1
|
Petrucci G, Giaretta A, Ranalli P, Cavalca V, Dragani A, Porro B, Hatem D, Habib A, Tremoli E, Patrono C, Rocca B. Platelet thromboxane inhibition by low-dose aspirin in polycythemia vera: Ex vivo and in vivo measurements and in silico simulation. Clin Transl Sci 2022; 15:2958-2970. [PMID: 36200184 PMCID: PMC9747129 DOI: 10.1111/cts.13415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 06/16/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Low-dose aspirin is currently recommended for patients with polycythemia vera (PV), a myeloproliferative neoplasm with increased risk of arterial and venous thromboses. Based on aspirin pharmacodynamics in essential thrombocythemia, a twice-daily regimen is recommended for patients with PV deemed at particularly high thrombotic risk. We investigated the effects of low-dose aspirin on platelet cyclooxygenase activity and in vivo platelet activation in 49 patients with PV, as assessed by serum thromboxane (TX) B2 and urinary TXA2 /TXB2 metabolite (TXM) measurements, respectively. A previously described pharmacokinetic-pharmacodynamic in silico model was used to simulate the degree of platelet TXA2 inhibition by once-daily (q.d.) and twice-daily (b.i.d.) aspirin, and to predict the effect of missing an aspirin dose during q.d. and b.i.d. regimens. Serum TXB2 averaged 8.2 (1.6-54.7) ng/ml and significantly correlated with the platelet count (γ = 0.39) and urinary TXM (γ = 0.52) in multivariable analysis. One-third of aspirin-treated patients with PV displayed less-than-maximal platelet TXB2 inhibition, and were characterized by significantly higher platelet counts and platelet-count corrected serum TXB2 than those with adequate inhibition. Eight patients with PV were sampled again after 12 ± 4 months, and had reproducible serum TXB2 and urinary TXM values. The in silico model predicted complete inhibition of platelet-derived TXB2 by b.i.d. aspirin, a prediction verified in a patient with PV with the highest TXB2 value while on aspirin q.d. and treated short-term with a b.i.d. regimen. In conclusion, one in three patients with PV on low-dose aspirin display less-than-maximal inhibition of platelet TXA2 production. Serum TXB2 measurement can be a valuable option to guide precision dosing of antiplatelet therapy in patients with PV.
Collapse
Affiliation(s)
- Giovanna Petrucci
- Department of Safety and Bioethics, Section of PharmacologyCatholic University School of MedicineRomeItaly
| | | | - Paola Ranalli
- Department of HematologyS. Spirito HospitalPescaraItaly
| | | | | | | | - Duaa Hatem
- Department of Safety and Bioethics, Section of PharmacologyCatholic University School of MedicineRomeItaly
| | - Aida Habib
- Department of Basic Medical Sciences, College of Medicine, QU HealthQatar UniversityDohaQatar
| | | | - Carlo Patrono
- Department of Safety and Bioethics, Section of PharmacologyCatholic University School of MedicineRomeItaly
| | - Bianca Rocca
- Department of Safety and Bioethics, Section of PharmacologyCatholic University School of MedicineRomeItaly
| |
Collapse
|
2
|
Petrucci G, Giaretta A, Ranalli P, Cavalca V, Dragani A, Porro B, Hatem D, Habib A, Tremoli E, Patrono C, Rocca B. Poster No. 005 Platelet Thromboxane Inhibition by Low-Dose Aspirin in Polycythemia Vera:Ex Vivo and In Vivo Measurements and In Silico Simulation. Cardiovasc Res 2022. [DOI: 10.1093/cvr/cvac157.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Low-dose aspirin is currently recommended for patients with polycythemia vera (PV), a myeloproliferative neoplasm with increased risk of arterial and venous thromboses. Based on aspirin pharmacodynamics in essential thrombocythemia, a twice-daily regimen is recommended for PV patients deemed at particularly high thrombotic risk.
Methods
We investigated the effects of low-dose aspirin on platelet cyclooxygenase activity and in vivo platelet activation in 49 PV patients, as assessed by serum thromboxane (TX)B2 and urinary TXA2/TXB2 metabolite (TXM) measurements, respectively. A previously described pharmacokinetic-pharmacodynamic in silico model was used to simulate the degree of platelet TXA2 inhibition by once-daily and twice-daily aspirin, and to predict the effect of missing an aspirin dose during qd and bid regimens.
Results
Serum TXB2 averaged 8.2 [1.6–54.7] ng/ml and significantly correlated with the platelet count (rho = 0.39) and urinary TXM (rho = 0.52) in multivariable analysis. One-third of aspirin-treated PV patients displayed less-than-maximal platelet TXB2 inhibition, and were characterized by significantly higher platelet counts and platelet-count corrected serum TXB2 than those with adequate inhibition. Eight PV patients were sampled again after 12 ± 4 months, and had reproducible serum TXB2 and urinary TXM values. The in silico model predicted complete inhibition of platelet-derived TXB2 by bid aspirin, a prediction verified in a PV patient with the highest TXB2 value while on aspirin qd and treated short-term with a bid regimen.
Conclusions
In conclusion, one in three PV patients on low-dose aspirin display less-than-maximal inhibition of platelet TXA2 production. A personalized approach to antiplatelet therapy can be guided by serum TXB2 measurements.
