Jole Costanza - Academia.edu (original) (raw)
Papers by Jole Costanza
Pediatric Research
Background Maternal dietary habits are contributors of maternal and fetal health; however, availa... more Background Maternal dietary habits are contributors of maternal and fetal health; however, available data are heterogeneous and not conclusive. Methods Nutrient intake during pregnancy was assessed in 503 women with uncomplicated pregnancies, using the validated Food Frequency Questionnaire developed by the European Prospective Investigation into Cancer and Nutrition (EPIC-FFQ). Results In all, 68% of women had a normal body mass index at the beginning of pregnancy, and 83% of newborns had an appropriate weight for gestational age. Maternal pre-pregnancy body mass index (BMI), gestational weight gain (GWG), and placental weight were independently correlated with birth weight. GWG was not related to the pre-pregnancy BMI. EPIC-FFQ evaluation showed that 30% of women adhered to the European Food Safety Authority (EFSA) ranges for macronutrient intake. In most pregnant women (98.1%), consumption of water was below recommendations. Comparing women with intakes within EFSA ranges for mac...
Italian Journal of Pediatrics, 2021
Background De novo pathogenic variants in the DDX3X gene are reported to account for 1–3% of unex... more Background De novo pathogenic variants in the DDX3X gene are reported to account for 1–3% of unexplained intellectual disability (ID) in females, leading to the rare disease known as DDX3X syndrome (MRXSSB, OMIM #300958). Besides ID, these patients manifest a variable clinical presentation, which includes neurological and behavioral defects, and abnormal brain MRIs. Case presentation We report a 10-year-old girl affected by delayed psychomotor development, delayed myelination, and polymicrogyria (PMG). We identified a novel de novo missense mutation in the DDX3X gene (c.625C > G) by whole exome sequencing (WES). The DDX3X gene encodes a DEAD-box ATP-dependent RNA-helicase broadly implicated in gene expression through regulation of mRNA metabolism. The identified mutation is located just upstream the helicase domain and is suggested to impair the protein activity, thus resulting in the altered translation of DDX3X-dependent mRNAs. The proband, presenting with the typical PMG pheno...
Additional file 1: Supplementary Table 1. Prediction of pathogenicity of the identified DDX3X var... more Additional file 1: Supplementary Table 1. Prediction of pathogenicity of the identified DDX3X variant by in silico tools.
It contains detailed results of our analyses in Figures S1-S4. (PDF 1180 kb)
Journal of Bone and Mineral Research, 2022
Skeletal disorders, including both isolated and syndromic brachydactyly type E, derive from genet... more Skeletal disorders, including both isolated and syndromic brachydactyly type E, derive from genetic defects affecting the fine tuning of the network of pathways involved in skeletogenesis and growth-plate development. Alterations of different genes of this network may result in overlapping phenotypes, as exemplified by disorders due to the impairment of the parathyroid hormone/parathyroid hormone-related protein pathway, and obtaining a correct diagnosis is sometimes challenging without a genetic confirmation. Five patients with "AHO-like" (Albright's Hereditary Osteodystrophy) skeletal malformations without a clear clinical diagnosis were analyzed by whole exome sequencing and novel potentially pathogenic variants in PTHLH (BDE with short stature, BDE2) and TRPS1 (tricho-rhino-phalangeal syndrome, TRPS) were discovered. The pathogenic impact of these variants was confirmed by in vitro functional studies. This study expands the spectrum of genetic defects associated with BDE2 and TRPS and demonstrates the pathogenicity of TRPS1 missense variants located outside both the nuclear localization signal and the GATA and Ikaros-like binding domains. Unfortunately, we could not find distinctive phenotypic features that might have led to an earlier clinical diagnosis, further highlighting the high degree of overlap among skeletal syndromes associated with brachydactyly and AHO-like features, and the need for a close interdisciplinary workout in these rare patients. This article is protected by copyright. All rights reserved.
