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Abstract Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus. 

The Elliott Wave principle is a time-honored, oft-used method for predicting variations in the financial markets. It is based on the notion that human emotions drive financial decisions. In the fight against the COVID-19 global pandemic, human emotions are similarly decisive, for instance in that they determine one’s willingness to be vaccinated, and/or to follow preventive measures including the personal wearing of masks, the application of social distancing protocols, and frequent handwashing. On this basis, we postulated that the Elliott Wave Principle may similarly be used to predict the future evolution of the COVID-19 pandemic. We demonstrated that this method reproduces the data pattern for various countries and the world (daily new cases). Potential scenarios were then extrapolated, from the best-case corresponding to a rapid, full vaccination of the population, to the utterly disastrous case of slow vaccination, and poor adherence to preventive protocols.

 

Pancreatic Ductal Adenocarcinoma (PDAC) is regarded as one of the most lethal cancer typesfor its challenges associated with early diagnosis and resistance to standard chemotherapeutic agents,thereby leading to a poor five-year survival rate. The complexity of the disease calls for a multidisciplinaryapproach to better manage the disease and improve the status quo in PDAC diagnosis, prognosis,and treatment. To this end, the application of quantitative tools can help improve the understanding ofdisease mechanisms, develop biomarkers for early diagnosis, and design patient-specific treatment strategiesto improve therapeutic outcomes. However, such approaches have only been minimally applied towardsthe investigation of PDAC, and we review the current status of mathematical modeling works inthis field. 

It is challenging to design effective drug delivery systems (DDS) that target metastatic breast cancers (MBC) because of lack of competent imaging and image analysis protocols that suitably capture the interactions between DDS and metastatic lesions. Here, we integrate high temporal resolution of in vivo whole-body PET-CT, ex vivo whole-organ optical imaging, high spatial resolution of confocal microscopy, and mathematical modeling, to systematically deconstruct the trafficking of injectable nanoparticle generators encapsulated with polymeric doxorubicin (iNPG-pDox) in pulmonary MBC. iNPG-pDox accumulated substantially in metastatic lungs, compared to healthy lungs. Intratumoral distribution and retention of iNPG-pDox varied with lesion size, possibly induced by locally remodeled microenvironment. We further used multiscale imaging and mathematical simulations to provide improved drug delivery strategies for MBC. Our work presents a multidisciplinary translational toolbox to evaluate transport and interactions of DDS within metastases. This knowledge can be recursively applied to rationally design advanced therapies for metastatic cancers. 

We present a mechanistic mathematical model of immune checkpoint inhibitor therapy to address the oncological need for early, broadly applicable readouts (biomarkers) of patient response to immunotherapy. The model is built upon the complex biological and physical interactions between the immune system and cancer, and is informed using only standard-of-care CT. We have retrospectively applied the model to 245 patients from multiple clinical trials treated with anti–CTLA-4 or anti–PD-1/PD-L1 antibodies. We found that model parameters distinctly identified patients with common ( n = 18) and rare ( n = 10) malignancy types who benefited and did not benefit from these monotherapies with accuracy as high as 88% at first restaging (median 53 days). Further, the parameters successfully differentiated pseudo-progression from true progression, providing previously unidentified insights into the unique biophysical characteristics of pseudo-progression. Our mathematical model offers a clinically relevant tool for personalized oncology and for engineering immunotherapy regimens. 

Ductal carcinoma in situ (DCIS) is commonly treated clinically through surgical resection. Although surgical options exist for resection, it is unclear which is optimal to reduce the likelihood of future invasive disease. This is further complicated by challenges in determining correct surgical margins from disease diagnostics, with mammographic imaging misidentifying surgical margins by as much as 2 cm vs. histological examination. We have implemented a threedimensional, hybrid multiscale model of DCIS to study disease initiation and progression. In order to shed new light on current biological questions and clinical challenges surrounding the disease, we present here an improved version of this model, with more biologically relevant molecular signaling pathways, cell phenotype hierarchies, and duct architecture variation. In particular, a cell necrosis, lysis and calcification pathway has been incorporated into the model to help better understand the relationship between diagnostic imaging and the true extent of disease invasion. We observe that deficiencies in availability of molecular signaling molecules that upregulate cell proliferation may be overcome by dynamic shifts in phenotypic distributions within the disease mass. Hypoxia, necrosis, and calcification together functioned as a hypoxia relief mechanism, and were observed to maintain a consistent distance between the DCIS leading edge and the site of necrosis onset, providing insights for improving surgical margins.