Collapse
Affiliation(s)
- Giovanna Petrucci
- Department of Safety and Bioethics, Section of Pharmacology, Catholic University School of Medicine , Rome , Italy
| | - Alberto Giaretta
- Department of Pathology, University of Cambridge , Cambridge , UK
| | - Paola Ranalli
- Department of Hematology, S. Spirito Hospital , Pescara , Italy
| | | | - Alfredo Dragani
- Department of Hematology, S. Spirito Hospital , Pescara , Italy
| | | | - Duaa Hatem
- Department of Safety and Bioethics, Section of Pharmacology, Catholic University School of Medicine , Rome , Italy
| | - Aida Habib
- Department of Basic Medical Sciences, QU Health, Qatar University , Doha , Qatar
| | | | - Carlo Patrono
- Department of Safety and Bioethics, Section of Pharmacology, Catholic University School of Medicine , Rome , Italy
| | - Bianca Rocca
- Department of Safety and Bioethics, Section of Pharmacology, Catholic University School of Medicine , Rome , Italy
| |
Collapse
|
3
|
Giaretta A, Petrucci G, Rocca B, Toffolo GM. Physiologically based modelling of the antiplatelet effect of aspirin: A tool to characterize drug responsiveness and inform precision dosing. PLoS One 2022; 17:e0268905. [PMID: 35976924 PMCID: PMC9385056 DOI: 10.1371/journal.pone.0268905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
A computational approach involving mathematical modeling and in silico experiments was used to characterize the determinants of extent and duration of platelet cyclooxygenase (COX)-1 inhibition by aspirin and design precision dosing in patients with accelerated platelet turnover or reduced drug bioavailability. To this purpose, a recently developed physiologically-based pharmacokinetics (PK) and pharmacodynamics (PD) model of low-dose aspirin in regenerating platelets and megakaryocytes, was used to predict the main features and determinants of platelet COX-1 inhibition. The response to different aspirin regimens in healthy subjects and in pathological conditions associated with alterations in aspirin PK (i.e., severely obese subjects) or PD (i.e., essential thrombocytemya patients), were simulated. A model sensitivity analysis was performed to identify the main processes influencing COX-1 dynamics. In silico experiments and sensitivity analyses indicated a major role for megakaryocytes and platelet turnover in determining the extent and duration of COX-1 inhibition by once-daily, low-dose aspirin. They also showed the superiority of reducing the dosing interval vs increasing the once-daily dose in conditions of increased platelet turnover, while suggested specific dose adjustments in conditions of possible reduction in drug bioavailability. In conclusion, the consistency of our model-based findings with experimental data from studies in healthy subjects and patients with essential thrombocythemia supports the potential of our approach for describing the determinants of platelet inhibition by aspirin and informing precision dosing which may guide personalized antithrombotic therapy in different patient populations, especially in those under-represented in clinical trials or in those associated with poor feasibility.
Collapse
Affiliation(s)
- Alberto Giaretta
- Department of Information Engineering, University of Padova, Padova, Italy
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: ,
| | - Giovanna Petrucci
- Department of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - Bianca Rocca
- Department of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | | |
Collapse
|
4
|
Giaretta A. Frequency response in splicing regulation under mRNA auto-depletion control. Annu Int Conf IEEE Eng Med Biol Soc 2022; 2022:2248-2253. [PMID: 36083926 DOI: 10.1109/embc48229.2022.9871147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nowadays, there exists a huge literature about stochastic model of transcriptional and translational control in gene networks. However, results related to post-transcriptional regulation via splicing and its connection with transcriptional and translational regulation are almost missing in the current literature and only related to the steady state moments investigation. Nowadays, it is becoming of paramount importance the need for modeling post-transcriptional regulation via splicing especially for DNA viruses or retroviruses. However, there exists only few studies in the literature about splicing regulation and none of them investigate its behavior in the frequency domain that can unveil important features of dynamical stochastic systems that cannot be revealed by the sole steady state moment investigation. The aim of this work is to theoretically investigate a simple gene network subject to splicing regulation with negative feedback control, implemented through mRNA auto-depletion under a frequency domain perspective. This study showed the pivotal role of the burst size, enhancing the noise power spectrum, as well as the splicing conversion rates capable to increase and decrease the noise power spectrum in the pre-mRNA and mRNA, respectively, for high values of conversion rates. Importantly, it shows the capability of the mRNA autodepletion control to modulate the noise as a frequency-dependent amplifying control as a function of the negative feedback strengths.