We propose a framework for the investigation and the au-tomated design of bacteria to allow the o... more We propose a framework for the investigation and the au-tomated design of bacteria to allow the overproduction of metabolites of industrial interest. Our framework, which consists of three main steps, includes the implementation of a sensitivity analysis method, a multi-objective optimiza-tion algorithm, and a robustness analysis algorithm. They exploit the Pareto optimality principle to explore species, re-actions, pathways, and knockout parameter space. Further-more, they provide theoretical and practical guidelines for design automation: applications on Escherichia coli, Geobac-ter sulfurreducens, Yersinia pestis, Methanosarcina barkery reveal a good performance on a variety of biotechnological products. The toolbox performs the following three inter-connected tasks: 1) the Pathway-oriented Sensitivity Anal-ysis, PoSA, evaluates the sensitive and insensitive parame-ters of the models of the four studied bacteria; 2) the Genetic Design Multi-Objective, GDMO, determines the Pareto ...
Table 1. Knockout strategies obtained through GDMO algorithm for maximising acetate production [m... more Table 1. Knockout strategies obtained through GDMO algorithm for maximising acetate production [mmolh −1 gDW −1]. For each strategy, we report the biomass formation [h −1], the knockout cost (k cost) and the genes and reactions switched off. The variation of acetate and biomass in comparison with the wild type is enclosed in brackets. We also provide a comparison between the robustness analysis. R values (Hafner et al., 2009)
If Turing were a first-year graduate student interested in computers, he would probably migrate i... more If Turing were a first-year graduate student interested in computers, he would probably migrate into the field of computational biology. During his studies, he presented a work about a mathematical and computational model of the morphogenesis process, in which chemical substances react together. Moreover, a protein can be thought of as a compu-tational element, i.e. a processing unit, able to transform an input into an output signal. Thus, in a biochemical pathway, an enzyme reads the amount of reactants (substrates) and converts them in products. In this work, we consider the biochemical pathway in unicellular organisms (e.g. bacteria) as a living computer, and we are able to program it in order to obtain desired outputs. The genome sequence is thought of as an executable code specified by a set of commands in a sort of ad-hoc low-level programming language. Each combination of genes is coded as a string of bits y ∈ {0, 1}L, each of which represents a gene set. By turning off a gen...
Cancer Research, 2020
Treatment of metastatic melanoma has been recently revolutionized by the use of targeted and immu... more Treatment of metastatic melanoma has been recently revolutionized by the use of targeted and immune inhibitors, though efficiently working only in a fraction of patients. Adverse effects still represent major challenges, as well as the rapid development of drug resistance upon treatment, thus suggesting that it is of utmost importance to elucidate additional molecular pathways and targets to better understand the biology of this tumor. In vivo RNAi screens done in patient-derived xenografts (PDXs) that fully phenocopy the original tumor of the patient represent a powerful tool to identify new putative essential and druggable candidates, and to repurpose drugs already approved for other indications. To this end we have recently generated a platform of melanoma PDXs with which we can recapitulate both melanoma growth and metastasization. We have performed in vivo shRNA screens, where we have found numerous and patient-specific epigenetic genes essential for tumor growth in vivo. With ...
International Journal of Molecular Sciences, 2019
Estrogen receptor (ER)-positive progesterone receptor (PR)-negative breast cancers are infrequent... more Estrogen receptor (ER)-positive progesterone receptor (PR)-negative breast cancers are infrequent but clinically challenging. Despite the volume of genomic data available on these tumors, their biology remains poorly understood. Here, we aimed to identify clinically relevant subclasses of ER+/PR− breast cancers based on their mutational landscape. The Cancer Genomics Data Server was interrogated for mutational and clinical data of all ER+ breast cancers with information on PR status from The Cancer Genome Atlas (TCGA), Memorial Sloan Kettering (MSK), and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) projects. Clustering analysis was performed using gplots, ggplot2, and ComplexHeatmap packages. Comparisons between groups were performed using the Student’s t-test and the test of Equal or Given Proportions. Survival curves were built according to the Kaplan–Meier method; differences in survival were assessed with the log-rank test. A total of 3570 ER+ breast c...
