Luca Zammataro | Yale University School of Medicine (original) (raw)

Papers by Luca Zammataro

In this paper we propose an immune algorithm (IA) to solve high dimensional global optimization p... more In this paper we propose an immune algorithm (IA) to solve high dimensional global optimization problems. To evaluate the effectiveness and quality of the IA we performed a large set of unconstrained numerical optimisation experiments, which is a crucial component of many real-world problem-solving settings. We extensively compare the IA against several Differential Evolution (DE) algorithms as these have been shown to perform better than many other Evolutionary Algorithms on similar problems. The DE algorithms were implemented using a range of recombination and mutation operators combinations. The algorithms were tested on 13 well known benchmark problems. Our results show that the proposed IA is effective, in terms of accuracy, and capable of solving large-scale instances of our benchmarks. We also show that the IA is comparable, and often outperforms, all the DE variants, including two Memetic algorithms.

Frontiers in Immunology, 2014

Lecture Notes in Computer Science, 2014

ABSTRACT In 1952, Turing outlined computational processes in the morphogenesis [8], thus thinking... more ABSTRACT In 1952, Turing outlined computational processes in the morphogenesis [8], thus thinking of the biological evolution of an organism as a consequence of the computation that it can perform. Following Turing’s idea on morphogenesis, many biological processes have been recently analysed from a computational standpoint. In 1995, Bray [2] argued that a single protein is a computational or information carrying element, being able to convert input signals into an output signal. Evolution had already been associated with computation many years before, by von Neumann and Burks [9], who constructed a self-replicating cellular automaton with the aim of developing synthetic models of a living organism. Starting from this concept, in this work we propose a relation between computation and metabolism.

Frontiers in Immunology, 2014

Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phe... more Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.

The Journal of Immunology, 2010

Journal of Bone and Mineral Research, 2012

Autosomal recessive osteopetrosis (ARO) is a genetically heterogeneous disorder attributed to red... more Autosomal recessive osteopetrosis (ARO) is a genetically heterogeneous disorder attributed to reduced bone resorption by osteoclasts. Most human AROs are classified as osteoclast rich, but recently two subsets of osteoclast-poor ARO have been recognized as caused by defects in either TNFSF11 or TNFRSF11A genes, coding the RANKL and RANK proteins, respectively. The RANKL/RANK axis drives osteoclast differentiation and also plays a role in the immune system. In fact, we have recently reported that mutations in the TNFRSF11A gene lead to osteoclast-poor osteopetrosis associated with hypogammaglobulinemia. Here we present the characterization of five additional unpublished patients from four unrelated families in which we found five novel mutations in the TNFRSF11A gene, including two missense and two nonsense mutations and a single-nucleotide insertion. Immunological investigation in three of them showed that the previously described defect in the B cell compartment was present only in some patients and that its severity seemed to increase with age and the progression of the disease. HSCT performed in all five patients almost completely cured the disease even when carried out in late infancy. Hypercalcemia was the most important posttransplant complication. Overall, our results further underline the heterogeneity of human ARO also deriving from the interplay between bone and the immune system, and highlight the prognostic and therapeutic implications of the molecular diagnosis. ß

Development, 2013

The capacity of the hematopoietic system to promptly respond to peripheral demands relies on adeq... more The capacity of the hematopoietic system to promptly respond to peripheral demands relies on adequate pools of progenitors able to transiently proliferate and differentiate in a regulated manner. However, little is known about factors that may restrain progenitor maturation to maintain their reservoirs. Conditional knockout mice for the Pbx1 proto-oncogene have a significant reduction in lineagerestricted progenitors in addition to a profound defect in hematopoietic stem cell (HSC) self-renewal. Through analysis of purified progenitor proliferation, differentiation capacity and transcriptional profiling, we demonstrate that Pbx1 regulates the lineage-specific output of multipotent and oligopotent progenitors. In the absence of Pbx1 multipotent progenitor (MPP) and common myeloid progenitor (CMP) pools are reduced due to aberrantly rapid myeloid maturation. This is associated with premature expression of myeloid differentiation genes and decreased maintenance of proto-oncogene transcriptional pathways, including reduced expression of Meis1, a Pbx1 dimerization partner, and its subordinate transcriptional program. Conversely, Pbx1 maintains the lymphoid differentiation potential of lymphoid-primed MPPs (LMPPs) and common lymphoid progenitors (CLPs), whose reduction in the absence of Pbx1 is associated with a defect in lymphoid priming that is also present in CMPs, which persistently express lymphoid and HSC genes underlying a previously unappreciated lineage promiscuity that is maintained by Pbx1. These results demonstrate a role for Pbx1 in restraining myeloid maturation while maintaining lymphoid potential to appropriately regulate progenitor reservoirs.