Collapse
|
5
|
Saunders-Wood T, Egawa N, Zheng K, Giaretta A, Griffin HM, Doorbar J. Role of E6 in Maintaining the Basal Cell Reservoir during Productive Papillomavirus Infection. J Virol 2022; 96:e0118121. [PMID: 35019722 PMCID: PMC8906426 DOI: 10.1128/jvi.01181-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/28/2021] [Indexed: 11/20/2022] Open
Abstract
Papillomaviruses exclusively infect stratified epithelial tissues and cause chronic infections. To achieve this, infected cells must remain in the epithelial basal layer alongside their uninfected neighbors for years or even decades. To examine how papillomaviruses achieve this, we used the in vivo MmuPV1 (Mus musculus papillomavirus 1) model of lesion formation and persistence. During early lesion formation, an increased cell density in the basal layer, as well as a delay in the infected cells' commitment to differentiation, was apparent in cells expressing MmuPV1 E6/E7 RNA. Using cell culture models, keratinocytes exogenously expressing MmuPV1 E6, but not E7, recapitulated this delay in differentiation postconfluence and also grew to a significantly higher density. Cell competition assays further showed that MmuPV1 E6 expression led to a preferential persistence of the cell in the first layer, with control cells accumulating almost exclusively in the second layer. Interestingly, the disruption of MmuPV1 E6 binding to MAML1 protein abrogated these phenotypes. This suggests that the interaction between MAML1 and E6 is necessary for the lower (basal)-layer persistence of MmuPV1 E6-expressing cells. Our results indicate a role for E6 in lesion establishment by facilitating the persistence of infected cells in the epithelial basal layer, a mechanism that is most likely shared by other papillomavirus types. Interruption of this interaction is predicted to impede persistent papillomavirus infection and consequently provides a novel treatment target. IMPORTANCE Persistent infection with high-risk HPV types can lead to development of HPV-associated cancers, and persistent low-risk HPV infection causes problematic diseases, such as recurrent respiratory papillomatosis. The management and treatment of these conditions pose a considerable economic burden. Maintaining a reservoir of infected cells in the basal layer of the epithelium is critical for the persistence of infection in the host, and our studies using the mouse papillomavirus model suggest that E6 gene expression leads to the preferential persistence of epithelial cells in the lower layers during stratification. The E6 interaction with MAML1, a component of the Notch pathway, is required for this phenotype and is linked to E6 effects on cell density and differentiation. These observations are likely to reflect a common E6 role that is preserved among papillomaviruses and provide us with a novel therapeutic target for the treatment of recalcitrant lesions.
Collapse
Affiliation(s)
| | - Nagayasu Egawa
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Ke Zheng
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Alberto Giaretta
- Department of Information Engineering, University of Padova, Padua, Italy
| | - Heather M. Griffin
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
6
|
Giaretta A. Stochasticity in transcriptional, splicing and translational regulations in time and frequency domains. Biosystems 2022; 212:104595. [DOI: 10.1016/j.biosystems.2021.104595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/13/2021] [Accepted: 12/22/2021] [Indexed: 11/02/2022]
|
7
|
Zorzan I, Del Favero S, Giaretta A, Manganelli R, Di Camillo B, Schenato L. Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response. BMC Bioinformatics 2021; 22:558. [PMID: 34798803 PMCID: PMC8605609 DOI: 10.1186/s12859-021-04372-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/11/2021] [Indexed: 12/19/2022] Open
Abstract
Background The ability to rapidly adapt to adverse environmental conditions represents the key of success of many pathogens and, in particular, of Mycobacterium tuberculosis. Upon exposition to heat shock, antibiotics or other sources of stress, appropriate responses in terms of genes transcription and proteins activity are activated leading part of a genetically identical bacterial population to express a different phenotype, namely to develop persistence. When the stress response network is mathematically described by an ordinary differential equations model, development of persistence in the bacterial population is associated with bistability of the model, since different emerging phenotypes are represented by different stable steady states. Results In this work, we develop a mathematical model of SigE stress response network that incorporates interactions not considered in mathematical models currently available in the literature. We provide, through involved analytical computations, accurate approximations of the system’s nullclines, and exploit the obtained expressions to determine, in a reliable though computationally efficient way, the number of equilibrium points of the system. Conclusions Theoretical analysis and perturbation experiments point out the crucial role played by the degradation pathway involving RseA, the anti-sigma factor of SigE, for coexistence of two stable equilibria and the emergence of bistability. Our results also indicate that a fine control on RseA concentration is a necessary requirement in order for the system to exhibit bistability. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04372-5.
Collapse
Affiliation(s)
- Irene Zorzan
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.
| | - Simone Del Favero
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Alberto Giaretta
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131, Padova, Italy.,Department of Comparative Biomedicine and Food Science, University of Padova, 35020, Legnaro (Padova), Italy
| | - Luca Schenato
- Department of Information Engineering, University of Padova, 35131, Padova, Italy
| |
Collapse
|
8
|
Giaretta A, Da Ros F, Mazzucato M, Pedersen MG, Visentin R. Modeling Pharmacokinetics of Doxorubicin in Multiple Myeloma Cells. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:4374-4378. [PMID: 34892189 DOI: 10.1109/embc46164.2021.9629493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Doxorubicin (DOXO) is a well-established chemotherapy drug for treatment of different tumors, ranging from breast cancer, melanoma to multiple myeloma (MM). Here, we present a coupled experimental/modeling approach to study DOXO pharmacokinetics in MM cells, investigate its distribution among the extracellular and intracellular compartments during time. Three model candidates are considered and identified. Model selection is performed based on its ability to describe the data both qualitatively and in terms of quantitative indexes. The most parsimonious model consists of a nonlinear structure with a saturation-threshold control of intracellular DOXO efflux by the DOXO bound to the cellular DNA. This structure could explain the hypothesis that MM cells are drug-resistant, likely due to the involvement of P-glycoproteins.The proposed model is able to predict the intracellular (free and bound) DOXO and suggests the presence of a saturation-threshold drug-resistant mechanism.Clinical Relevance- The model can be used to properly understand and guide further experimental setup, e.g., to investigate multiple myeloma cell variability among different cell lines.