Lecture Notes in Computer Science, 2016
We present a thorough in silico analysis and optimization of the genome-scale metabolic model of ... more We present a thorough in silico analysis and optimization of the genome-scale metabolic model of the mycolic acid pathway in M. tuberculosis. We apply and further extend meGDMO to account for finer sensitivity analysis and post-processing analysis, thanks to the combination of statistical evaluation of strains robustness, and clustering analysis to map the phenotype-genotype relationship among Pareto optimal strains. In the first analysis scenario, we find 12 Pareto-optimal single gene set knockout, which completely shut down the pathway, hence critically reducing the pathogenicity of M. tuberculosis; as well as 34 genotypically different strains in which the production of mycolic acid is severely reduced.
Una volta effettuato il sequenziamento Sanger di un campione di DNA, e necessario valutare la cor... more Una volta effettuato il sequenziamento Sanger di un campione di DNA, e necessario valutare la correttezza del sequenziamento analizzando i segnali Raw Data ed Analyzed Data forniti dal sequenziatore per poter risalire ai problemi, legati alle tecniche di preparazione del campione o alla procedura di sequenziamento, che possono generare errori nella determinazione della sequenza. Tali analisi, detta in gergo troubleshooting, attualmente viene effettuata da biologi esperti, in quanto non esistono software che realizzano automaticamente questa analisi. In questa tesi e stato realizzato un algoritmo che compie l'analisi automatica dei segnali e classifica le problematiche in opportune categorie al fine di fornire un supporto efficiente e veloce al troubleshooting. Per realizzare l'algoritmo e stato utilizzato un training set di 167 sequenze con problematiche note. L'algoritmo, implementato in Matlab, utilizza tecniche di filtro a media mobile, di peak detection e altre metodologie tipiche dell'analisi del segnale. Per validare l'algoritmo sono state utilizzate 1200 sequenze con problematiche note. Per ogni problematica e stata testata la performance dell'algoritmo, valutando quante classificazioni corrette vengono da esso compiute. I risultati ottenuti sono buoni, superando per ogni problematica mediamente il 93% dell'assegnazione corretta, definita come il rapporto tra il numero dato dalla somma dei veri positivi e negativi e il numero di sequenze del validation test.
Advances in Experimental Medicine and Biology, 2011
Understanding and optimizing the CO 2 fixation process would allow human beings to address better... more Understanding and optimizing the CO 2 fixation process would allow human beings to address better current energy and biotechnology issues. We focused on modeling the C 3 photosynthetic Carbon metabolism pathway with the aim of identifying the minimal set of enzymes whose biotechnological alteration could allow a functional re-engineering of the pathway. To achieve this result we merged in a single powerful pipeline Sensitivity Analysis (SA), Single-(SO) and Multi-Objective Optimization (MO), and Robustness Analysis (RA). By using our recently developed multipurpose optimization algorithms (PAO and PMO2) here we extend our work exploring a large combinatorial solution space and most importantly, here we present an important reduction of the problem search space. From the initial number of 23 enzymes we have identified 11 enzymes whose targeting
The placental methylation pattern is crucial for the regulation of genes involved in trophoblast ... more The placental methylation pattern is crucial for the regulation of genes involved in trophoblast invasion and placental development, both key events for fetal growth. We investigated LINE-1 methylation and methylome profiling using a methylation EPIC array and the targeted methylation sequencing of 154 normal, full-term pregnancies, stratified by birth weight percentiles. LINE-1 methylation showed evidence of a more pronounced hypomethylation in small neonates compared with normal and large for gestational age. Genome-wide methylation, performed in two subsets of pregnancies, showed very similar methylation profiles among cord blood samples while placentae from different pregnancies appeared very variable. A unique methylation profile emerged in each placenta, which could represent the sum of adjustments that the placenta made during the pregnancy to preserve the epigenetic homeostasis of the fetus. Investigations into the 1000 most variable sites between cord blood and the placenta...
