Service robotics, as it has been intended so far, views the accomplishment of a service mission m... more Service robotics, as it has been intended so far, views the accomplishment of a service mission mainly as the result of the action of a single robot. Swarm robotics tackles the very same problem from a different stance, ie as the result of a team effort of simple units. The project described here shows this particular approach. It defines first one simple unit (s-bot) capable of independently moving about on the ground and of dynamically establishing rigid or semi-rigid connections with other fellow units, and then it shows how a large group of them can, as a whole entity (swarm-bot), carry out a given task. Thanks to the ductility in assembling and forming its connections, a swarm-bot can readily cope with occasional failures of some components and promptly reshape the remaining swarm so as to replace the role of the failing units. Given such a plasticity, their possible applications is rather large ranging from harsh environment exploration to goods harvesting or goods transportat...
The present document is the User Manual of the Swarmbot3d simulator. It contains a description of... more The present document is the User Manual of the Swarmbot3d simulator. It contains a description of the software components included in it as well as a the procedure to install the whole package. A detailed discussion concerning how the simulator’s components have been implemented and concerning the reasons which lead to their implementation are reported in the associated Technical Report ”Definition, Implementation, and Calibration of the Swarmbot3d Simulator”. This document concentrates on the presentation of the application programming interface (API) with which users can design their own customized robot control. A simple behaviour-based control example is also presentented and discussed.
DLBCL is a biologically heterogeneous disease. Depending on a gene expression profiling of DLBCL ... more DLBCL is a biologically heterogeneous disease. Depending on a gene expression profiling of DLBCL has revealed a molecular subtypes that include germinal center B cell-like (GCB) and activated B cell-like (ABC or non-GCB). The prognosis of pediatric DLBCL mostly GCB has improved since short intensive multi-agent chemotherapy regimens like NHL-BFM 90 was introduced. We hypothesized that AYA with the GCB DLBCL may benefit of such treatment. The purpose of this study was to determine the efficacy of NHL-BFM 90 protocol for AYA with DLBCL. Materials and methods: From 10.1998 to 04.2008, 28 (m-14, f-14) patients (pts) with de novo DLBCL were treated with 6 chemotherapy cycles similar to those in NHL-BFM 90. Before 2006, 18 pts received a modified treatment cycles with the reduction of methotrexate (1 g/m2/36h instead 5 g/m2/24h). Since 2006, 10 pts received therapy on a national pediatric protocol B-NHL 2004M. This protocol differed from BFM by adding rituximab 375 mg/m2 on the first day of each cycle and reduction of methotrexate doses only in the first 2 cycles (1 g/m2/24h instead 5 g/m2/24h). The cases were classified as GCB or non-GC by immunohistochemistry (Hans, 2004). Results: Median age pts was 21.0 years (range, 15−38). 24 (86%) pts were diagnosed in advanced (III-IV) stages. The molecular subtypes of DLBCL were evaluated for 16 pts: 8 (50%) classified as GCB and 8 (50%)-non-GCB. Complete response (CR) achieved 8 (100%) pts with GCB and 5 (63%) pts with non-GCB (p > 0.05). 5y-EFS was 1.0 (SE 0.0) vs. 0.50 (SE 0.18) respectively (p = 0.046). 5y-OS was 1.0 (SE 0.0) vs. 0.50 (SE 0.23) respectively (p = 0.071). Median follow-up was 3.4 years. The GCB and non-GCB group did not differ in their international prognostic index scores, presence of bulky disease and frequency of rituximab treatment. Conclusions: AYA with immunohistochemically determined GCB-type DLBCL have an improved prognosis as a result of intensive BFM-like therapy in contrast to non-GCB.
The swarm intelligence paradigm has proven to have very interesting properties such as robustness... more The swarm intelligence paradigm has proven to have very interesting properties such as robustness, flexibility and ability to solve complex problems exploiting parallelism and self-organization. Several robotics implementations of this paradigm confirm that these properties can be exploited for the control of a population of physically independent mobile robots.The work presented here introduces a new robotic concept called swarm-bot in which the collective interaction exploited by the swarm intelligence mechanism goes beyond the control layer and is extended to the physical level. This implies the addition of new mechanical functionalities on the single robot, together with new electronics and software to manage it. These new functionalities, even if not directly related to mobility and navigation, allow to address complex mobile robotics problems, such as extreme all-terrain exploration.The work shows also how this new concept is investigated using a simulation tool (swarmbot3d) s...
This work has evaluated the potential superiority of a morphomolecular classification based on th... more This work has evaluated the potential superiority of a morphomolecular classification based on the combination of clinicopathologic and molecular features of colorectal cancers. A cohort of 126 colorectal carcinomas was investigated by unsupervised hierarchical clustering analysis to combine 13 routinely assessed clinicopathologic features and all five molecular markers recently suggested by Jass' classification to distinguish four molecular subtypes of sporadic colorectal carcinomas. Survival analysis was assessed by a Cox proportional hazards model. A clear separation into three prognostically significant groups was identified: cluster A and cluster C were associated with good prognosis and cluster B with poor prognosis (P ¼ 0.006). Clinicopathologic and molecular features of cluster A and cluster B tumors were strongly concordant with colorectal cancer profiles characterized by microsatellite instability or by chromosomal instability, respectively. The clinicopathologic features of cluster C tumors were suggestive of a less aggressive disease than cluster B tumors. Genetically, they appeared intermediate between cluster A and cluster B tumors, as they were mainly microsatellite stable tumors showing high levels of both MGMT methylation and loss of heterozygosity. Chromosomal instability was significantly lower in cluster C than in cluster B tumors. A more accurate tumor classification should combine the prognostic power of clinicopathologic parameters with molecular biomarkers that provide information regarding the natural history of the cancer. Hierarchical clustering seems to be a useful, promising and powerful tool for further translational studies and should lead us to define a diagnostic and prognostic signature for different carcinomas.