Collapse
|
9
|
Giaretta A. Frequency analysis of splicing regulation. Annu Int Conf IEEE Eng Med Biol Soc 2021; 2021:4487-4492. [PMID: 34892215 DOI: 10.1109/embc46164.2021.9629722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In the past decades, mathematical modelers developed a huge literature to model and analyze gene networks under both deterministic and stochastic formalisms. Such literature is predominantly focused on modeling transcriptional and translational regulation, while the development of proper mathematical frameworks to model and study post-transcriptional regulation via splicing and its connection with transcriptional and translational regulation are almost missing. Nowadays, it is becoming of paramount importance the need for modeling post-transcriptional regulation via splicing especially for bacteria or viruses. However, current literature is focused on investigating splicing regulation at steady state and none of them have the purpose to investigate gene networks behavior in the frequency domain, thus providing only a partial investigation about the system dynamical response. The aim of this work is to theoretically investigate a simple gene network subjects to splicing regulation with/without negative feedback control under a frequency domain perspective. This study showed the pivotal role of the burst size, as well as splicing conversion rates to modulate the noise and the power spectrum response. It also shows an interesting behavior under the frequency domain induced by the merging effect of burst size, splicing conversion rates and negative feedback strength.
Collapse
|
10
|
Giaretta A. A Human Papillomavirus Early Promoter Minimal Model: Viral Population and Stochasticity. Annu Int Conf IEEE Eng Med Biol Soc 2020; 2020:2471-2474. [PMID: 33018507 DOI: 10.1109/embc44109.2020.9176564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
HPV infection starts with the activation of the early promoter (EP) regulatory core and the replication of the viral particles to around 10-100 per cell at the beginning of the infection. For this reason, understanding the deterministic and stochastic role of the population number of viruses inside the cell is of pivotal importance to understand the regulation of the EP and the viral latency.The aim of this study is to extend a recently published minimal model of the EP transcriptional regulation in order to consider the effect of the viral population on gene regulation, to perform the bifurcation analysis and to understand the role of the stochasticity at the beginning of the infection.The bifurcation analysis showed how modeling the viral population number is pivotal to exhibit a bistable behavior, potentially linked to the viral latency. Moreover, the viral population number was identified as an important source of stochasticity, which is of paramount importance to drive the bistable switching mechanism in the first stages of infection.
Collapse
|
11
|
Abstract
In the past decades an extensive mathematical literature was developed to model and analyze gene networks under both deterministic and stochastic formalisms. However, such literature is predominantly focused to deal with the modeling of transcriptional and translational regulation, but results related to post-transcriptional regulation and its connection with transcriptional regulation are poorly investigated. However, it is becoming of paramount importance the need for modeling post-transcriptional regulation via splicing especially for minor organisms or viruses.The aim of this study is to propose a first general basic modeling scheme for modeling gene expression via alternative splicing and investigating the basic deterministic and stochastic features of the pre-mRNA, mRNAs and proteins under different biological conditions.This first study showed the dynamical properties of alternative splicing, the faster kinetics of the pre-mRNA compared to the mRNA and the importance to stochastically model gene networks when considering the post-transcriptional regulation.
Collapse
|
12
|
Giaretta A, Toffolo GM, Elston TC. Stochastic modeling of human papillomavirusearly promoter gene regulation. J Theor Biol 2020; 486:110057. [PMID: 31672406 PMCID: PMC6937396 DOI: 10.1016/j.jtbi.2019.110057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/01/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022]
Abstract
High risk forms of human papillomaviruses (HPVs) promote cancerous lesions and are implicated in almost all cervical cancer. Of particular relevance to cancer progression is regulation of the early promoter that controls gene expression in the initial phases of infection and can eventually lead to pre-cancer progression. Our goal was to develop a stochastic model to investigate the control mechanisms that regulate gene expression from the HPV early promoter. Our model integrates modules that account for transcriptional, post-transcriptional, translational and post-translational regulation of E1 and E2 early genes to form a functioning gene regulatory network. Each module consists of a set of biochemical steps whose stochastic evolution is governed by a chemical Master Equation and can be simulated using the Gillespie algorithm. To investigate the role of noise in gene expression, we compared our stochastic simulations with solutions to ordinary differential equations for the mean behavior of the system that are valid under the conditions of large molecular abundances and quasi-equilibrium for fast reactions. The model produced results consistent with known HPV biology. Our simulation results suggest that stochasticity plays a pivotal role in determining the dynamics of HPV gene expression. In particular, the combination of positive and negative feedback regulation generates stochastic bursts of gene expression. Analysis of the model reveals that regulation at the promoter affects burst amplitude and frequency, whereas splicing is more specialized to regulate burst frequency. Our results also suggest that splicing enhancers are a significant source of stochasticity in pre-mRNA abundance and that the number of viruses infecting the host cell represents a third important source of stochasticity in gene expression.
