Publications by authors named "Alexander Anderson"

162 Publications

Mechanism of peptidoglycan -acetyltransferase A as an -acyltransferase.

Proc Natl Acad Sci U S A 2021 Sep;118(36)

Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;

The O-acetylation of exopolysaccharides, including the essential bacterial cell wall polymer peptidoglycan, confers resistance to their lysis by exogenous hydrolases. Like the enzymes catalyzing the O-acetylation of exopolysaccharides in the Golgi of animals and fungi, peptidoglycan -acetyltransferase A (OatA) is predicted to be an integral membrane protein comprised of a membrane-spanning acyltransferase-3 (AT-3) domain and an extracytoplasmic domain; for OatA, these domains are located in the N- and C-terminal regions of the enzyme, respectively. The recombinant C-terminal domain (OatA) has been characterized as an SGNH acetyltransferase, but nothing was known about the function of the N-terminal AT-3 domain (OatA) or its homologs associated with other acyltransferases. We report herein the experimental determination of the topology of OatA, which differs markedly from that predicted in silico. We present the biochemical characterization of OatA as part of recombinant OatA and demonstrate that acetyl-CoA serves as the substrate for OatA Using in situ and in vitro assays, we characterized 35 engineered OatA variants which identified a catalytic triad of Tyr-His-Glu residues. We trapped an acetyl group from acetyl-CoA on the catalytic Tyr residue that is located on an extracytoplasmic loop of OatA Further enzymatic characterization revealed that -acetyl-Tyr represents the substrate for OatA We propose a model for OatA action involving the translocation of acetyl groups from acetyl-CoA across the cytoplasmic membrane by OatA and their subsequent intramolecular transfer to OatA for the O-acetylation of peptidoglycan via the concerted action of catalytic Tyr and Ser residues.
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http://dx.doi.org/10.1073/pnas.2103602118DOI Listing
September 2021

Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques.

Proc Natl Acad Sci U S A 2021 09;118(38)

US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910.

Emergence of novel variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for next-generation vaccines able to elicit broad and durable immunity. Here we report the evaluation of a ferritin nanoparticle vaccine displaying the receptor-binding domain of the SARS-CoV-2 spike protein (RFN) adjuvanted with Army Liposomal Formulation QS-21 (ALFQ). RFN vaccination of macaques using a two-dose regimen resulted in robust, predominantly Th1 CD4+ T cell responses and reciprocal peak mean serum neutralizing antibody titers of 14,000 to 21,000. Rapid control of viral replication was achieved in the upper and lower airways of animals after high-dose SARS-CoV-2 respiratory challenge, with undetectable replication within 4 d in seven of eight animals receiving 50 µg of RFN. Cross-neutralization activity against SARS-CoV-2 variant B.1.351 decreased only approximately twofold relative to WA1/2020. In addition, neutralizing, effector antibody and cellular responses targeted the heterotypic SARS-CoV-1, highlighting the broad immunogenicity of RFN-ALFQ for SARS-CoV-like Sarbecovirus vaccine development.
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http://dx.doi.org/10.1073/pnas.2106433118DOI Listing
September 2021

The role of memory in non-genetic inheritance and its impact on cancer treatment resistance.

PLoS Comput Biol 2021 Aug 30;17(8):e1009348. Epub 2021 Aug 30.

Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida, United States of America.

Intra-tumour heterogeneity is a leading cause of treatment failure and disease progression in cancer. While genetic mutations have long been accepted as a primary mechanism of generating this heterogeneity, the role of phenotypic plasticity is becoming increasingly apparent as a driver of intra-tumour heterogeneity. Consequently, understanding the role of this plasticity in treatment resistance and failure is a key component of improving cancer therapy. We develop a mathematical model of stochastic phenotype switching that tracks the evolution of drug-sensitive and drug-tolerant subpopulations to clarify the role of phenotype switching on population growth rates and tumour persistence. By including cytotoxic therapy in the model, we show that, depending on the strategy of the drug-tolerant subpopulation, stochastic phenotype switching can lead to either transient or permanent drug resistance. We study the role of phenotypic heterogeneity in a drug-resistant, genetically homogeneous population of non-small cell lung cancer cells to derive a rational treatment schedule that drives population extinction and avoids competitive release of the drug-tolerant sub-population. This model-informed therapeutic schedule results in increased treatment efficacy when compared against periodic therapy, and, most importantly, sustained tumour decay without the development of resistance.
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http://dx.doi.org/10.1371/journal.pcbi.1009348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8432806PMC
August 2021

Super-resolution microscopy reveals the arrangement of inner membrane protein complexes in mammalian mitochondria.