The aim of the study was to identify the impact on prognosis of hypoxia-inducible factor-1 geneti... more The aim of the study was to identify the impact on prognosis of hypoxia-inducible factor-1 genetic program in colorectal carcinomas and to develop an experimental procedure that would allow a reliable quantitative gene expression analysis in formalin-fixed and paraffin-embedded tissue. The expression of hypoxia-inducible factor-1α and 13 hypoxia-inducible factor-1 target genes (AMF, CAIX, VEGF, VEGFR1, VEGFR2, HGF, MET, TGFα, EGFR, IGF2, MMP2, PLAUR, NIX) was quantified by real-time polymerase chain reaction in 18 colorectal, poorly differentiated neuroendocrine carcinomas and in 60 invasive colorectal carcinomas. Moreover, hypoxia-inducible factor-1α protein expression was evaluated by immunohistochemistry. High levels of hypoxia-inducible factor-1α were positively associated with poorly differentiated neuroendocrine carcinoma histology (P b .005), poor differentiation (P b .025), presence of necrosis, and presence of microsatellite instability (P b .05). AMF, TGFα, IGF2, NIX, VEGF, and VEGFR2 transcripts were significantly higher in the very aggressive poorly differentiated neuroendocrine carcinomas than in exocrine colorectal carcinomas and TGFα expression was significantly associated with presence of lymph nodal metastases (P b .05). High levels of TGFα and NIX were significantly associated with decreased overall survival (P b .001; P b .01). The multivariate analysis showed that advanced stage, presence of lymph node metastases, and high TGFα expression had an independent effect on survival (P b .006; P b .01; P b .0006). Our study suggests an up-regulation of the hypoxia-inducible factor-1 transcriptional pathway in colorectal carcinomas. hypoxia-inducible factor-1α overexpression alone, has no impact on the prognosis of colorectal carcinomas likely because the consequences of hypoxia-inducible factor-1α expression/stabilization strongly depend on the genetic background of the transformed cells. Mechanisms leading to increased synthesis of hypoxia-inducible factor-1α mRNA via autocrine growth factor loops may play a crucial role in invasive growth in this site.
Primary central nervous system lymphoma (PCNSL) is a rare form of extranodal non-Hodgkin’s lympho... more Primary central nervous system lymphoma (PCNSL) is a rare form of extranodal non-Hodgkin’s lymphoma with continuously increasing incidence in both immunosuppressed and immunocompetent individuals. PCNSL is a very aggressive tumor with a poor outcome, and its clinical outcome is much worse than for nodal lymphomas. Differently from lymphomas arising in lymph nodes or in other extranodal sites, the treatment of PCNSL remains very unsatisfactory. Current biologic knowledge of PCNSL is still limited and several fundamental questions remain to be answered. This is mainly due to the paucity of PCNSL material for adequate translational research. With the aim of providing biologic material to investigators interested in PCNSL, we have implemented a virtual tissue bank (VTB) for PCNSL in immunocompetent patients. After registration, the VTB is accessible via any web browser at www.ielsg.org. Only anonymous data are centralized at the website of the International Extranodal Lymphoma Study Gro...
The aureolic acid antibiotic mithramycin (MTM) binds selectively to GC-rich DNA sequences and blo... more The aureolic acid antibiotic mithramycin (MTM) binds selectively to GC-rich DNA sequences and blocks preferentially binding of proteins, like Sp1 transcription factors, to GC-rich elements in gene promoters. Genetic approaches can be applied to alter the MTM biosynthetic pathway in the producing microorganism and obtain new products with improved pharmacological properties. Here, we report on a new analog, MTM SDK, obtained by targeted gene inactivation of the ketoreductase MtmW catalyzing the last step in MTM biosynthesis. SDK exhibited greater activity as transcriptional inhibitor compared to MTM. SDK was a potent inhibitor of Sp1-dependent reporter activity and interfered minimally with reporters of other transcription factors, indicating that it retained a high degree of selectivity toward GC-rich DNAbinding transcription factors. RT-PCR and microarray analysis showed that SDK repressed transcription of multiple genes implicated in critical aspects of cancer development and progression, including cell cycle, apoptosis, migration, invasion and angiogenesis, consistent with the pleiotropic role of Sp1 family transcription factors. SDK inhibited proliferation and was a potent inducer of apoptosis in ovarian cancer cells while it had minimal effects on viability of normal cells. The new MTM derivative SDK could be an effective agent for treatment of cancer and other diseases with abnormal expression or activity of GC-rich DNA-binding transcription factors.
