Review
Computer Science, Interdisciplinary Applications
Anna Procopio, Giuseppe Cesarelli, Leandro Donisi, Alessio Merola, Francesco Amato, Carlo Cosentino
Summary: Mechanistic-based models (MMs) and Machine Learning (ML) techniques are often used separately to investigate biological systems. This review investigates the combination of MMs and ML in systems biology research and highlights the great potential of this hybrid approach at both micro and macro biological scales.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Biochemical Research Methods
Anna Niarakis, Tomas Helikar
Summary: The passage discusses the use of mechanistic computational models in studying regulatory mechanisms in biological processes, and presents a detailed protocol for model construction. The protocol outlines steps including defining scope, choosing validation criteria, selecting modeling approach, constructing and simulating the model.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Patrick A. Giolando, Kelsey Hopkins, Barrett F. Davis, Nicole Vike, Adib Ahmadzadegan, Arezoo M. Ardekani, Pavlos P. Vlachos, Joseph V. Rispoli, Luis Solorio, Tamara L. Kinzer-Ursem
Summary: Implantable, bioresorbable drug delivery systems provide a patient-tailored drug dosage with increased patient compliance. Mechanistic mathematical modeling accelerates the design of release systems by predicting physical anomalies and short- and long-term drug release profiles. This study investigates the impact of various parameters on drug release and offers new insight into the design process for tailored release systems.
ADVANCED MATERIALS
(2023)
Review
Biotechnology & Applied Microbiology
Antonio Gaetano Cardillo, Maria Monica Castellanos, Benoit Desailly, Sandrine Dessoy, Marco Mariti, Rui M. C. Portela, Bernadette Scutella, Moritz von Stosch, Emanuele Tomba, Christos Varsakelis
Summary: Chemical, manufacturing, and control development timelines are crucial in the end-to-end development of vaccines. In the race to accelerate timelines, in silico process development using a mechanistically oriented approach is a viable strategy. Modeling competencies including fluid mechanics, thermodynamics, transport phenomena, intracellular modeling, hybrid modeling, and data science are essential pillars for vaccine development. A generic pathway has been crafted to incorporate these modeling competencies into an in silico process development strategy.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Immunology
Giuditta Guerrini, Antonio Vivi, Sabrina Gioria, Jessica Ponti, Davide Magri, Arnd Hoeveler, Donata Medaglini, Luigi Calzolai
Summary: Physicochemical properties of adjuvant-protein antigen complexes impact vaccine efficacy and safety, and a multi-staged characterization strategy has been developed for accurate assessment of nanoaluminum-ovalbumin complex, which can be adapted for various adjuvant-protein antigen combinations to control quality and improve immunological outcomes of vaccines.
Editorial Material
Immunology
Abu Salim Mustafa
Summary: Efforts towards developing new vaccines against TB mainly focus on using Mycobacterium tuberculosis antigens as subunit vaccines, requiring appropriate adjuvants and delivery systems to induce immune responses. Additionally, studies have examined the pathogenesis of BCG in children and explored the potential use of BCG as a vaccine against asthma, alongside different adjuvants and delivery systems in inducing protective immune responses after immunization with subunit vaccines.
Review
Biochemical Research Methods
Karthik Nagarajan, Congjian Ni, Ting Lu
Summary: This review provides a comprehensive overview of recent advances in agent-based modeling of microbial communities, including algorithms for simulating intracellular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments, as well as applications of agent-based modeling. It also discusses challenges and potential mitigation strategies.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Coral Fung Shek, Pavlos Kotidis, Michael Betenbaugh
Summary: Modulation of glycosylation is crucial in the development of therapeutic proteins, as different glycan moieties can significantly affect efficacy and safety. Computational tools, including mechanistic models and data-driven models, are used to understand and quantify the impact of glycosylation on therapeutic proteins. These tools help researchers gain insights into the glycosylation pathway and identify process levers for glycosylation.
CURRENT OPINION IN CHEMICAL ENGINEERING
(2021)
Article
Engineering, Biomedical
Birkan Tunc, David A. Hormuth, George Biros, Thomas E. Yankeelov
Summary: This study evaluated the performance of three mathematical models of tumor growth using MRI data from a murine model of glioma. The RDM model most accurately predicts tumor growth, while the RDAM model demonstrates the least variation in estimates of diffusion coefficient and proliferation rate. The mathematical models successfully capture tumor development and mass effect observed in experiments.