J Cell Sci 2021 07 13;134(13). Epub 2021 Jul 13.

Department of Biochemistry and Pharmacology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.

The mitochondrial inner membrane is a protein-rich environment containing large multimeric complexes, including complexes of the mitochondrial electron transport chain, mitochondrial translocases and quality control machineries. Although the inner membrane is highly proteinaceous, with 40-60% of all mitochondrial proteins localised to this compartment, little is known about the spatial distribution and organisation of complexes in this environment. We set out to survey the arrangement of inner membrane complexes using stochastic optical reconstruction microscopy (STORM). We reveal that subunits of the TIM23 complex, TIM23 and TIM44 (also known as TIMM23 and TIMM44, respectively), and the complex IV subunit COXIV, form organised clusters and show properties distinct from the outer membrane protein TOM20 (also known as TOMM20). Density based cluster analysis indicated a bimodal distribution of TIM44 that is distinct from TIM23, suggesting distinct TIM23 subcomplexes. COXIV is arranged in larger clusters that are disrupted upon disruption of complex IV assembly. Thus, STORM super-resolution microscopy is a powerful tool for examining the nanoscale distribution of mitochondrial inner membrane complexes, providing a 'visual' approach for obtaining pivotal information on how mitochondrial complexes exist in a cellular context.
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http://dx.doi.org/10.1242/jcs.252197DOI Listing
July 2021

The orthopaedic waiting list crisis : two sides of the story.

Bone Jt Open 2021 Jul;2(7):530-534

Rotherham District General Hospital, Rotherham NHS Foundation Trust, Rotherham, UK.

Aims: Due to widespread cancellations in elective orthopaedic procedures, the number of patients on waiting list for surgery is rising. We aim to determine and quantify if disparities exist between inpatient and day-case orthopaedic waiting list numbers; we also aim to determine if there is a 'hidden burden' that already exists due to reductions in elective secondary care referrals.

Methods: Retrospective data were collected between 1 April 2020 and 31 December 2020 and compared with the same nine-month period the previous year. Data collected included surgeries performed (day-case vs inpatient), number of patients currently on the orthopaedic waiting list (day-case vs inpatient), and number of new patient referrals from primary care and therapy services.

Results: There was a 52.8% reduction in our elective surgical workload in 2020. The majority of surgeries performed in 2020 were day case surgeries (739; 86.6%) with 47.2% of these performed in the independent sector on a 'lift and shift' service. The total number of patients on our waiting lists has risen by 30.1% in just 12 months. As we have been restricted in performing inpatient surgery, the inpatient waiting lists have risen by 73.2%, compared to a 1.6% rise in our day-case waiting list. New patient referral from primary care and therapy services have reduced from 3,357 in 2019 to 1,722 in 2020 (49.7% reduction).

Conclusion: This study further exposes the increasing number of patients on orthopaedic waiting lists. We observed disparities between inpatient and day-case waiting lists, with dramatic increases in the number of inpatients on the waiting lists. The number of new patient referrals has decreased, and we predict an influx of referrals as the pandemic eases, further adding to the pressure on inpatient waiting lists. Robust planning and allocation of adequate resources is essential to deal with this backlog. Cite this article:  2021;2(7):530-534.
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http://dx.doi.org/10.1302/2633-1462.27.BJO-2021-0044.R1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8325974PMC
July 2021

Conserved Influenza Hemagglutinin, Neuraminidase and Matrix Peptides Adjuvanted with ALFQ Induce Broadly Neutralizing Antibodies.

Vaccines (Basel) 2021 Jun 25;9(7). Epub 2021 Jun 25.

Longhorn Vaccines and Diagnostics, Gaithersburg, MD 20878, USA.