Collapse
Affiliation(s)
- Alberto Giaretta
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Timothy C Elston
- Department of Pharmacology, University of North Carolina, Chapel Hill, United States of America.
| |
Collapse
|
13
|
Abstract
High risk human papillomavirus (HPV) can induce cervical and oropharyngeal cancerous lesions. Different HPV strains, as well as still unknown mechanisms can be associated to a range of biochemical parameters that can importantly affect the HPV gene expression dynamics. For this reason, it is of pivotal importance to investigate how parameters variation can induce interesting behaviors such as viral latency in place of the normal gene replication activity. The aim of this study is to perform bifurcation analysis on a minimal model of the early promoter regulatory core controlled by E2 transcriptional regulation. The bifurcation analysis showed how E2 regulation can induce a bistability on the early promoter gene expression that could explain the interplay between viral latency and gene replication regimen.
Collapse
|
14
|
Giaretta A, Toffolo GM. Sensitivity Analysis of a Model of Human Papillomavirus Late Promoter Regulation. Annu Int Conf IEEE Eng Med Biol Soc 2019; 2019:2913-2916. [PMID: 31946500 DOI: 10.1109/embc.2019.8856475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A mathematical model of Human Papillomavirus late promoter regulation was recently developed, able to predict the main features of HPV gene expression during cellular differentiation under productive infection. A sensitivity analysis is performed to characterize the influence of transcriptional, post-transcriptional and translational regulations on the viral species related to E1, E2, E4 and Li genes. Sensitivity analysis indicates strong influence of parameters related to transcriptional and translational regulation. It also shows a strong influence on the parameters related to post-transcriptional regulation, showing the importance of modeling splicing regulation to well describe the biology of the late promoter.
Collapse
|
15
|
Petrucci G, Zaccardi F, Giaretta A, Cavalca V, Capristo E, Cardillo C, Pitocco D, Porro B, Schinzari F, Toffolo G, Tremoli E, Rocca B. Obesity is associated with impaired responsiveness to once-daily low-dose aspirin and in vivo platelet activation. J Thromb Haemost 2019; 17:885-895. [PMID: 30933424 DOI: 10.1111/jth.14445] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The prevalence and degree of obesity is rising worldwide, increases cardiovascular risk, modifies body composition and organ function, and potentially affects the pharmacokinetics and/or pharmacodynamics of drugs. OBJECTIVES To investigate the pharmacodynamics of once-daily low-dose aspirin in healthy obese subjects, and to assess whether body weight (BW) and body mass index (BMI) affect the pharmacology of aspirin. PATIENTS/METHODS Otherwise healthy, obese (BMI > 30 kg/m2 ) subjects were studied before and after 3-4 weeks of 100-mg once-daily aspirin intake. Aspirin pharmacodynamics were assessed according to serum thromboxane (TX) B2 levels measured at 4 hours, 24 hours (i.e., posologic interval) and 48 hours after the last witnessed intake; age-matched and sex-matched non-obese controls were included. A previously calibrated pharmacokinetic/pharmacodynamic in silico model of aspirin was used to fit serum TXB2 data from obese subjects. At baseline, the major urinary TXA2 and prostacyclin metabolites, urinary isoprostane and plasma inflammatory biomarkers were measured. RESULTS In 16 obese subjects (aged 47 ± 11 years; BMI of 39.4 ± 5.1 kg/m2 ), residual serum TXB2 values between 4 and 48 hours after aspirin intake were increased 3- to 5-fold as compared with controls. At 24 hours, the residual serum TXB2 level was log-linearly associated with body size over a wide range of BMI and BW values, without any apparent threshold. The in silico model predicted that reduced aspirin bioavailability would be inversely related to body size and rescued by 200 mg of aspirin once daily or 85 mg twice daily. Baseline urinary TXA2 metabolite, isoprostane and plasma C-reactive protein levels were significantly increased in obese subjects. CONCLUSIONS Obesity is associated with impaired aspirin responsiveness, largely because of body size. Impaired inhibition of platelet activation by conventional low-dose aspirin may affect antithrombotic efficacy.