High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtain... more High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtained in the context of leukemia. Using chronic lymphocytic leukemia as a model, saliva DNA was frequently devoid of tumor DNA also during overt disease, and passed quality controls for SNP-array (77/102, 75.4%) and next generation sequencing (71/102, 69.6%). Compared to saliva, urine provides germline DNA of similar quality but in lower amounts. Saliva DNA was successfully run on SNP 6.0 arrays, and passed quality control call rate thresholds. On these bases, saliva represents a useful source of germline DNA for high-throughput genomic studies of hematologic neoplasia.
Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors.... more Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors. Here, we present the cytogenetic and molecular characterization of an amplification affecting 11q23.1 in four cell lines derived from B-cell lymphoid tumors. A minimal common region of amplification of 330 kb was identified in three cell lines using Affymetrix Human Mapping 250K arrays. When analyzed with three BAC clones, the amplifications appeared different at cytogenetic level in each cell line. Possibly affected transcripts were evaluated using tiling arrays, and validated by real time PCR. Since no effect of the amplification at the local transcription level was observed, it is possible that 11q23 amplification might mainly represent the effect of unstable chromosomal region.
Knowledge on the impact of pharmacogenetics in predicting outcome and toxicity in diffuse large B... more Knowledge on the impact of pharmacogenetics in predicting outcome and toxicity in diffuse large B-cell lymphoma (DLBCL) is scant. We tested 106 consecutive DLBCL treated with R-CHOP21 for 19 single nucleotide polymorphisms (SNPs) from 15 genes potentially relevant to rituximab-CHOP (R-CHOP) pharmacogenetics. Associations of SNPs with event-free survival (EFS) and toxicity were controlled for multiple testing. Genotypic variants of nicotinamide adenine dinucleotide phosphate (NAD(P)H) oxidase p22phox (CYBA rs4673) and alpha1 class glutathione S-transferase (GSTA1 rs3957357) were independent predictors of EFS (CYBA rs4673 TT genotype: HR 2.06, P ¼ 0.038; GSTA1 rs3957357 CT/TT genotypes: HR 0.38, P ¼ 0.003), after adjusting for International Prognostic Index (IPI). CYBA rs4673 and GSTA1 rs3957357 also predicted outcome in DLBCL subgroups by IPI. Impact of SNPs on toxicity was evaluated in 658 R-CHOP21 courses utilizing generalized estimating equations. NCF4 rs1883112 was an independent predictor against hematologic (odds ratios (OR): 0.45; P ¼ 0.018), infectious (OR: 0.46; P ¼ 0.003) and cardiac toxicity (OR: 0.37; P ¼ 0.023). Overall, host SNPs affecting doxorubicin pharmacodynamics (CYBA rs4673) and alkylator detoxification (GSTA1 rs3957357) may predict outcome in R-CHOP21-treated DLBCL. Also, NCF4 rs1883112, a SNP of NAD(P)H oxidase p40phox, may have a function in protecting against hematologic and nonhematologic toxicity. These results highlight the need to improve characterization of the host genetic background for a better prognostication of DLBCL.
Richter's syndrome (RS) represents the transformation of chronic lymphocytic leukaemia (CLL) to a... more Richter's syndrome (RS) represents the transformation of chronic lymphocytic leukaemia (CLL) to aggressive lymphoma and is mostly represented by diffuse large B-cell lymphoma (DLBCL), with a post-germinal centre (GC) phenotype, clonally related to the pre-existing CLL. RS has a very poor prognosis and its pathogenetic mechanisms are poorly understood. In order to gain additional hints in RS pathogenesis, we performed a genome-wide DNA profiling study of 13 RS phases and eight matched CLL phases using the Affymetrix Human Mapping 250K NspI SNP arrays. Individual genomic profiles were heterogeneous, with no individual lesions occurring in more than half of the cases. However, several observations suggest that MYC pathway might be involved in RS. The 13q13.3-qter region containing MIRHG1 (MIR-17-92), a cluster of microRNA interacting with c-MYC, was acquired at the time of transformation. The 13q gain was coupled with the gain of c-MYC and loss of TP53. Translocation of c-MYC was acquired at transformation in a fraction of cases and this event appeared mutually exclusive with gain of MIRHG1. MYCN, a c-MYC homologue, was also recurrently gained. By comparing RS with 48 de novo DLBCL, RS presented a significantly lower prevalence of deletions affecting the PRDM1 and TNFAIP3, genes on 6q, known to be associated with a post-GC phenotype. In conclusion, the genomic profile of RS seems to differ from what observed in de novo DLBCL and in other transformed DLBCL. Genomic lesions occurring in RS are heterogeneous suggesting the existence of different RS subsets, possibly due to different transforming mechanisms. A deregulation of MYC pathway might represent one of the main transformation events in the pathogenesis of a subset of RS clonally related to the previous CLL.
Bone marrow (BM) involvement in diffuse large B-cell lymphoma (DLBCL) can be morphologically disc... more Bone marrow (BM) involvement in diffuse large B-cell lymphoma (DLBCL) can be morphologically discordant from the primary tumor. Concordant BM infiltration has been shown associated with a poorer outcome in patients treated with CHOP. In order to evaluate tumor-related factors leading to BM involvement in DLBCL, we performed an integrated analysis of i) genomic profiles obtained with a high-density genome wide SNPbased arrays ii) immunomorphological and iii) clinical data from 133 patients uniformly treated with R-CHOP. BM infiltration was found in 27 of 133 (20%) cases; and it was concordant in 18/27 (67%) cases. Concordant infiltration, but not discordant, influenced negatively OS, PFS and DFS and was associated with higher serum LDH, lower CR and higher PD rates. No association with cell of origin was found between BMþ and BM-DLBCL. As compared with BM-cases, BMþ DLBCL showed absence of 7q gain.