Pediatric Research
Background Maternal dietary habits are contributors of maternal and fetal health; however, availa... more Background Maternal dietary habits are contributors of maternal and fetal health; however, available data are heterogeneous and not conclusive. Methods Nutrient intake during pregnancy was assessed in 503 women with uncomplicated pregnancies, using the validated Food Frequency Questionnaire developed by the European Prospective Investigation into Cancer and Nutrition (EPIC-FFQ). Results In all, 68% of women had a normal body mass index at the beginning of pregnancy, and 83% of newborns had an appropriate weight for gestational age. Maternal pre-pregnancy body mass index (BMI), gestational weight gain (GWG), and placental weight were independently correlated with birth weight. GWG was not related to the pre-pregnancy BMI. EPIC-FFQ evaluation showed that 30% of women adhered to the European Food Safety Authority (EFSA) ranges for macronutrient intake. In most pregnant women (98.1%), consumption of water was below recommendations. Comparing women with intakes within EFSA ranges for mac...
Italian Journal of Pediatrics, 2021
Background De novo pathogenic variants in the DDX3X gene are reported to account for 1–3% of unex... more Background De novo pathogenic variants in the DDX3X gene are reported to account for 1–3% of unexplained intellectual disability (ID) in females, leading to the rare disease known as DDX3X syndrome (MRXSSB, OMIM #300958). Besides ID, these patients manifest a variable clinical presentation, which includes neurological and behavioral defects, and abnormal brain MRIs. Case presentation We report a 10-year-old girl affected by delayed psychomotor development, delayed myelination, and polymicrogyria (PMG). We identified a novel de novo missense mutation in the DDX3X gene (c.625C > G) by whole exome sequencing (WES). The DDX3X gene encodes a DEAD-box ATP-dependent RNA-helicase broadly implicated in gene expression through regulation of mRNA metabolism. The identified mutation is located just upstream the helicase domain and is suggested to impair the protein activity, thus resulting in the altered translation of DDX3X-dependent mRNAs. The proband, presenting with the typical PMG pheno...
Additional file 1: Supplementary Table 1. Prediction of pathogenicity of the identified DDX3X var... more Additional file 1: Supplementary Table 1. Prediction of pathogenicity of the identified DDX3X variant by in silico tools.
It contains detailed results of our analyses in Figures S1-S4. (PDF 1180 kb)
Journal of Bone and Mineral Research, 2022
Skeletal disorders, including both isolated and syndromic brachydactyly type E, derive from genet... more Skeletal disorders, including both isolated and syndromic brachydactyly type E, derive from genetic defects affecting the fine tuning of the network of pathways involved in skeletogenesis and growth-plate development. Alterations of different genes of this network may result in overlapping phenotypes, as exemplified by disorders due to the impairment of the parathyroid hormone/parathyroid hormone-related protein pathway, and obtaining a correct diagnosis is sometimes challenging without a genetic confirmation. Five patients with "AHO-like" (Albright's Hereditary Osteodystrophy) skeletal malformations without a clear clinical diagnosis were analyzed by whole exome sequencing and novel potentially pathogenic variants in PTHLH (BDE with short stature, BDE2) and TRPS1 (tricho-rhino-phalangeal syndrome, TRPS) were discovered. The pathogenic impact of these variants was confirmed by in vitro functional studies. This study expands the spectrum of genetic defects associated with BDE2 and TRPS and demonstrates the pathogenicity of TRPS1 missense variants located outside both the nuclear localization signal and the GATA and Ikaros-like binding domains. Unfortunately, we could not find distinctive phenotypic features that might have led to an earlier clinical diagnosis, further highlighting the high degree of overlap among skeletal syndromes associated with brachydactyly and AHO-like features, and the need for a close interdisciplinary workout in these rare patients. This article is protected by copyright. All rights reserved.