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Zhihui Liang, Xin Wang, Ge Yu, Min Li, Shuting Shi, Hang Bao, Chen Chen, Duo Fu, Wei Ma, Changying Xue, Bingbing Sun
Summary: The aspect ratio of AlOOH nanorods plays a critical role in modulating adjuvanticity by affecting cellular uptake, dendritic cell activation, and antigen trafficking. Nanorods with higher aspect ratio elicit more potent immune responses.
Review
Chemistry, Physical
Aihua Qu, Maozhong Sun, Liguang Xu, Liqiang Liu, Lingling Guo, Panpan Chen, Qing Wang, Zhiyong Du, Zhimeng Wu, Chuanlai Xu, Hua Kuang
Summary: Chiral nanomaterials play a crucial role in the field of vaccines by promoting antigen presentation and activating the immune system for tumor immunotherapy. However, there are still challenges in this research, such as finding better synthesis methods and addressing the issue of immune system regulation.
Article
Medicine, General & Internal
Rebecca A. Clark, Chathika K. Weerasuriya, Allison Portnoy, Christinah Mukandavire, Matthew Quaife, Roel Bakker, Danny Scarponi, Rebecca C. Harris, Kirankumar Rade, Sanjay Kumar Mattoo, Dheeraj Tumu, Nicolas A. Menzies, Richard G. White
Summary: The potential health and economic impact of M72/AS01(E) and BCG-revaccination in India were evaluated. The results showed that M72/AS01(E) vaccine could prevent more tuberculosis cases and deaths compared to BCG-revaccination, and almost all scenarios were cost-effective. However, there is uncertainty regarding the vaccine characteristics that requires further investment.
Article
Oncology
Stephen Joseph McMahon, Kevin M. Prise
Summary: Variations in intrinsic radiosensitivity of different cells to ionizing radiation play a significant role in response to radiotherapy. The Medras model provides a mechanistic framework to model different radiation responses and predict individual responses, by simulating repair of radiation-induced DNA damage and predicting a range of biological endpoints. Validation of the model against various exposure types, including different radiation qualities and dose-rates, supports its potential in informing mechanistic predictions of radiation sensitivity and supporting developments in treatment personalization.
FRONTIERS IN ONCOLOGY
(2021)
Article
Geriatrics & Gerontology
Emerson Santiago, David F. Moreno, Murat Acar
Summary: Aging is a complex phenomenon of functional decay in biological organisms, with the cause(s) still poorly understood. Computational biology offers a unique opportunity to generate models that can help us understand the fundamental nature of aging, identify unaccounted aging factors, and demonstrate the mechanics of aging.
EXPERIMENTAL GERONTOLOGY
(2021)
Article
Microbiology
Alex J. Metcalf, Nanette R. Boyle
Summary: In this study, the researchers developed a transient metabolic model for diurnal growth of algae that can predict phenotype from genotype. This model allows evaluation of the impact of genetic and environmental changes on growth, biomass composition, and intracellular fluxes.
Article
Infectious Diseases
Arnaud G. L'Huillier, Benjamin Meyer, Diego O. Andrey, Isabelle Arm-Vernez, Stephanie Baggio, Arnaud Didierlaurent, Christiane S. Eberhardt, Isabella Eckerle, Carole Grasset-Salomon, Angela Huttner, Klara M. Posfay-Barbe, Irene Sabater Royo, Jacques A. Pralong, Nicolas Vuilleumier, Sabine Yerly, Claire-Anne Siegrist, Laurent Kaiser
Summary: This study evaluated the persistence of antibodies against SARS-CoV-2 in hospital employees with mild COVID-19, finding that neutralizing antibodies were detectable in almost all participants at 6 months post infection. Anti-RBD antibodies showed better persistence and even increased over time, possibly due to the detection of progressively higher-affinity antibodies.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Immunology
Cedric Bosteels, Kaat Fierens, Sofie De Prijck, Justine Van Moorleghem, Manon Vanheerswynghels, Caroline De Wolf, Aurelie Chalon, Catherine Collignon, Hamida Hammad, Arnaud M. Didierlaurent, Bart N. Lambrecht