Clinical & Experimental Immunology, 2012

Scleroderma (SSc) is a rare connective tissue disease characterized by fibrosis, microvasculopath... more Scleroderma (SSc) is a rare connective tissue disease characterized by fibrosis, microvasculopathy and autoimmune features. The role of genetics is limited in SSc, as suggested by similar concordance rates in monozygotic and dizygotic twin pairs, while environmental factors may act through epigenetic changes, as demonstrated for specific genes. Further, sex chromosome changes have been reported in SSc and may explain the female preponderance. In the present study we compared the methylation profile of all X chromosome genes in peripheral blood mononuclear cells from monozygotic twins discordant (n = 7) and concordant (n = 1) for SSc. Methylated DNA immunoprecipitations from each discordant twin pair were hybridized to a custom-designed array included 998 sites encompassing promoters of all X chromosome genes and randomly chosen autosomal genes. Biostatistical tools identified sites with an elevated probability to be consistently hypermethylated (n = 18) or hypomethylated (n = 25) in affected twins. Identified genes include transcription factors (ARX, HSFX1, ZBED1, ZNF41) and surface antigens (IL1RAPL2, PGRMC1), and pathway analysis suggests their involvement in cell proliferation (PGK1, SMS, UTP14A, SSR4), apoptosis (MTM1), inflammation (ARAF) and oxidative stress (ENOX2). In conclusion, we propose that X chromosome genes with different methylation profiles in monozygotic twin pairs may constitute candidates for SSc susceptibility.

Cancer Research, 2004

Growth inhibition by transforming growth factor (TGF)-beta 1 has been attributed to the induction... more Growth inhibition by transforming growth factor (TGF)-beta 1 has been attributed to the induction of cyclin-dependent kinase inhibitors, among which p21/Waf1 plays a major role in many biological contexts. In the present study, two new intracellular mediators for the induction of p21/Waf1 by TGF-beta 1 were identified in a human hepatocellular carcinoma cell line (JHH-5) expressing mutant-type p53. After addition of TGF-beta 1 to JHH-5 cells, a marked increase of the p21/Waf1 expression preceded the inhibition of DNA synthesis. Expression of IFN regulatory factor (IRF)-1, a known transacting factor for p21/Waf1 promoter, was elevated just before or in parallel with the increase of p21/Waf1. Transduction of antisense IRF-1 inhibited the increase in p21/Waf1 in JHH-5 cells treated with TGF-beta 1 and partially released the cells from the growth arrest by TGF-beta 1. Expression of S100C/A11, a member of the Ca(2+)-binding S100 protein family, also markedly increased after addition of TGF-beta 1. S100C/A11 protein was translocated to and accumulated in nuclei of TGF-beta 1-treated JHH-5 cells, where p21/Waf1 was concomitantly accumulated. When a recombinant S100C/A11 protein was introduced into nuclei of JHH-5 cells, DNA synthesis was markedly inhibited in a dose-dependent manner in the absence of TGF-beta 1. Prior transfection of p21/Waf1-targeted small interfering RNA efficiently blocked decrease of DNA synthesis in JHH-5 cells caused by TAT-S100C/A11 or TGF-beta 1 and markedly inhibited expression of p21/Waf1 protein in the cells. These results indicate that IRF-1 and S100C/A11 mediate growth inhibition by TGF-beta 1 via induction of p21/Waf1.

BMC Bioinformatics, 2014

Background: Modern genomic technologies produce large amounts of data that can be mapped to speci... more Background: Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results: Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user.