To investigate the patterns of genetic lesions in a panel of 23 human multiple myeloma cell lines... more To investigate the patterns of genetic lesions in a panel of 23 human multiple myeloma cell lines (HMCLs), we made a genomic integrative analysis involving FISH, and both gene expression and genome‐wide profiling approaches. The expression profiles of the genes targeted by the main IGH translocations showed that the WHSC1/MMSET gene involved in t(4;14)(p16;q32) was expressed at different levels in all of the HMCLs, and that the expression of the MAF gene was not restricted to the HMCLs carrying t(14;16)(q32;q23). Supervised analyses identified a limited number of genes specifically associated with t(4;14) and involved in different biological processes. The signature related to MAF/MAFB expression included the known MAF target genes CCND2 and ITGB7, as well as genes controlling cell shape and cell adhesion. Genome‐wide DNA profiling allowed the identification of a gain on chromosome arm 1q in 88% of the analyzed cell lines, together with recurrent gains on 8q, 18q, 7q, and 20q; the m...
Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocyti... more Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion Chronic lymphocytic leukaemia (CLL) is a B-cell neoplasm with heterogeneous survival, ranging from few months to more than 20 years (Krober et al, 2002). Heterogeneity is also identified by distinct chromosomal abnormalities that can predict outcome (Krober et al, 2002). Deletion of 17p13 (17p-CLL), the locus of the TP53 gene, identifies the most aggressive subset (Krober et al, 2002). Cases of 17p-CLL typically are resistant to alkylating agents and purine analogues, have a high risk of transformation and a median survival of only 36 months, with outcome independent of clinical stage or immunoglobulin heavy chain gene (IGHV) status (Krober et al, 2002). However, not all 17p-CLL behave poorly, and intrinsic mechanisms of dismal prognosis cannot simply be recapitulated by the genes deleted at the 17p locus (Kienle et al, 2005). Genome-wide DNA analysis of copy number (CN) changes and loss of heterozygosity (LOH) is providing a new tool to identify common recurrent chromosomal changes of pathogenetic significance in cancer. In CLL, this approach can overcome the methodological limitations of conventional
Post-transplant lymphoproliferative disorders (PTLD) are a major complication of solid organ tran... more Post-transplant lymphoproliferative disorders (PTLD) are a major complication of solid organ transplantation, representing a cause of severe morbidity and mortality. Apart from Epstein-Barr virus infection, knowledge of the pathogenesis of monoclonal PTLD is limited. Powerful analysis techniques, such as whole genomic DNA profiling (array comparative genomic hybridisation), can improve our understanding of PTLD pathogenesis. Whole genome profiling using the Affymetrix GeneChip Human Mapping 10 k 2.0 was performed on 20 PTLD cases and 25 cases of diffuse large B-cell lymphoma (DLBCL) from immunocompetent patients as a control group. Recurrent lesions were detected among all the samples. Chromosome 18q, 7q, 3q and 12 were the most common gains in the control group. Chromosomes 5p and 11p were commonly gained in PTLD-DLBCL. The latter had frequent losses of 6q, 17p, 1p and 9p. Chromosome 12p was the most frequent target of deletions among PTLD-DLBCL cases. Loss of heterozygosity (LOH) did not always match DNA loss: chromosome 10 seemed to be targeted by uniparental disomy in PTLD. Small deletions and gains, involving both known (BCL2 and PAX5) and unknown genes (ZDHHC14), were identified. These data suggest that PTLD share, at a lower frequency, common genetic aberrations with DLBCL from immunocompetent patients. The demonstration of 9p13 amplification emphasises the importance of PAX5 in PTLD. The combination of DNA copy number and LOH assessment lead to the hypothesis that uniparental disomy may be a potential mechanism in B-cell lymphomagenesis.
SummaryDespite recent therapeutic improvements, the clinical course of diffuse large B‐cell lymph... more SummaryDespite recent therapeutic improvements, the clinical course of diffuse large B‐cell lymphoma (DLBCL) still differs considerably among patients. We conducted this retrospective multi‐centre study to evaluate the impact of genomic aberrations detected using a high‐density genome wide‐single nucleotide polymorphism‐based array on clinical outcome in a population of DLBCL patients treated with R‐CHOP‐21 (rituximab, cyclophosphamide, doxorubicine, vincristine and prednisone repeated every 21 d). 166 DNA samples were analysed using the GeneChip Human Mapping 250K NspI. Genomic anomalies were analysed regarding their impact on the clinical course of 124 patients treated with R‐CHOP‐21. Unsupervised clustering was performed to identify genetically related subgroups of patients with different clinical outcomes. Twenty recurrent genetic lesions showed an impact on the clinical course. Loss of genomic material at 8p23.1 showed the strongest statistical significance and was associated w...
