierend auf gut charakterisierten, tumorspezifischen Antigenen ein vielversprechendes Konzept in der Tumor-Therapie dar. Für das kutane T-Zell Lymphom (CTCL) sind bislang nur wenige tumorassoziierte Antigene bekannt. In dieser Arbeit konnten ein mögliches Onkogen (PAR-3ta), ein weiteres, putativ Virus-induziertes Antigen (se57-1), neue Antigene und ihre Splicing-Varianten (se70-2, cTAGE-1/2, cTAGE-5), sowie lymphozytenspezifische Differenzierungsantigene (se20-10-Familie) für das CTCL gefunden werden. Auf Grund des Cancer-Testis spezifischen Expressionsprofils kommen die Antigene cTAGE-1 (46% CTCL-Expression), cTAGE-1B (31%) und cTAGE-5A (44%) für eine CTCL-Immuntherapie in Frage. Einige bekannte, spezifische Tumorantigene konnten auch im CTCL nachgewiesen werden: MAGE-A9 (21%), GAGE 3-7b (46%) und MUC-1 (44%). Die Immunogenität konnte mittels der SEREX-Technologie durch reaktive Antikörper gegen rekombinantes MAGE-A9 in 22% der getesteten CTCL-Seren, gegen GAGE in 16% und gegen cTAGE-5A in 15% bewiesen werden. Die cTAGE-mRNAs bilden eine neue Cancer-Testis Antigenfamilie. Die Multigenfamilie ist durch Retrotransposition eines aktiven Gens (cTAGE-5) entstanden, wobei 7 aktive, transkribierte und 7 nicht transkribierte Pseudogene unterschieden werden müssen. Die aktiven Gene cTAGE-1, cTAGE-1B und cTAGE-5A werden tumorspezifisch aus den Chromosomen 18p11.2 und 14 gespliced. Die Testis-CTCL spezifischen mRNAs können häufig auch in anderen Tumoren gefunden werden. Die Antigene cTAGE-1, cTAGE-5, MAGE-A9 und GAGE 3-7b gehören zu den ersten spezifischen Zielstrukturen des CTCLs, die somit für mögliche Immuntherapien in Betracht kommen.

Comparative genomic sequencing analysis of a region in human chromosome 11p15.3, mouse chromosome 7 and analysis of the novel STK33, Stk33 gene

The comparative genomic sequence analysis of a region in human chromosome 11p15.3 and its homologous segment in mouse chromosome 7 between ST5 and LMO1 genes has been performed. 158,201 bases were sequenced in the mouse and compared with the syntenic region in human, partially available in the public databases. The analysed region exhibits the typical eukaryotic genomic structure and compared with the close neighbouring regions, strikingly reflexes the mosaic pattern distribution of (G+C) and repeats content despites its relative short size. Within this region the novel gene STK33 was discovered (Stk33 in the mouse), that codes for a serine/threonine kinase. The finding of this gene constitutes an excellent example of the strength of the comparative sequencing approach. Poor gene-predictions in the mouse genomic sequence were corrected and improved by the comparison with the unordered data from the human genomic sequence publicly available. Phylogenetical analysis suggests that STK33 belongs to the calcium/calmodulin-dependent protein kinases group and seems to be a novelty in the chordate lineage. The gene, as a whole, seems to evolve under purifying selection whereas some regions appear to be under strong positive selection. Both human and mouse versions of serine/threonine kinase 33, consists of seventeen exons highly conserved in the coding regions, particularly in those coding for the core protein kinase domain. Also the exon/intron structure in the coding regions of the gene is conserved between human and mouse. The existence and functionality of the gene is supported by the presence of entries in the EST databases and was in vivo fully confirmed by isolating specific transcripts from human uterus total RNA and from several mouse tissues. Strong evidence for alternative splicing was found, which may result in tissue-specific starting points of transcription and in some extent, different protein N-termini. RT-PCR and hybridisation experiments suggest that STK33/Stk33 is differentially expressed in a few tissues and in relative low levels. STK33 has been shown to be reproducibly down-regulated in tumor tissues, particularly in ovarian tumors. RNA in-situ hybridisation experiments using mouse Stk33-specific probes showed expression in dividing cells from lung and germinal epithelium and possibly also in macrophages from kidney and lungs. Preliminary experimentation with antibodies designed in this work, performed in parallel to the preparation of this manuscript, seems to confirm this expression pattern. The fact that the chromosomal region 11p15 in which STK33 is located may be associated with several human diseases including tumor development, suggest further investigation is necessary to establish the role of STK33 in human health.