Blood, 2012

In response to microenvironmental signals, macrophages undergo different activation, including th... more In response to microenvironmental signals, macrophages undergo different activation, including the "classic" proinflammatory phenotype (also called M1), the "alternative" activation induced by the IL-4/IL-13 trigger, and the related but distinct heterogeneous M2 polarization associated with the anti-inflammatory profile. The latter is induced by several stimuli, including IL-10 and TGF-␤. Macrophagepolarized activation has profound effects on immune and inflammatory responses and in tumor biology, but information on the underlying molecular pathways is scarce. In the present study, we report that alternative polarization of macrophages requires the transcription factor c-MYC. In macrophages, IL-4 and different stimuli sustaining M2-like polarization induce c-MYC expression and its translocation to the nucleus. c-MYC controls the induction of a subset (45%) of genes associated with alternative activation. ChIP assays indicate that c-MYC directly regulates some genes associated with alternative activation, including SCARB1, ALOX15, and MRC1, whereas others, including CD209, are indirectly regulated by c-MYC. c-MYC up-regulates the IL-4 signaling mediators signal transducer and activator of transcription-6 and peroxisome proliferator-activated receptor␥, is also expressed in tumorassociated macrophages, and its inhibition blocks the expression of protumoral genes including VEGF, MMP9, HIF-1␣, and TGF-␤. We conclude that c-MYC is a key player in alternative macrophage activation, and is therefore a potential therapeutic target in pathologies related to these cells, including tumors. (Blood. 2012;119(2):411-421)

Knowing every single component of a given biological system is not enough to understand the compl... more Knowing every single component of a given biological system is not enough to understand the complexity of the system but rather it becomes crucial to understand how these components interact with each others. It is not only important the knowledge of genes and proteins, but also knowing their structures and primarily the laws and parameters governing their dynamics, which is often unknown and impossible to measure directly. The Gene Regulatory Networks explain exactly how a genomic sequence encodes the ...

The Immune System is, together with Central Nervous System, one of the most important and complex... more The Immune System is, together with Central Nervous System, one of the most important and complex unit of our organism. Despite great advances in recent years that shed light on its understanding and in the unraveling of key mechanisms behind its functions, there are still many areas of the Immune System that remain object of active research. The development of in-silico models, bridged with proper biological considerations, have recently improved the understanding of important complex systems [1,2]. In this paper, after introducing major role players and principal functions of the mammalian Immune System, we present two computational approaches to its modeling; i.e., two in-silico Immune Systems. (i) A large-scale model, with a complexity of representation of 106 − 108 cells (e.g., APC, T, B and Plasma cells) and molecules (e.g., immunocomplexes), is here presented, and its evolution in time is shown to be mimicking an important region of a real immune response. (ii) Additionally, a viral infection model, stochastic and light-weight, is here presented as well: its seamless design from biological considerations, its modularity and its fast simulation times are strength points when compared to (i). Finally we report, with the intent of moving towards the virtual lymph note, a cost-benefits comparison among Immune System models presented in this paper.

Digestive and Liver Disease, 2010

Journal of Hepatology, 2010

A human betaretrovirus resembling the mouse mammary tumor virus has been cloned from biliary epit... more A human betaretrovirus resembling the mouse mammary tumor virus has been cloned from biliary epithelium and lymph nodes of patients with primary biliary cirrhosis (PBC). The virus has been detected by RT-PCR in 75% of peri-hepatic lymph nodes by PCR and immunohistochemistry but is difficult to find in the liver. Aims: To address the first and second of Koch's postulates (i) to isolate an infectious betaretrovirus and (ii) demonstrate absolute proof of viral infection by identifying integration sites in bile ducts. Methods: Lymph node homogenates from PBC patients were co-cultured with Hs578T cells and infected cells were tested for betaretrovirus production. DNA was extracted from biliary epithelium cultured from the liver at transplantation, perihepatic lymph nodes as well as the co-cultured HS578T cells. Integration sites were identified in the DNA using linker mediated-PCR with virus-specific primers and a linker primer. A genuine integration site had to include the 3' end of the viral LTR, followed a human genomic sequence within 3 bases and then the linker sequence. Results: Betaretrovirus was detected by RT-PCR in 16 supernatants from 28 subcloned Hs578T co-cultured cells. Betaretrovirus particles were identified by electron microscopy and 20 unique integration sites were identified in infected Hs578T DNA but not in controls. Unique betaretrovirus integration sites were identified in biliary epithelial cells from 5/9 PBC vs. 1/9 control samples as well as 9/13 PBC lymph nodes. Of the 79 human betaretrovirus integration identified, 58 (73%) were within genes or within 100kb of transcription start sites. Clustering of 3 or more sites within 15,000 Kb was observed on chromosomes 4, 5, 6, 8 and 11. Conclusions: The viral isolation studies and unequivocal detection of viral integration sites in the human genome provide proof that patients with PBC have infection with a transmissible betaretrovirus. The majority of PBC patients tested by linker mediated-PCR to date have evidence of viral infection. The detection of betaretrovirus within genes and in close proximity to transcription start sites suggests a hypothesis that integration may effect gene regulation in patients with PBC.