Summary: The AS01 adjuvant system containing MPL and QS-21 in liposomal formulation is crucial for the recruitment and activation of dendritic cells, particularly cDC2s and inf-cDC2s, which play a significant role in priming antigen-specific T cell responses post-vaccination. Depletion of these DC subsets results in the abrogation of adaptive immune responses, highlighting their importance in the adjuvant activity of AS01.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Infectious Diseases
Pauline Vetter, Samuel Cordey, Manuel Schibler, Laure Vieux, Lena Despres, Florian Laubscher, Diego O. Andrey, Romain Martischang, Stephan Harbarth, Clemence Cuvelier, Meriem Bekliz, Isabella Eckerle, Claire-Anne Siegrist, Arnaud M. Didierlaurent, Christiane S. Eberhardt, Benjamin Meyer, Laurent Kaiser
Summary: This study reported a case of SARS-CoV-2 reinfection in a young healthy female physician 6 months after the first infection, both resulting in mild COVID-19. Whole-genome sequencing confirmed the reinfection. Neutralizing antibodies quickly declined after the first infection but were boosted rapidly after symptom onset in the reinfection, indicating cellular memory responses elicited by the first infection.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Review
Immunology
Flor M. Munoz, Jakob P. Cramer, Cornelia L. Dekker, Matthew Z. Dudley, Barney S. Graham, Marc Gurwith, Barbara Law, Stanley Perlman, Fernando P. Polack, Jonathan M. Spergel, Eva Van Braeckel, Brian J. Ward, Arnaud M. Didierlaurent, Paul Henri Lambert
Summary: This is a case definition developed by a group of experts convened by CEPI to assess adverse events following immunization. It follows the case definition format of the Brighton Collaboration and defines levels of certainty after an exhaustive literature review and expert consultation.
Article
Cell Biology
Maria Vono, Angela Huttner, Sylvain Lemeille, Paola Martinez-Murillo, Benjamin Meyer, Stephanie Baggio, Shilpee Sharma, Anais Thiriard, Arnaud Marchant, Gert-Jan Godeke, Chantal Reusken, Catia Alvarez, Francisco Perez-Rodriguez, Isabella Eckerle, Laurent Kaiser, Natasha Loevy, Christiane S. Eberhardt, Geraldine Blanchard-Rohner, Claire-Anne Siegrist, Arnaud M. Didierlaurent
Summary: Compared to adults, children with mild SARS-CoV-2 infection display less severe symptoms despite similar initial viral load and show a faster resolution of antiviral response, with more transient activation of monocytes and dendritic cells and earlier appearance of genes associated with B cell activation.
Article
Immunology
Sonia Budroni, Francesca Buricchi, Andrea Cavallone, Patricia Bourguignon, Magalie Caubet, Vincent Dewar, Ugo D'Oro, Oretta Finco, Nathalie Garcon, Mohamed El Idrissi, Michel Janssens, Geert Leroux-Roels, Arnaud Marchant, Tino Schwarz, Pierre Van Damme, Gianfranco Volpini, Robbert van der Most, Arnaud M. Didierlaurent, Wivine Burny
Summary: Differences in innate immune 'imprinting' between vaccine adjuvants may mediate dissimilar effects on the quantity and quality of persisting adaptive responses. Specific combinations of immunoenhancers in the adjuvant systems increase antibody persistence and avidity maturation. Different adjuvants have varied effects on the duration and maturity of adaptive immune responses.
Review
Immunology
Derek T. O'Hagan, Robbert van der Most, Rushit N. Lodaya, Margherita Coccia, Giuseppe Lofano
Summary: Emulsion adjuvants like MF59 and AS03 have been widely used in vaccines for over 20 years, showing effectiveness, safety, and ease of manufacturing. They allow for antigen dose sparing, rapid immune responses, and enhanced quality and quantity of adaptive immune responses. These adjuvants induce distinct immunological responses, including a mixed T cell response, long-lived plasma cells, and high titers of cross-neutralizing antibodies.
Article
Immunology
Wivine Burny, Caroline Herve, Magalie Caubet, Juan Pablo Yarzabal, Arnaud M. Didierlaurent
Summary: Plasma cytokines are useful indicators of the inflammatory response to vaccination, and urinary cytokine levels may serve as potential biomarkers. However, the study found limited correlation between urinary cytokines and the reactogenicity or immunogenicity of the AS01(B)-adjuvanted vaccine, except for IP-10 which showed some association with systemic reactogenicity. Further research is needed to substantiate the utility of urinary IP-10 as a complementary biomarker.