We propose a framework for the investigation and the au-tomated design of bacteria to allow the o... more We propose a framework for the investigation and the au-tomated design of bacteria to allow the overproduction of metabolites of industrial interest. Our framework, which consists of three main steps, includes the implementation of a sensitivity analysis method, a multi-objective optimiza-tion algorithm, and a robustness analysis algorithm. They exploit the Pareto optimality principle to explore species, re-actions, pathways, and knockout parameter space. Further-more, they provide theoretical and practical guidelines for design automation: applications on Escherichia coli, Geobac-ter sulfurreducens, Yersinia pestis, Methanosarcina barkery reveal a good performance on a variety of biotechnological products. The toolbox performs the following three inter-connected tasks: 1) the Pathway-oriented Sensitivity Anal-ysis, PoSA, evaluates the sensitive and insensitive parame-ters of the models of the four studied bacteria; 2) the Genetic Design Multi-Objective, GDMO, determines the Pareto ...
Table 1. Knockout strategies obtained through GDMO algorithm for maximising acetate production [m... more Table 1. Knockout strategies obtained through GDMO algorithm for maximising acetate production [mmolh −1 gDW −1]. For each strategy, we report the biomass formation [h −1], the knockout cost (k cost) and the genes and reactions switched off. The variation of acetate and biomass in comparison with the wild type is enclosed in brackets. We also provide a comparison between the robustness analysis. R values (Hafner et al., 2009)
If Turing were a first-year graduate student interested in computers, he would probably migrate i... more If Turing were a first-year graduate student interested in computers, he would probably migrate into the field of computational biology. During his studies, he presented a work about a mathematical and computational model of the morphogenesis process, in which chemical substances react together. Moreover, a protein can be thought of as a compu-tational element, i.e. a processing unit, able to transform an input into an output signal. Thus, in a biochemical pathway, an enzyme reads the amount of reactants (substrates) and converts them in products. In this work, we consider the biochemical pathway in unicellular organisms (e.g. bacteria) as a living computer, and we are able to program it in order to obtain desired outputs. The genome sequence is thought of as an executable code specified by a set of commands in a sort of ad-hoc low-level programming language. Each combination of genes is coded as a string of bits y ∈ {0, 1}L, each of which represents a gene set. By turning off a gen...
Cancer Research, 2020
Treatment of metastatic melanoma has been recently revolutionized by the use of targeted and immu... more Treatment of metastatic melanoma has been recently revolutionized by the use of targeted and immune inhibitors, though efficiently working only in a fraction of patients. Adverse effects still represent major challenges, as well as the rapid development of drug resistance upon treatment, thus suggesting that it is of utmost importance to elucidate additional molecular pathways and targets to better understand the biology of this tumor. In vivo RNAi screens done in patient-derived xenografts (PDXs) that fully phenocopy the original tumor of the patient represent a powerful tool to identify new putative essential and druggable candidates, and to repurpose drugs already approved for other indications. To this end we have recently generated a platform of melanoma PDXs with which we can recapitulate both melanoma growth and metastasization. We have performed in vivo shRNA screens, where we have found numerous and patient-specific epigenetic genes essential for tumor growth in vivo. With ...
International Journal of Molecular Sciences, 2019
Estrogen receptor (ER)-positive progesterone receptor (PR)-negative breast cancers are infrequent... more Estrogen receptor (ER)-positive progesterone receptor (PR)-negative breast cancers are infrequent but clinically challenging. Despite the volume of genomic data available on these tumors, their biology remains poorly understood. Here, we aimed to identify clinically relevant subclasses of ER+/PR− breast cancers based on their mutational landscape. The Cancer Genomics Data Server was interrogated for mutational and clinical data of all ER+ breast cancers with information on PR status from The Cancer Genome Atlas (TCGA), Memorial Sloan Kettering (MSK), and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) projects. Clustering analysis was performed using gplots, ggplot2, and ComplexHeatmap packages. Comparisons between groups were performed using the Student’s t-test and the test of Equal or Given Proportions. Survival curves were built according to the Kaplan–Meier method; differences in survival were assessed with the log-rank test. A total of 3570 ER+ breast c...