Cell Death and Differentiation, 2003

Nature, 2003

The motility and morphogenesis of endothelial cells is controlled by spatio-temporally regulated ... more The motility and morphogenesis of endothelial cells is controlled by spatio-temporally regulated activation of integrin adhesion receptors, and integrin activation is stimulated by major determinants of vascular remodelling. In order for endothelial cells to be responsive to changes in activator gradients, the adhesiveness of these cells to the extracellular matrix must be dynamic, and negative regulators of integrins could be required. Here we show that during vascular development and experimental angiogenesis, endothelial cells generate autocrine chemorepulsive signals of class 3 semaphorins (SEMA3 proteins) that localize at nascent adhesive sites in spreading endothelial cells. Disrupting endogenous SEMA3 function in endothelial cells stimulates integrin-mediated adhesion and migration to extracellular matrices, whereas exogenous SEMA3 proteins antagonize integrin activation. Misexpression of dominant negative SEMA3 receptors in chick embryo endothelial cells locks integrins in an active conformation, and severely impairs vascular remodelling. Sema3a null mice show vascular defects as well. Thus during angiogenesis endothelial SEMA3 proteins endow the vascular system with the plasticity required for its reshaping by controlling integrin function.

In this paper we propose an immune algorithm (IA) to solve high dimensional global optimization p... more In this paper we propose an immune algorithm (IA) to solve high dimensional global optimization problems. To evaluate the effectiveness and quality of the IA we performed a large set of unconstrained numerical optimisation experiments, which is a crucial component of many real-world problem-solving settings. We extensively compare the IA against several Differential Evolution (DE) algorithms as these have been shown to perform better than many other Evolutionary Algorithms on similar problems. The DE algorithms were implemented using a range of recombination and mutation operators combinations. The algorithms were tested on 13 well known benchmark problems. Our results show that the proposed IA is effective, in terms of accuracy, and capable of solving large-scale instances of our benchmarks. We also show that the IA is comparable, and often outperforms, all the DE variants, including two Memetic algorithms.

Frontiers in Immunology, 2014

Lecture Notes in Computer Science, 2014

ABSTRACT In 1952, Turing outlined computational processes in the morphogenesis [8], thus thinking... more ABSTRACT In 1952, Turing outlined computational processes in the morphogenesis [8], thus thinking of the biological evolution of an organism as a consequence of the computation that it can perform. Following Turing’s idea on morphogenesis, many biological processes have been recently analysed from a computational standpoint. In 1995, Bray [2] argued that a single protein is a computational or information carrying element, being able to convert input signals into an output signal. Evolution had already been associated with computation many years before, by von Neumann and Burks [9], who constructed a self-replicating cellular automaton with the aim of developing synthetic models of a living organism. Starting from this concept, in this work we propose a relation between computation and metabolism.

Frontiers in Immunology, 2014

Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phe... more Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.