Collapse
Affiliation(s)
- Giovanna Petrucci
- Istituto di Farmacologia, Università Cattolica, Rome, Italy
- Fondazione Policlinico Universitario IRCCS, A. Gemelli, Rome, Italy
| | | | - Alberto Giaretta
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Esmeralda Capristo
- Fondazione Policlinico Universitario IRCCS, A. Gemelli, Rome, Italy
- Internal Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Carmine Cardillo
- Fondazione Policlinico Universitario IRCCS, A. Gemelli, Rome, Italy
- Istituto di Patologia Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Dario Pitocco
- Fondazione Policlinico Universitario IRCCS, A. Gemelli, Rome, Italy
- Diabetology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Francesca Schinzari
- Istituto di Patologia Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianna Toffolo
- Department of Information Engineering, University of Padova, Padova, Italy
| | | | - Bianca Rocca
- Istituto di Farmacologia, Università Cattolica, Rome, Italy
- Fondazione Policlinico Universitario IRCCS, A. Gemelli, Rome, Italy
| |
Collapse
|
16
|
Giaretta A. Stochastic Modeling of the Co-Regulation between Early and E8 Promoters in Human Papillomavirus. Annu Int Conf IEEE Eng Med Biol Soc 2018; 2018:5026-5029. [PMID: 30441470 DOI: 10.1109/embc.2018.8513406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
High risk HPV can induce cervical and oropharyngeal cancerous Iesions. The initial phase of the infection is characterized by a fine regulation of the viral DNA replication, in order to maintain 10-100 DNA copies per cell. Such regulation is primarily controlled by El and E2 proteins produced by the early promoter. The recently discovered E8 promoter is capable to co-regulate the early one in order to maintain a low and constant viral DNA copy number.The aim of this study is to develop a novel stochastic mathematical model of the co-regulation between the E8 and the early promoter, with the main purpose to rigorously show the E8 promoter capability to finely regulate the HPV transcripts which control the DNA replication in the first stages of the infection.The model, condensing the biological knowledge present in literature, describes the interaction between the two promoters and shows how the E8 co-regulation is capable to reject the stochastic noise of E2 gene expression to a higher extent than the early promoter negative auto-feedback. This proves the capability of the E8 promoter to finely control the HPV genomes copy number.
Collapse
|
17
|
Abstract
High risk HPV can induce cervical and oropharyngeal Iesions. HPV productive infection is strictly linked by differentiation-dependent control of the late promoter. This latter produces HPV transcripts at different epithelial layers through a complex post-transcriptional control. The aim of this study is to develop a novel mathematical model of the late promoter condensing the biological knowledge present in literature. The model describes the interaction among primary transcript, spliced transcripts and their proteins and includes the major splicing mechanisms. When used as an in silico tool it shows the crucial role of splicing regulation to explain the HPV gene expression. Novel testing hypothesis are then formulated to uncover this still elusive but pivotal promoter.
Collapse
|
18
|
Schiavon M, Acciaroli G, Vettoretti M, Giaretta A, Visentin R. A Model of Acetaminophen Pharmacokinetics and its Effect on Continuous Glucose Monitoring Sensor Measurements. Annu Int Conf IEEE Eng Med Biol Soc 2018; 2018:159-162. [PMID: 30440363 DOI: 10.1109/embc.2018.8512257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Some of commercial continuous glucose monitoring (CGM) devices, i.e., minimally-invasive sensors able to measure almost continuously glucose concentration in the subcutaneous tissue, recently received the regulatory approval to be used for making therapeutic decisions in diabetes management. A fundamental requirement for its safe and effective use is represented by the accuracy of CGM measurements. However, despite recent advances in sensors accuracy and reliability, CGM still suffers from inaccuracy problems in presence of pharmacologic interferences, e.g., the common orally administered acetaminophen (APAP), which artificially raises CGM glucose readings for several hours. A model of the artifact induced by APAP on CGM measurements would be useful to design algorithms to compensate such a distortion. The aim of this work is to exploit the data published by previous literature studies to design a model of oral APAP pharmacokinetics and its effect on glucose concentration measured by CGM sensors. Specifically, the developed model was identified on average data of both plasma APAP concentration and the APAP effect on CGM profiles after an oral administration of 1000 mg of APAP. The APAP effect on CGM readings was estimated from the difference observed, in the same study, between the glucose profile measured by a Dexcom G4 Platinum sensor and the plasma glucose concentration. The model was validated by comparing the simulated effect of mealtime APAP administration in CGM measurements of 100 virtual subjects generated by the UVA/Padova Type 1 Diabetes (TID) Simulator vs. the effect observed in a clinical study by Maahs et al. (Diabetes Care, 2015) in 40 TID subjects taking APAP at breakfast. Results suggest that the proposed model is able to reliably describe the mean APAP effect on CGM measurements.
Collapse
|
19
|
Spognardi A, Donno MD, Dragoni N, Giaretta A. Analysis of DDoS-Capable IoT Malwares. ANNALS OF COMPUTER SCIENCE AND INFORMATION SYSTEMS 2017. [DOI: 10.15439/2017f288] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
20
|
Giaretta A, Rocca B, Di Camillo B, Toffolo GM, Patrono C. In Silico Modeling of the Antiplatelet Pharmacodynamics of Low-dose Aspirin in Health and Disease. Clin Pharmacol Ther 2017; 102:823-831. [PMID: 28378909 DOI: 10.1002/cpt.694] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/06/2017] [Accepted: 03/11/2017] [Indexed: 01/25/2023]
Abstract
The influence of platelet turnover on cyclooxygenase (COX-1) inhibition by low-dose aspirin remains largely uncharacterized due to limited feasibility of studying aspirin pharmacodynamics in bone marrow precursors. We developed an in silico compartmental model describing the aspirin effects on COX-1 activity in a population of megakaryocytes (MK) and in peripheral platelets. Model parameters were inferred from the literature and calibrated using measurements of serum thromboxane B2 (sTXB2 ), as proxy of COX-1 activity in peripheral platelets, in 17 healthy subjects and 24 patients with essential thrombocythemia (ET). The model reproduced well the average time-course of sTXB2 inhibition in healthy (accuracy = 10.4%), the reduced inhibition of sTXB2 observed in ET, and the effect of different dosing regimens. In conclusion, the in silico model accurately describes COX-1 inactivation by low-dose aspirin in MK and platelets in different clinical settings, and might help personalize aspirin regimens in conditions of altered megakaryopoiesis.