Service robotics, as it has been intended so far, views the accomplishment of a service mission m... more Service robotics, as it has been intended so far, views the accomplishment of a service mission mainly as the result of the action of a single robot. Swarm robotics tackles the very same problem from a different stance, ie as the result of a team effort of simple units. The project described here shows this particular approach. It defines first one simple unit (s-bot) capable of independently moving about on the ground and of dynamically establishing rigid or semi-rigid connections with other fellow units, and then it shows how a large group of them can, as a whole entity (swarm-bot), carry out a given task. Thanks to the ductility in assembling and forming its connections, a swarm-bot can readily cope with occasional failures of some components and promptly reshape the remaining swarm so as to replace the role of the failing units. Given such a plasticity, their possible applications is rather large ranging from harsh environment exploration to goods harvesting or goods transportat...
The present document is the User Manual of the Swarmbot3d simulator. It contains a description of... more The present document is the User Manual of the Swarmbot3d simulator. It contains a description of the software components included in it as well as a the procedure to install the whole package. A detailed discussion concerning how the simulator’s components have been implemented and concerning the reasons which lead to their implementation are reported in the associated Technical Report ”Definition, Implementation, and Calibration of the Swarmbot3d Simulator”. This document concentrates on the presentation of the application programming interface (API) with which users can design their own customized robot control. A simple behaviour-based control example is also presentented and discussed.
DLBCL is a biologically heterogeneous disease. Depending on a gene expression profiling of DLBCL ... more DLBCL is a biologically heterogeneous disease. Depending on a gene expression profiling of DLBCL has revealed a molecular subtypes that include germinal center B cell-like (GCB) and activated B cell-like (ABC or non-GCB). The prognosis of pediatric DLBCL mostly GCB has improved since short intensive multi-agent chemotherapy regimens like NHL-BFM 90 was introduced. We hypothesized that AYA with the GCB DLBCL may benefit of such treatment. The purpose of this study was to determine the efficacy of NHL-BFM 90 protocol for AYA with DLBCL. Materials and methods: From 10.1998 to 04.2008, 28 (m-14, f-14) patients (pts) with de novo DLBCL were treated with 6 chemotherapy cycles similar to those in NHL-BFM 90. Before 2006, 18 pts received a modified treatment cycles with the reduction of methotrexate (1 g/m2/36h instead 5 g/m2/24h). Since 2006, 10 pts received therapy on a national pediatric protocol B-NHL 2004M. This protocol differed from BFM by adding rituximab 375 mg/m2 on the first day of each cycle and reduction of methotrexate doses only in the first 2 cycles (1 g/m2/24h instead 5 g/m2/24h). The cases were classified as GCB or non-GC by immunohistochemistry (Hans, 2004). Results: Median age pts was 21.0 years (range, 15−38). 24 (86%) pts were diagnosed in advanced (III-IV) stages. The molecular subtypes of DLBCL were evaluated for 16 pts: 8 (50%) classified as GCB and 8 (50%)-non-GCB. Complete response (CR) achieved 8 (100%) pts with GCB and 5 (63%) pts with non-GCB (p > 0.05). 5y-EFS was 1.0 (SE 0.0) vs. 0.50 (SE 0.18) respectively (p = 0.046). 5y-OS was 1.0 (SE 0.0) vs. 0.50 (SE 0.23) respectively (p = 0.071). Median follow-up was 3.4 years. The GCB and non-GCB group did not differ in their international prognostic index scores, presence of bulky disease and frequency of rituximab treatment. Conclusions: AYA with immunohistochemically determined GCB-type DLBCL have an improved prognosis as a result of intensive BFM-like therapy in contrast to non-GCB.
The swarm intelligence paradigm has proven to have very interesting properties such as robustness... more The swarm intelligence paradigm has proven to have very interesting properties such as robustness, flexibility and ability to solve complex problems exploiting parallelism and self-organization. Several robotics implementations of this paradigm confirm that these properties can be exploited for the control of a population of physically independent mobile robots.The work presented here introduces a new robotic concept called swarm-bot in which the collective interaction exploited by the swarm intelligence mechanism goes beyond the control layer and is extended to the physical level. This implies the addition of new mechanical functionalities on the single robot, together with new electronics and software to manage it. These new functionalities, even if not directly related to mobility and navigation, allow to address complex mobile robotics problems, such as extreme all-terrain exploration.The work shows also how this new concept is investigated using a simulation tool (swarmbot3d) s...
This work has evaluated the potential superiority of a morphomolecular classification based on th... more This work has evaluated the potential superiority of a morphomolecular classification based on the combination of clinicopathologic and molecular features of colorectal cancers. A cohort of 126 colorectal carcinomas was investigated by unsupervised hierarchical clustering analysis to combine 13 routinely assessed clinicopathologic features and all five molecular markers recently suggested by Jass' classification to distinguish four molecular subtypes of sporadic colorectal carcinomas. Survival analysis was assessed by a Cox proportional hazards model. A clear separation into three prognostically significant groups was identified: cluster A and cluster C were associated with good prognosis and cluster B with poor prognosis (P ¼ 0.006). Clinicopathologic and molecular features of cluster A and cluster B tumors were strongly concordant with colorectal cancer profiles characterized by microsatellite instability or by chromosomal instability, respectively. The clinicopathologic features of cluster C tumors were suggestive of a less aggressive disease than cluster B tumors. Genetically, they appeared intermediate between cluster A and cluster B tumors, as they were mainly microsatellite stable tumors showing high levels of both MGMT methylation and loss of heterozygosity. Chromosomal instability was significantly lower in cluster C than in cluster B tumors. A more accurate tumor classification should combine the prognostic power of clinicopathologic parameters with molecular biomarkers that provide information regarding the natural history of the cancer. Hierarchical clustering seems to be a useful, promising and powerful tool for further translational studies and should lead us to define a diagnostic and prognostic signature for different carcinomas.