The Journal of Immunology, 2010

Journal of Bone and Mineral Research, 2012

Autosomal recessive osteopetrosis (ARO) is a genetically heterogeneous disorder attributed to red... more Autosomal recessive osteopetrosis (ARO) is a genetically heterogeneous disorder attributed to reduced bone resorption by osteoclasts. Most human AROs are classified as osteoclast rich, but recently two subsets of osteoclast-poor ARO have been recognized as caused by defects in either TNFSF11 or TNFRSF11A genes, coding the RANKL and RANK proteins, respectively. The RANKL/RANK axis drives osteoclast differentiation and also plays a role in the immune system. In fact, we have recently reported that mutations in the TNFRSF11A gene lead to osteoclast-poor osteopetrosis associated with hypogammaglobulinemia. Here we present the characterization of five additional unpublished patients from four unrelated families in which we found five novel mutations in the TNFRSF11A gene, including two missense and two nonsense mutations and a single-nucleotide insertion. Immunological investigation in three of them showed that the previously described defect in the B cell compartment was present only in some patients and that its severity seemed to increase with age and the progression of the disease. HSCT performed in all five patients almost completely cured the disease even when carried out in late infancy. Hypercalcemia was the most important posttransplant complication. Overall, our results further underline the heterogeneity of human ARO also deriving from the interplay between bone and the immune system, and highlight the prognostic and therapeutic implications of the molecular diagnosis. ß

Development, 2013

The capacity of the hematopoietic system to promptly respond to peripheral demands relies on adeq... more The capacity of the hematopoietic system to promptly respond to peripheral demands relies on adequate pools of progenitors able to transiently proliferate and differentiate in a regulated manner. However, little is known about factors that may restrain progenitor maturation to maintain their reservoirs. Conditional knockout mice for the Pbx1 proto-oncogene have a significant reduction in lineagerestricted progenitors in addition to a profound defect in hematopoietic stem cell (HSC) self-renewal. Through analysis of purified progenitor proliferation, differentiation capacity and transcriptional profiling, we demonstrate that Pbx1 regulates the lineage-specific output of multipotent and oligopotent progenitors. In the absence of Pbx1 multipotent progenitor (MPP) and common myeloid progenitor (CMP) pools are reduced due to aberrantly rapid myeloid maturation. This is associated with premature expression of myeloid differentiation genes and decreased maintenance of proto-oncogene transcriptional pathways, including reduced expression of Meis1, a Pbx1 dimerization partner, and its subordinate transcriptional program. Conversely, Pbx1 maintains the lymphoid differentiation potential of lymphoid-primed MPPs (LMPPs) and common lymphoid progenitors (CLPs), whose reduction in the absence of Pbx1 is associated with a defect in lymphoid priming that is also present in CMPs, which persistently express lymphoid and HSC genes underlying a previously unappreciated lineage promiscuity that is maintained by Pbx1. These results demonstrate a role for Pbx1 in restraining myeloid maturation while maintaining lymphoid potential to appropriately regulate progenitor reservoirs.

Clinical & Experimental Immunology, 2012

Scleroderma (SSc) is a rare connective tissue disease characterized by fibrosis, microvasculopath... more Scleroderma (SSc) is a rare connective tissue disease characterized by fibrosis, microvasculopathy and autoimmune features. The role of genetics is limited in SSc, as suggested by similar concordance rates in monozygotic and dizygotic twin pairs, while environmental factors may act through epigenetic changes, as demonstrated for specific genes. Further, sex chromosome changes have been reported in SSc and may explain the female preponderance. In the present study we compared the methylation profile of all X chromosome genes in peripheral blood mononuclear cells from monozygotic twins discordant (n = 7) and concordant (n = 1) for SSc. Methylated DNA immunoprecipitations from each discordant twin pair were hybridized to a custom-designed array included 998 sites encompassing promoters of all X chromosome genes and randomly chosen autosomal genes. Biostatistical tools identified sites with an elevated probability to be consistently hypermethylated (n = 18) or hypomethylated (n = 25) in affected twins. Identified genes include transcription factors (ARX, HSFX1, ZBED1, ZNF41) and surface antigens (IL1RAPL2, PGRMC1), and pathway analysis suggests their involvement in cell proliferation (PGK1, SMS, UTP14A, SSR4), apoptosis (MTM1), inflammation (ARAF) and oxidative stress (ENOX2). In conclusion, we propose that X chromosome genes with different methylation profiles in monozygotic twin pairs may constitute candidates for SSc susceptibility.