Collapse
Affiliation(s)
- A Giaretta
- Department of Information Engineering, University of Padova, Padova, Italy
| | - B Rocca
- Department of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - B Di Camillo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - G M Toffolo
- Department of Information Engineering, University of Padova, Padova, Italy
| | - C Patrono
- Department of Pharmacology, Catholic University School of Medicine, Rome, Italy
| |
Collapse
|
21
|
Abstract
In high risk forms, human papillomaviruses (HPV) can either induce or promote cancerous lesions, especially cervical cancer which is considered the second most common cancer in the women worldwide. HPV life cycle is tightly linked to the infected cell differentiation program and its evolution is strictly joined to the switch between the early and the late viral polycistronic promoters.The aim of this study is to develop a novel mathematical model which collects and structures the available biologic knowledge on the early promoter regulation for HPV in episomal form. The model includes the main regulation by E2 viral protein as well as a novel discovered co-regulation function mediated by the viral E1 protein. Only by including both E2 and E1 regulatory effect the model is able to correctly predict the temporal behaviour of the early promoter switching off. A possible use of the model as in silico tool to evaluate new antiviral therapies is discussed.
Collapse
|
22
|
Carraro A, Fabbri P, Giaretta A, Peruzzo L, Tateo F, Tellini F. Effects of redox conditions on the control of arsenic mobility in shallow alluvial aquifers on the Venetian Plain (Italy). Sci Total Environ 2015; 532:581-594. [PMID: 26115337 DOI: 10.1016/j.scitotenv.2015.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 06/04/2023]
Abstract
The Venetian Plain is known for the occurrence of areas with high concentrations of arsenic in groundwater (greater than 400 μg/L). The study area represents the typical residential, industrial and agricultural features of most Western countries and is devoid of hydrothermal, volcanic or anthropogenic sources of arsenic. The aim of the study is to model the arsenic mobilization and the water-rock interaction by a complete hydrogeochemical investigation (analyses of filtered and unfiltered groundwater sediment mineralogy and geochemistry). The groundwater arsenic contamination and redox conditions are highly variable. Groundwaters with oxidizing and strongly reducing potentials have much lower arsenic concentrations than do mildly reducing waters. The grain size of the aquifer sediments includes gravels, sands and silty-clays. A continuous range of organic material concentrations is observed (from zero to 40%). The amount of sedimentary organic matter is highly correlated with the arsenic content of the sediments (up to 300 mg/kg), whereas no relationships are detectable between arsenic and other chemical parameters. The occurrence of arsenic minerals was observed as a peculiar feature under the scanning electron microscope. Arsenic and sulfur are the sole constituents of small tufts or thin crystals concentrated in small masses. These arsenic minerals were clearly observed in the peat sediments, in agreement with the geochemical modeling that requires very reducing conditions for their precipitation from the groundwater. The modeling suggests that, under oxidizing conditions, arsenic is adsorbed; moreover, a continuous decrease in the redox potential causes increasing desorption of arsenic. If the reducing conditions become more intense, the formation of As-S minerals would explain the lower concentration of arsenic measured in the strongly reducing groundwater. Even if As-sulfides are rare under low-temperature conditions, the anomalous abundance of reductants (organic matter) can locally stabilize As-S minerals, which can scavenge large quantities of groundwater arsenic.
Collapse
Affiliation(s)
- A Carraro
- Institute of Geosciences and Earth Resources, National Research Council (CNR) of Italy, Padova, Italy c/o Department of Geosciences, University of Padova, 35131 Padova, Italy
| | - P Fabbri
- Institute of Geosciences and Earth Resources, National Research Council (CNR) of Italy, Padova, Italy c/o Department of Geosciences, University of Padova, 35131 Padova, Italy; Department of Geosciences, University of Padova, 35131 Padova, Italy
| | - A Giaretta
- Institute of Geosciences and Earth Resources, National Research Council (CNR) of Italy, Padova, Italy c/o Department of Geosciences, University of Padova, 35131 Padova, Italy
| | - L Peruzzo
- Institute of Geosciences and Earth Resources, National Research Council (CNR) of Italy, Padova, Italy c/o Department of Geosciences, University of Padova, 35131 Padova, Italy
| | - F Tateo
- Institute of Geosciences and Earth Resources, National Research Council (CNR) of Italy, Padova, Italy c/o Department of Geosciences, University of Padova, 35131 Padova, Italy
| | - F Tellini
- Institute of Geosciences and Earth Resources, National Research Council (CNR) of Italy, Padova, Italy c/o Department of Geosciences, University of Padova, 35131 Padova, Italy
| |
Collapse
|
23
|
Giaretta A, Rocca B, Di Camillo B, Toffolo G, Patrono C. An in silico model of aspirin-iduced inactivation of platelet and Megakaryocyte Cyclooxygenase-1. Clin Ther 2015. [DOI: 10.1016/j.clinthera.2015.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
24
|