Lecture Notes in Computer Science, 2016
We present a thorough in silico analysis and optimization of the genome-scale metabolic model of ... more We present a thorough in silico analysis and optimization of the genome-scale metabolic model of the mycolic acid pathway in M. tuberculosis. We apply and further extend meGDMO to account for finer sensitivity analysis and post-processing analysis, thanks to the combination of statistical evaluation of strains robustness, and clustering analysis to map the phenotype-genotype relationship among Pareto optimal strains. In the first analysis scenario, we find 12 Pareto-optimal single gene set knockout, which completely shut down the pathway, hence critically reducing the pathogenicity of M. tuberculosis; as well as 34 genotypically different strains in which the production of mycolic acid is severely reduced.
Una volta effettuato il sequenziamento Sanger di un campione di DNA, e necessario valutare la cor... more Una volta effettuato il sequenziamento Sanger di un campione di DNA, e necessario valutare la correttezza del sequenziamento analizzando i segnali Raw Data ed Analyzed Data forniti dal sequenziatore per poter risalire ai problemi, legati alle tecniche di preparazione del campione o alla procedura di sequenziamento, che possono generare errori nella determinazione della sequenza. Tali analisi, detta in gergo troubleshooting, attualmente viene effettuata da biologi esperti, in quanto non esistono software che realizzano automaticamente questa analisi. In questa tesi e stato realizzato un algoritmo che compie l'analisi automatica dei segnali e classifica le problematiche in opportune categorie al fine di fornire un supporto efficiente e veloce al troubleshooting. Per realizzare l'algoritmo e stato utilizzato un training set di 167 sequenze con problematiche note. L'algoritmo, implementato in Matlab, utilizza tecniche di filtro a media mobile, di peak detection e altre metodologie tipiche dell'analisi del segnale. Per validare l'algoritmo sono state utilizzate 1200 sequenze con problematiche note. Per ogni problematica e stata testata la performance dell'algoritmo, valutando quante classificazioni corrette vengono da esso compiute. I risultati ottenuti sono buoni, superando per ogni problematica mediamente il 93% dell'assegnazione corretta, definita come il rapporto tra il numero dato dalla somma dei veri positivi e negativi e il numero di sequenze del validation test.
Advances in Experimental Medicine and Biology, 2011
Understanding and optimizing the CO 2 fixation process would allow human beings to address better... more Understanding and optimizing the CO 2 fixation process would allow human beings to address better current energy and biotechnology issues. We focused on modeling the C 3 photosynthetic Carbon metabolism pathway with the aim of identifying the minimal set of enzymes whose biotechnological alteration could allow a functional re-engineering of the pathway. To achieve this result we merged in a single powerful pipeline Sensitivity Analysis (SA), Single-(SO) and Multi-Objective Optimization (MO), and Robustness Analysis (RA). By using our recently developed multipurpose optimization algorithms (PAO and PMO2) here we extend our work exploring a large combinatorial solution space and most importantly, here we present an important reduction of the problem search space. From the initial number of 23 enzymes we have identified 11 enzymes whose targeting
The placental methylation pattern is crucial for the regulation of genes involved in trophoblast ... more The placental methylation pattern is crucial for the regulation of genes involved in trophoblast invasion and placental development, both key events for fetal growth. We investigated LINE-1 methylation and methylome profiling using a methylation EPIC array and the targeted methylation sequencing of 154 normal, full-term pregnancies, stratified by birth weight percentiles. LINE-1 methylation showed evidence of a more pronounced hypomethylation in small neonates compared with normal and large for gestational age. Genome-wide methylation, performed in two subsets of pregnancies, showed very similar methylation profiles among cord blood samples while placentae from different pregnancies appeared very variable. A unique methylation profile emerged in each placenta, which could represent the sum of adjustments that the placenta made during the pregnancy to preserve the epigenetic homeostasis of the fetus. Investigations into the 1000 most variable sites between cord blood and the placenta...