Cancer Research, 2004

Growth inhibition by transforming growth factor (TGF)-beta 1 has been attributed to the induction... more Growth inhibition by transforming growth factor (TGF)-beta 1 has been attributed to the induction of cyclin-dependent kinase inhibitors, among which p21/Waf1 plays a major role in many biological contexts. In the present study, two new intracellular mediators for the induction of p21/Waf1 by TGF-beta 1 were identified in a human hepatocellular carcinoma cell line (JHH-5) expressing mutant-type p53. After addition of TGF-beta 1 to JHH-5 cells, a marked increase of the p21/Waf1 expression preceded the inhibition of DNA synthesis. Expression of IFN regulatory factor (IRF)-1, a known transacting factor for p21/Waf1 promoter, was elevated just before or in parallel with the increase of p21/Waf1. Transduction of antisense IRF-1 inhibited the increase in p21/Waf1 in JHH-5 cells treated with TGF-beta 1 and partially released the cells from the growth arrest by TGF-beta 1. Expression of S100C/A11, a member of the Ca(2+)-binding S100 protein family, also markedly increased after addition of TGF-beta 1. S100C/A11 protein was translocated to and accumulated in nuclei of TGF-beta 1-treated JHH-5 cells, where p21/Waf1 was concomitantly accumulated. When a recombinant S100C/A11 protein was introduced into nuclei of JHH-5 cells, DNA synthesis was markedly inhibited in a dose-dependent manner in the absence of TGF-beta 1. Prior transfection of p21/Waf1-targeted small interfering RNA efficiently blocked decrease of DNA synthesis in JHH-5 cells caused by TAT-S100C/A11 or TGF-beta 1 and markedly inhibited expression of p21/Waf1 protein in the cells. These results indicate that IRF-1 and S100C/A11 mediate growth inhibition by TGF-beta 1 via induction of p21/Waf1.

BMC Bioinformatics, 2014

Background: Modern genomic technologies produce large amounts of data that can be mapped to speci... more Background: Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results: Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user.

Blood, 2012

In response to microenvironmental signals, macrophages undergo different activation, including th... more In response to microenvironmental signals, macrophages undergo different activation, including the "classic" proinflammatory phenotype (also called M1), the "alternative" activation induced by the IL-4/IL-13 trigger, and the related but distinct heterogeneous M2 polarization associated with the anti-inflammatory profile. The latter is induced by several stimuli, including IL-10 and TGF-␤. Macrophagepolarized activation has profound effects on immune and inflammatory responses and in tumor biology, but information on the underlying molecular pathways is scarce. In the present study, we report that alternative polarization of macrophages requires the transcription factor c-MYC. In macrophages, IL-4 and different stimuli sustaining M2-like polarization induce c-MYC expression and its translocation to the nucleus. c-MYC controls the induction of a subset (45%) of genes associated with alternative activation. ChIP assays indicate that c-MYC directly regulates some genes associated with alternative activation, including SCARB1, ALOX15, and MRC1, whereas others, including CD209, are indirectly regulated by c-MYC. c-MYC up-regulates the IL-4 signaling mediators signal transducer and activator of transcription-6 and peroxisome proliferator-activated receptor␥, is also expressed in tumorassociated macrophages, and its inhibition blocks the expression of protumoral genes including VEGF, MMP9, HIF-1␣, and TGF-␤. We conclude that c-MYC is a key player in alternative macrophage activation, and is therefore a potential therapeutic target in pathologies related to these cells, including tumors. (Blood. 2012;119(2):411-421)

Knowing every single component of a given biological system is not enough to understand the compl... more Knowing every single component of a given biological system is not enough to understand the complexity of the system but rather it becomes crucial to understand how these components interact with each others. It is not only important the knowledge of genes and proteins, but also knowing their structures and primarily the laws and parameters governing their dynamics, which is often unknown and impossible to measure directly. The Gene Regulatory Networks explain exactly how a genomic sequence encodes the ...