Identifikation transkriptioneller Alterationen menschlicher Tumoren und Entwicklung eines neuen auf RNA-Transfer basierenden Verfahrens zur Bestimmung der Genfunktion

Zielvorgaben der vorliegenden Arbeit war die Identifikation neuer selektiv in Tumoren aktivierter Gene sowie die Entwicklung eines methodischen Prozesses, um die molekularen Effekte der fehlerhaften Aktivierung solcher Gene zu untersuchen. Für die erste Fragestellung haben wir zwei komplementäre Methoden entwickelt. Zum einen haben wir nach neuen Mitglieder der Cancer/Germline (CG) Familie von Genen gesucht, die bereits attraktive Zielstrukturen laufender Phase I/IIa Studien sind. Zu diesem Zweck wurde ein bioinformatischer Data Mining Ansatz generiert. Dieser führte zur erfolgreichen in silico Klonierung neuer CG Gene. Zur Identifikation von in Tumorzellen überexprimierten Genen nutzten wir einen cDNA Mikroarray mit 1152 ausgewählten Genen mit direkter oder indirekter tumorimmunologischer oder tumorbiologischer Relevanz. Die komparative transkriptionelle Untersuchung von humanen Tumor- und Normalgeweben mit diesem Array führte zur Wiederentdeckung bereits bekannter, aber auch zur Aufdeckung bisher nicht beschriebener tumor-assoziierter Transkriptionsveränderungen. Der zweite große Schwerpunkt dieser Arbeit war die Technologieentwicklung eines versatilen Prozesses zur Untersuchung von molekularen Effekten eines aberrant in Zellen exprimierten Gens. Zur Simulation dieser Situation stellten wir in vitro transkribierte RNA dieses Gens her und elektroporierten diese in Zielzellen. Transkriptionsanalysen solcher Transfektanden mit Affymetrix Oligonukleotid Mikroarray deckten auf gesamt-genomischer Ebene ganze Kaskaden konsekutiver, transkriptioneller Alterationen auf.

Strukturelle und funktionelle Untersuchungen zur Bedeutung der endogenen retroviralen Insertion HERV-K(C4) im C4-Gen des Menschen

Der Längenpolymorphismus des C4-Gens beruht auf der An- oder Abwesenheit einer 6.4 kb langen Insertion im Intron 9. Es handelt sich dabei um einen eigenständigen bisher noch nicht beschriebenen Virus-Typ, der alle Sequenzmerkmale der Familie der humanen endogenen Retroviren (HERV) trägt und zu den HERV-K Viren gehört. Der Provirus wurde als HERV-K(C4) bezeichnet. Die Orientierung dieses retroviralen Elements ist entgegengesetzt zu der Transkriptionsrichtung des C4-Gens. Mittels RT-PCR, RNase Protection Assays und Northern-Blot Analysen konnte der Nachweis von HERV-K(C4)-Antisense mRNA-Transkripten in verschiedenen humanen Zellinien und Geweben erbracht werden. Die retroviralen Transkripte schlossen am 5'- und 3'-Ende Sequenzen des C4-Exon 9 und Exon 10 ein, so daß diese wahrscheinlich "readthrough" Transkripte darstellen, die durch einen 5' des LTR2 gelegenen Promotor initiiert oder im Zusammenhang mit der C4-Expression transkribiert und reguliert werden. Weiterhin konnten insgesamt 4 HERV-K(C4)-mRNA Spezies, einschließlich einer Vollängen-RNA detektiert werden. Die drei subgenomischen mRNAs werden vermutlich durch einfaches und mehrfaches Spleißen generiert. Die quantitative Analyse in verschiedenen humanen Zellinien ergab, daß HERV-K(C4) durchschnittlich mit einer Kopienanzahl zwischen ca.1 bis 100 Transkripten in einer Zelle vorkommt, so daß es sich um low abundance mRNAs handelt. Mittels eines Reportergen-System konnte eine Aktivität des LTR2-Promotors in der Sense-Orientierung des Retrovirus nachgewiesen werden, die nach Stimulation mit IFN- signifikant abnahm. Ein humanes Modell-Systems wurde etabliert, um die Theorie einer Antisense-Abwehr gegen exogene Retroviren in HepG2-Zellen zu überprüfen. Die Theorie basiert auf dem Nachweis von HERV-K(C4)-Antisense-Transkripten, die über eine Heteroduplexbildung mit der Sense-mRNA von verwandten, infektiösen Retroviren eine mögliche Blockierung deren Translation erwirken könnten. Es konnte eine signifikante Abnahme der retroviralen Expression von bis zu 45% nach steigenden Dosen an IFN- in HepG2-Zellen nachgewiesen werden. Der funktionell aktive 3'-LTR-Sense Promotor sowie der Nachweis von HERV-K(C4)-Antisense Transkripten sprechen für die bedeutende Rolle von HERV-K(C4) bei der Genregulation und Schutz gegen exogene Retroviren, wodurch eine Selektion stattgefunden hat.