Giaretta A, Rocca B, Di Camillo B, Toffolo G, Patrono C. An in silico model of aspirin-iduced inactivation of platelet and Megakaryocyte Cyclooxygenase-1. Clin Ther 2015. [DOI: 10.1016/j.clinthera.2015.05.293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
25
|
Cariati E, Botta C, Danelli SG, Forni A, Giaretta A, Giovanella U, Lucenti E, Marinotto D, Righetto S, Ugo R. Solid state and solution fine tuning of the linear and nonlinear optical properties of (2-pyrene-1-yl-vinyl)pyridine by protonation–deprotonation reactions. Chem Commun (Camb) 2014; 50:14225-8. [DOI: 10.1039/c4cc05891g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
26
|
Valente M, Pettenazzo E, Thiene G, Molin GM, Martignago F, De Giorgi G, Gatti AM, Giaretta A, Pasquino E, Talenti E, Rinaldi S. Detoxified glutaraldehyde cross-linked pericardium: tissue preservation and mineralization mitigation in a subcutaneous rat model. J Heart Valve Dis 1998; 7:283-91. [PMID: 9651841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIM OF THE STUDY Glutaraldehyde is considered a promoter of calcification by the action of toxic aldehyde group residuals from cross-linking. Post-fixation treatment with homocysteic acid (HA), besides bonding aldehyde groups and neutralizing toxicity, should enhance biocompatibility due to the strongly electronegative sulfonic group. The aim of this investigation was to evaluate HA efficacy on tissue preservation and dystrophic calcification mitigation in glutaraldehyde cross-linked bovine pericardium (BP) using a subcutaneous rat model. METHODS Four samples of BP, two with glutaraldehyde-HA and two with glutaraldehyde treatment, were implanted in each of 24 male Sprague-Dawley rats. Three rats were killed at 14 days, eight at 28 days, eight at 56 days and five at 84 days. Unimplanted glutaraldehyde-HA- and glutaraldehyde-treated samples served as controls. All samples were studied by gross examination, mammography, light transmission and scanning electron microscopy, and atomic absorption spectroscopy. The nature of mineralization was investigated by coupling techniques of scanning electron microscopy, electron microprobe analysis and X-ray powder diffraction. RESULTS No histological and ultrastructural differences were found between glutaraldehyde-HA- and glutaraldehyde-treated BP, whether implanted or unimplanted. In both groups, calcification progressed with time, but significantly less after glutaraldehyde-HA treatment than after glutaraldehyde alone and at all time intervals (14.63 +/- 21.34 versus 43.17 +/- 15.99 at 28 days, p = 0.003; 56.42 +/- 40.20 versus 90.59 +/- 32.90 at 56 days, p = 0.008; 91.68 +/- 67.68 versus 156.23 +/- 17.85 at 84 days, p = 0.01). Differences were evident by mammography and histology (von Kossa stain). Electron microprobe analysis in both groups showed the composition of calcified nuclei to be calcium phosphate, stoichiometrically close to apatite (Ca5(PO4)3(OH)). The occurrence of crystallized apatite was supported by X-ray powder diffraction findings, the amount of crystallized apatite being higher in glutaraldehyde-treated samples. CONCLUSIONS Post-fixation treatment with HA preserves BP structural properties and significantly mitigates mineralization of long-term subcutaneous implants.
Collapse
Affiliation(s)
- M Valente
- University of Padua and Modena, Sorin Biomedica-Cardio, Saluggia, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Cantanna R, Morini M, Risuglia S, Lopez T, Danieli D, Giaretta A, Anni R, Rotunno L. [Carotid thromboendarterectomy. Comparison of two anesthesiologic techniques]. Minerva Anestesiol 1991; 57:149-53. [PMID: 1922862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The authors have examined two homogeneous groups of patients suffering from "carotid stenosis", operated by TEAC with two different techniques of anaesthesia: general and local-regional (block). Neurological and cardiovascular complications have been recorded in pre and post-operative period. The results analysed statistically with the Pearson test, were homogeneous. However the authors, on the basis of their experience, prefer local-regional (block) anaesthesia for good haemodynamic stability and a better neurologic control. Moreover the block anaesthesia was better in patients.
Collapse
Affiliation(s)
- R Cantanna
- Servizio di Anestesia e Rianimazione, USSL n. 8 - Stabilimento Ospedaliero di Vicenza
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Cantanna R, Morini M, Risuglia S, Torelli L, Danieli D, Giaretta A, Anni R, Dall'Antonia F. [Block of the cervical plexus in surgery of the carotid artery. Our experience with 142 cases]. Minerva Anestesiol 1989; 55:301-5. [PMID: 2622542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The main anesthesiological problem in TEAC operations is the possibility of evaluating the degree of tolerance after carotid artery clamping. When facing this situation, some anesthesiologists prefer to administer general anesthesia, others prefer loco-regional anesthesia. On the basis of their background and experience, the Authors, from 1.1.1987 to 12.31.1988, have performed 142 nerve blocks of the superficial and the cervical plexus. The proposed technique is simple. No side effects are observed. Moreover it is gratifying for the surgeon and safe from risks for patients. Loco-regional anesthesia permits a close neurologic monitoring that is easily understandable and inexpensive. When performing this kind of surgery, this technique seems to be valid and effective.
Collapse
|