The Immune System is, together with Central Nervous System, one of the most important and complex... more The Immune System is, together with Central Nervous System, one of the most important and complex unit of our organism. Despite great advances in recent years that shed light on its understanding and in the unraveling of key mechanisms behind its functions, there are still many areas of the Immune System that remain object of active research. The development of in-silico models, bridged with proper biological considerations, have recently improved the understanding of important complex systems [1,2]. In this paper, after introducing major role players and principal functions of the mammalian Immune System, we present two computational approaches to its modeling; i.e., two in-silico Immune Systems. (i) A large-scale model, with a complexity of representation of 106 − 108 cells (e.g., APC, T, B and Plasma cells) and molecules (e.g., immunocomplexes), is here presented, and its evolution in time is shown to be mimicking an important region of a real immune response. (ii) Additionally, a viral infection model, stochastic and light-weight, is here presented as well: its seamless design from biological considerations, its modularity and its fast simulation times are strength points when compared to (i). Finally we report, with the intent of moving towards the virtual lymph note, a cost-benefits comparison among Immune System models presented in this paper.

Digestive and Liver Disease, 2010

Journal of Hepatology, 2010

A human betaretrovirus resembling the mouse mammary tumor virus has been cloned from biliary epit... more A human betaretrovirus resembling the mouse mammary tumor virus has been cloned from biliary epithelium and lymph nodes of patients with primary biliary cirrhosis (PBC). The virus has been detected by RT-PCR in 75% of peri-hepatic lymph nodes by PCR and immunohistochemistry but is difficult to find in the liver. Aims: To address the first and second of Koch's postulates (i) to isolate an infectious betaretrovirus and (ii) demonstrate absolute proof of viral infection by identifying integration sites in bile ducts. Methods: Lymph node homogenates from PBC patients were co-cultured with Hs578T cells and infected cells were tested for betaretrovirus production. DNA was extracted from biliary epithelium cultured from the liver at transplantation, perihepatic lymph nodes as well as the co-cultured HS578T cells. Integration sites were identified in the DNA using linker mediated-PCR with virus-specific primers and a linker primer. A genuine integration site had to include the 3' end of the viral LTR, followed a human genomic sequence within 3 bases and then the linker sequence. Results: Betaretrovirus was detected by RT-PCR in 16 supernatants from 28 subcloned Hs578T co-cultured cells. Betaretrovirus particles were identified by electron microscopy and 20 unique integration sites were identified in infected Hs578T DNA but not in controls. Unique betaretrovirus integration sites were identified in biliary epithelial cells from 5/9 PBC vs. 1/9 control samples as well as 9/13 PBC lymph nodes. Of the 79 human betaretrovirus integration identified, 58 (73%) were within genes or within 100kb of transcription start sites. Clustering of 3 or more sites within 15,000 Kb was observed on chromosomes 4, 5, 6, 8 and 11. Conclusions: The viral isolation studies and unequivocal detection of viral integration sites in the human genome provide proof that patients with PBC have infection with a transmissible betaretrovirus. The majority of PBC patients tested by linker mediated-PCR to date have evidence of viral infection. The detection of betaretrovirus within genes and in close proximity to transcription start sites suggests a hypothesis that integration may effect gene regulation in patients with PBC.

Cell Death and Differentiation, 2003

Nature, 2003

The motility and morphogenesis of endothelial cells is controlled by spatio-temporally regulated ... more The motility and morphogenesis of endothelial cells is controlled by spatio-temporally regulated activation of integrin adhesion receptors, and integrin activation is stimulated by major determinants of vascular remodelling. In order for endothelial cells to be responsive to changes in activator gradients, the adhesiveness of these cells to the extracellular matrix must be dynamic, and negative regulators of integrins could be required. Here we show that during vascular development and experimental angiogenesis, endothelial cells generate autocrine chemorepulsive signals of class 3 semaphorins (SEMA3 proteins) that localize at nascent adhesive sites in spreading endothelial cells. Disrupting endogenous SEMA3 function in endothelial cells stimulates integrin-mediated adhesion and migration to extracellular matrices, whereas exogenous SEMA3 proteins antagonize integrin activation. Misexpression of dominant negative SEMA3 receptors in chick embryo endothelial cells locks integrins in an active conformation, and severely impairs vascular remodelling. Sema3a null mice show vascular defects as well. Thus during angiogenesis endothelial SEMA3 proteins endow the vascular system with the plasticity required for its reshaping by controlling integrin function.