The aim of the study was to identify the impact on prognosis of hypoxia-inducible factor-1 geneti... more The aim of the study was to identify the impact on prognosis of hypoxia-inducible factor-1 genetic program in colorectal carcinomas and to develop an experimental procedure that would allow a reliable quantitative gene expression analysis in formalin-fixed and paraffin-embedded tissue. The expression of hypoxia-inducible factor-1α and 13 hypoxia-inducible factor-1 target genes (AMF, CAIX, VEGF, VEGFR1, VEGFR2, HGF, MET, TGFα, EGFR, IGF2, MMP2, PLAUR, NIX) was quantified by real-time polymerase chain reaction in 18 colorectal, poorly differentiated neuroendocrine carcinomas and in 60 invasive colorectal carcinomas. Moreover, hypoxia-inducible factor-1α protein expression was evaluated by immunohistochemistry. High levels of hypoxia-inducible factor-1α were positively associated with poorly differentiated neuroendocrine carcinoma histology (P b .005), poor differentiation (P b .025), presence of necrosis, and presence of microsatellite instability (P b .05). AMF, TGFα, IGF2, NIX, VEGF, and VEGFR2 transcripts were significantly higher in the very aggressive poorly differentiated neuroendocrine carcinomas than in exocrine colorectal carcinomas and TGFα expression was significantly associated with presence of lymph nodal metastases (P b .05). High levels of TGFα and NIX were significantly associated with decreased overall survival (P b .001; P b .01). The multivariate analysis showed that advanced stage, presence of lymph node metastases, and high TGFα expression had an independent effect on survival (P b .006; P b .01; P b .0006). Our study suggests an up-regulation of the hypoxia-inducible factor-1 transcriptional pathway in colorectal carcinomas. hypoxia-inducible factor-1α overexpression alone, has no impact on the prognosis of colorectal carcinomas likely because the consequences of hypoxia-inducible factor-1α expression/stabilization strongly depend on the genetic background of the transformed cells. Mechanisms leading to increased synthesis of hypoxia-inducible factor-1α mRNA via autocrine growth factor loops may play a crucial role in invasive growth in this site.
Primary central nervous system lymphoma (PCNSL) is a rare form of extranodal non-Hodgkin’s lympho... more Primary central nervous system lymphoma (PCNSL) is a rare form of extranodal non-Hodgkin’s lymphoma with continuously increasing incidence in both immunosuppressed and immunocompetent individuals. PCNSL is a very aggressive tumor with a poor outcome, and its clinical outcome is much worse than for nodal lymphomas. Differently from lymphomas arising in lymph nodes or in other extranodal sites, the treatment of PCNSL remains very unsatisfactory. Current biologic knowledge of PCNSL is still limited and several fundamental questions remain to be answered. This is mainly due to the paucity of PCNSL material for adequate translational research. With the aim of providing biologic material to investigators interested in PCNSL, we have implemented a virtual tissue bank (VTB) for PCNSL in immunocompetent patients. After registration, the VTB is accessible via any web browser at www.ielsg.org. Only anonymous data are centralized at the website of the International Extranodal Lymphoma Study Gro...
The aureolic acid antibiotic mithramycin (MTM) binds selectively to GC-rich DNA sequences and blo... more The aureolic acid antibiotic mithramycin (MTM) binds selectively to GC-rich DNA sequences and blocks preferentially binding of proteins, like Sp1 transcription factors, to GC-rich elements in gene promoters. Genetic approaches can be applied to alter the MTM biosynthetic pathway in the producing microorganism and obtain new products with improved pharmacological properties. Here, we report on a new analog, MTM SDK, obtained by targeted gene inactivation of the ketoreductase MtmW catalyzing the last step in MTM biosynthesis. SDK exhibited greater activity as transcriptional inhibitor compared to MTM. SDK was a potent inhibitor of Sp1-dependent reporter activity and interfered minimally with reporters of other transcription factors, indicating that it retained a high degree of selectivity toward GC-rich DNAbinding transcription factors. RT-PCR and microarray analysis showed that SDK repressed transcription of multiple genes implicated in critical aspects of cancer development and progression, including cell cycle, apoptosis, migration, invasion and angiogenesis, consistent with the pleiotropic role of Sp1 family transcription factors. SDK inhibited proliferation and was a potent inducer of apoptosis in ovarian cancer cells while it had minimal effects on viability of normal cells. The new MTM derivative SDK could be an effective agent for treatment of cancer and other diseases with abnormal expression or activity of GC-rich DNA-binding transcription factors.