Article
Clinical Neurology
Natacha Madelon, Nelli Heikkila, Irene Sabater Royo, Paola Fontannaz, Gautier Breville, Kim Lauper, Rachel Goldstein, Alba Grifoni, Alessandro Sette, Claire-Anne Siegrist, Axel Finckh, Patrice H. Lalive, Arnaud M. Didierlaurent, Christiane S. Eberhardt
Summary: This study aimed to investigate T-cell responses to the Omicron spike protein in patients with multiple sclerosis (MS) treated with anti-CD20 therapy before and after a third mRNA COVID-19 vaccination. The results showed that the third dose enhanced T-cell responses to all variants, suggesting that COVID-19 vaccination may protect patients taking B-cell-depleting drugs against severe complications from infection.
Article
Immunology
Benjamin Meyer, Paola Andrea Martinez-Murillo, Barbara Lemaitre, Geraldine Blanchard-Rohner, Arnaud M. Didierlaurent, Paola Fontannaz, Chloe Eugercios Manzanas, Paul-Henri Lambert, Natasha Loevy, Laurent Kaiser, Julie Sartoretti, Chantal Tougne, Jean Villard, Angela Huttner, Claire-Anne Siegrist, Christiane S. Eberhardt
Summary: In mild COVID-19 cases, stable levels of SARS-CoV-2 specific memory B cells and neutralizing antibodies against current variants of concern can be observed up to one year post infection. Care should be taken when predicting neutralizing titers using commercial assays that measure binding antibodies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Meriem Bekliz, Kenneth Adea, Pauline Vetter, Christiane S. Eberhardt, Krisztina Hosszu-Fellous, Diem-Lan Vu, Olha Puhach, Manel Essaidi-Laziosi, Sophie Waldvogel-Abramowski, Caroline Stephan, Arnaud G. L'Huillier, Claire-Anne Siegrist, Arnaud M. Didierlaurent, Laurent Kaiser, Benjamin Meyer, Isabella Eckerle
Summary: Emerging SARS-CoV-2 variants pose concerns about protective immunity, as convalescent sera from individuals infected with different variants show reduced neutralization against Omicron-BA.1. However, vaccine-breakthrough infections with Omicron-BA.1 or Delta lead to robust neutralization against both variants. Understanding the antigenic relationship between variants is crucial due to the complexity of population immunity resulting from prior infections and vaccinations.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Margherita Coccia, Wivine Burny, Marie-Ange Demoitie, Paul Gillard, Robert A. van den Berg, Robbert van der Most
Summary: Transcriptional responses to adjuvanted vaccines can vary among populations due to individual differences in pathogen exposure and immunological memory. This study found that individuals with higher cell-mediated memory responses to TB had stronger transcriptional responses to the AS01-adjuvanted vaccine. However, after a second vaccination, the heterogeneity in responses decreased and became similar across all groups.
Correction
Immunology
Derek T. O'Hagan, Robbert van der Most, Rushit N. Lodaya, Margherita Coccia, Giuseppe Lofano
Article
Immunology
Carolin Loos, Margherita Coccia, Arnaud M. M. Didierlaurent, Ahmed Essaghir, Jonathan K. K. Fallon, Douglas Lauffenburger, Corinne Luedemann, Ashlin Michell, Robbert van der Most, Alex Lee Zhu, Galit Alter, Wivine Burny
Summary: The mechanisms by which antibodies confer protection vary across vaccines. Adjuvants play a role in shaping the maturation of antibody-effector functions. Different adjuvants induce different responses and have different effects on immunoglobulin titers or Fc-effector functions. Selective vaccine formulation using adjuvants with different immunological properties may direct antigen-specific antibody functions.
Article
Infectious Diseases
Serge Grazioli, Fedora Tavaglione, Giulia Torriani, Noemie Wagner, Marie Rohr, Arnaud G. L'Huillier, Charlotte Leclercq, Anne Perrin, Alice Bordessoule, Maurice Beghetti, Jana Pachlopnik Schmid, Stefano Vavassori, Matthieu Perreau, Christiane Eberhardt, Arnaud Didierlaurent, Laurent Kaiser, Isabella Eckerle, Pascale Roux-Lombard, Geraldine Blanchard-Rohner
Summary: This study reported 4 pediatric patients with MIS-C related to COVID-19, showing a postinfectious inflammatory syndrome with elevation in all cytokines, and markers of recent T-cell activation. While some features overlap with HLH, the patients in this study exhibited different perforin expression and NK cell degranulation compared to primary HLH cases.
JOURNAL OF THE PEDIATRIC INFECTIOUS DISEASES SOCIETY
(2021)