High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtain... more High-throughput genomics requires tumor DNA matched to germline DNA, that cannot be easily obtained in the context of leukemia. Using chronic lymphocytic leukemia as a model, saliva DNA was frequently devoid of tumor DNA also during overt disease, and passed quality controls for SNP-array (77/102, 75.4%) and next generation sequencing (71/102, 69.6%). Compared to saliva, urine provides germline DNA of similar quality but in lower amounts. Saliva DNA was successfully run on SNP 6.0 arrays, and passed quality control call rate thresholds. On these bases, saliva represents a useful source of germline DNA for high-throughput genomic studies of hematologic neoplasia.
Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors.... more Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors. Here, we present the cytogenetic and molecular characterization of an amplification affecting 11q23.1 in four cell lines derived from B-cell lymphoid tumors. A minimal common region of amplification of 330 kb was identified in three cell lines using Affymetrix Human Mapping 250K arrays. When analyzed with three BAC clones, the amplifications appeared different at cytogenetic level in each cell line. Possibly affected transcripts were evaluated using tiling arrays, and validated by real time PCR. Since no effect of the amplification at the local transcription level was observed, it is possible that 11q23 amplification might mainly represent the effect of unstable chromosomal region.
Knowledge on the impact of pharmacogenetics in predicting outcome and toxicity in diffuse large B... more Knowledge on the impact of pharmacogenetics in predicting outcome and toxicity in diffuse large B-cell lymphoma (DLBCL) is scant. We tested 106 consecutive DLBCL treated with R-CHOP21 for 19 single nucleotide polymorphisms (SNPs) from 15 genes potentially relevant to rituximab-CHOP (R-CHOP) pharmacogenetics. Associations of SNPs with event-free survival (EFS) and toxicity were controlled for multiple testing. Genotypic variants of nicotinamide adenine dinucleotide phosphate (NAD(P)H) oxidase p22phox (CYBA rs4673) and alpha1 class glutathione S-transferase (GSTA1 rs3957357) were independent predictors of EFS (CYBA rs4673 TT genotype: HR 2.06, P ¼ 0.038; GSTA1 rs3957357 CT/TT genotypes: HR 0.38, P ¼ 0.003), after adjusting for International Prognostic Index (IPI). CYBA rs4673 and GSTA1 rs3957357 also predicted outcome in DLBCL subgroups by IPI. Impact of SNPs on toxicity was evaluated in 658 R-CHOP21 courses utilizing generalized estimating equations. NCF4 rs1883112 was an independent predictor against hematologic (odds ratios (OR): 0.45; P ¼ 0.018), infectious (OR: 0.46; P ¼ 0.003) and cardiac toxicity (OR: 0.37; P ¼ 0.023). Overall, host SNPs affecting doxorubicin pharmacodynamics (CYBA rs4673) and alkylator detoxification (GSTA1 rs3957357) may predict outcome in R-CHOP21-treated DLBCL. Also, NCF4 rs1883112, a SNP of NAD(P)H oxidase p40phox, may have a function in protecting against hematologic and nonhematologic toxicity. These results highlight the need to improve characterization of the host genetic background for a better prognostication of DLBCL.
Richter's syndrome (RS) represents the transformation of chronic lymphocytic leukaemia (CLL) to a... more Richter's syndrome (RS) represents the transformation of chronic lymphocytic leukaemia (CLL) to aggressive lymphoma and is mostly represented by diffuse large B-cell lymphoma (DLBCL), with a post-germinal centre (GC) phenotype, clonally related to the pre-existing CLL. RS has a very poor prognosis and its pathogenetic mechanisms are poorly understood. In order to gain additional hints in RS pathogenesis, we performed a genome-wide DNA profiling study of 13 RS phases and eight matched CLL phases using the Affymetrix Human Mapping 250K NspI SNP arrays. Individual genomic profiles were heterogeneous, with no individual lesions occurring in more than half of the cases. However, several observations suggest that MYC pathway might be involved in RS. The 13q13.3-qter region containing MIRHG1 (MIR-17-92), a cluster of microRNA interacting with c-MYC, was acquired at the time of transformation. The 13q gain was coupled with the gain of c-MYC and loss of TP53. Translocation of c-MYC was acquired at transformation in a fraction of cases and this event appeared mutually exclusive with gain of MIRHG1. MYCN, a c-MYC homologue, was also recurrently gained. By comparing RS with 48 de novo DLBCL, RS presented a significantly lower prevalence of deletions affecting the PRDM1 and TNFAIP3, genes on 6q, known to be associated with a post-GC phenotype. In conclusion, the genomic profile of RS seems to differ from what observed in de novo DLBCL and in other transformed DLBCL. Genomic lesions occurring in RS are heterogeneous suggesting the existence of different RS subsets, possibly due to different transforming mechanisms. A deregulation of MYC pathway might represent one of the main transformation events in the pathogenesis of a subset of RS clonally related to the previous CLL.
Bone marrow (BM) involvement in diffuse large B-cell lymphoma (DLBCL) can be morphologically disc... more Bone marrow (BM) involvement in diffuse large B-cell lymphoma (DLBCL) can be morphologically discordant from the primary tumor. Concordant BM infiltration has been shown associated with a poorer outcome in patients treated with CHOP. In order to evaluate tumor-related factors leading to BM involvement in DLBCL, we performed an integrated analysis of i) genomic profiles obtained with a high-density genome wide SNPbased arrays ii) immunomorphological and iii) clinical data from 133 patients uniformly treated with R-CHOP. BM infiltration was found in 27 of 133 (20%) cases; and it was concordant in 18/27 (67%) cases. Concordant infiltration, but not discordant, influenced negatively OS, PFS and DFS and was associated with higher serum LDH, lower CR and higher PD rates. No association with cell of origin was found between BMþ and BM-DLBCL. As compared with BM-cases, BMþ DLBCL showed absence of 7q gain.
To investigate the patterns of genetic lesions in a panel of 23 human multiple myeloma cell lines... more To investigate the patterns of genetic lesions in a panel of 23 human multiple myeloma cell lines (HMCLs), we made a genomic integrative analysis involving FISH, and both gene expression and genome‐wide profiling approaches. The expression profiles of the genes targeted by the main IGH translocations showed that the WHSC1/MMSET gene involved in t(4;14)(p16;q32) was expressed at different levels in all of the HMCLs, and that the expression of the MAF gene was not restricted to the HMCLs carrying t(14;16)(q32;q23). Supervised analyses identified a limited number of genes specifically associated with t(4;14) and involved in different biological processes. The signature related to MAF/MAFB expression included the known MAF target genes CCND2 and ITGB7, as well as genes controlling cell shape and cell adhesion. Genome‐wide DNA profiling allowed the identification of a gain on chromosome arm 1q in 88% of the analyzed cell lines, together with recurrent gains on 8q, 18q, 7q, and 20q; the m...
Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocyti... more Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion Chronic lymphocytic leukaemia (CLL) is a B-cell neoplasm with heterogeneous survival, ranging from few months to more than 20 years (Krober et al, 2002). Heterogeneity is also identified by distinct chromosomal abnormalities that can predict outcome (Krober et al, 2002). Deletion of 17p13 (17p-CLL), the locus of the TP53 gene, identifies the most aggressive subset (Krober et al, 2002). Cases of 17p-CLL typically are resistant to alkylating agents and purine analogues, have a high risk of transformation and a median survival of only 36 months, with outcome independent of clinical stage or immunoglobulin heavy chain gene (IGHV) status (Krober et al, 2002). However, not all 17p-CLL behave poorly, and intrinsic mechanisms of dismal prognosis cannot simply be recapitulated by the genes deleted at the 17p locus (Kienle et al, 2005). Genome-wide DNA analysis of copy number (CN) changes and loss of heterozygosity (LOH) is providing a new tool to identify common recurrent chromosomal changes of pathogenetic significance in cancer. In CLL, this approach can overcome the methodological limitations of conventional
Post-transplant lymphoproliferative disorders (PTLD) are a major complication of solid organ tran... more Post-transplant lymphoproliferative disorders (PTLD) are a major complication of solid organ transplantation, representing a cause of severe morbidity and mortality. Apart from Epstein-Barr virus infection, knowledge of the pathogenesis of monoclonal PTLD is limited. Powerful analysis techniques, such as whole genomic DNA profiling (array comparative genomic hybridisation), can improve our understanding of PTLD pathogenesis. Whole genome profiling using the Affymetrix GeneChip Human Mapping 10 k 2.0 was performed on 20 PTLD cases and 25 cases of diffuse large B-cell lymphoma (DLBCL) from immunocompetent patients as a control group. Recurrent lesions were detected among all the samples. Chromosome 18q, 7q, 3q and 12 were the most common gains in the control group. Chromosomes 5p and 11p were commonly gained in PTLD-DLBCL. The latter had frequent losses of 6q, 17p, 1p and 9p. Chromosome 12p was the most frequent target of deletions among PTLD-DLBCL cases. Loss of heterozygosity (LOH) did not always match DNA loss: chromosome 10 seemed to be targeted by uniparental disomy in PTLD. Small deletions and gains, involving both known (BCL2 and PAX5) and unknown genes (ZDHHC14), were identified. These data suggest that PTLD share, at a lower frequency, common genetic aberrations with DLBCL from immunocompetent patients. The demonstration of 9p13 amplification emphasises the importance of PAX5 in PTLD. The combination of DNA copy number and LOH assessment lead to the hypothesis that uniparental disomy may be a potential mechanism in B-cell lymphomagenesis.
SummaryDespite recent therapeutic improvements, the clinical course of diffuse large B‐cell lymph... more SummaryDespite recent therapeutic improvements, the clinical course of diffuse large B‐cell lymphoma (DLBCL) still differs considerably among patients. We conducted this retrospective multi‐centre study to evaluate the impact of genomic aberrations detected using a high‐density genome wide‐single nucleotide polymorphism‐based array on clinical outcome in a population of DLBCL patients treated with R‐CHOP‐21 (rituximab, cyclophosphamide, doxorubicine, vincristine and prednisone repeated every 21 d). 166 DNA samples were analysed using the GeneChip Human Mapping 250K NspI. Genomic anomalies were analysed regarding their impact on the clinical course of 124 patients treated with R‐CHOP‐21. Unsupervised clustering was performed to identify genetically related subgroups of patients with different clinical outcomes. Twenty recurrent genetic lesions showed an impact on the clinical course. Loss of genomic material at 8p23.1 showed the strongest statistical significance and was associated w...
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Papers by Ivo W Kwee