A universal influenza candidate vaccine that targets multiple conserved influenza virus epitopes from hemagglutinin (HA), neuraminidase (NA) and matrix (M2e) proteins was combined with the potent Army liposomal adjuvant (ALFQ) to promote induction of broad immunity to seasonal and pandemic influenza strains. The unconjugated and CRM-conjugated composite peptides formulated with ALFQ were highly immunogenic and induced both humoral and cellular immune responses in mice. Broadly reactive serum antibodies were induced across various IgG isotypes. Mice immunized with the unconjugated composite peptide developed antibody responses earlier than mice immunized with conjugated peptides, and the IgG antibodies were broadly reactive and neutralizing across Groups 1 and 2 influenza viruses. Multi-epitope unconjugated influenza composite peptides formulated with ALFQ provide a novel strategy for the development of a universal influenza vaccine. These synthetic peptide vaccines avoid the pitfalls of egg-produced influenza vaccines and production can be scaled up rapidly and economically.
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http://dx.doi.org/10.3390/vaccines9070698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310080PMC
June 2021

A SARS-CoV-2 spike ferritin nanoparticle vaccine protects against heterologous challenge with B.1.1.7 and B.1.351 virus variants in Syrian golden hamsters.

bioRxiv 2021 Jun 16. Epub 2021 Jun 16.

The emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the B.1.1.7 and B.1.351 VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 μg) or low (0.2 μg) immunogen dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose two vaccinations. SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.
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http://dx.doi.org/10.1101/2021.06.16.448525DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8219092PMC
June 2021

SARS-CoV-2 ferritin nanoparticle vaccines elicit broad SARS coronavirus immunogenicity.

bioRxiv 2021 May 10. Epub 2021 May 10.

The need for SARS-CoV-2 next-generation vaccines has been highlighted by the rise of variants of concern (VoC) and the long-term threat of other coronaviruses. Here, we designed and characterized four categories of engineered nanoparticle immunogens that recapitulate the structural and antigenic properties of prefusion Spike (S), S1 and RBD. These immunogens induced robust S-binding, ACE2-inhibition, and authentic and pseudovirus neutralizing antibodies against SARS-CoV-2 in mice. A Spike-ferritin nanoparticle (SpFN) vaccine elicited neutralizing titers more than 20-fold higher than convalescent donor serum, following a single immunization, while RBD-Ferritin nanoparticle (RFN) immunogens elicited similar responses after two immunizations. Passive transfer of IgG purified from SpFN- or RFN-immunized mice protected K18-hACE2 transgenic mice from a lethal SARS-CoV-2 virus challenge. Furthermore, SpFN- and RFN-immunization elicited ACE2 blocking activity and neutralizing ID50 antibody titers >2,000 against SARS-CoV-1, along with high magnitude neutralizing titers against major VoC. These results provide design strategies for pan-coronavirus vaccine development.

Highlights: Iterative structure-based design of four Spike-domain Ferritin nanoparticle classes of immunogensSpFN-ALFQ and RFN-ALFQ immunization elicits potent neutralizing activity against SARS-CoV-2, variants of concern, and SARS-CoV-1Passively transferred IgG from immunized C57BL/6 mice protects K18-hACE2 mice from lethal SARS-CoV-2 challenge.
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http://dx.doi.org/10.1101/2021.05.09.443331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8132231PMC
May 2021

Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques.

bioRxiv 2021 Apr 10. Epub 2021 Apr 10.

Emergence of novel variants of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) underscores the need for next-generation vaccines able to elicit broad and durable immunity. Here we report the evaluation of a ferritin nanoparticle vaccine displaying the receptor-binding domain of the SARS-CoV-2 spike protein (RFN) adjuvanted with Army Liposomal Formulation QS-21 (ALFQ). RFN vaccination of macaques using a two-dose regimen resulted in robust, predominantly Th1 CD4+ T cell responses and reciprocal peak mean neutralizing antibody titers of 14,000-21,000. Rapid control of viral replication was achieved in the upper and lower airways of animals after high-dose SARS-CoV-2 respiratory challenge, with undetectable replication within four days in 7 of 8 animals receiving 50 µg RFN. Cross-neutralization activity against SARS-CoV-2 variant B.1.351 decreased only ∼2-fold relative to USA-WA1. In addition, neutralizing, effector antibody and cellular responses targeted the heterotypic SARS-CoV-1, highlighting the broad immunogenicity of RFN-ALFQ for SARS-like betacoronavirus vaccine development.

Significance Statement: The emergence of SARS-CoV-2 variants of concern (VOC) that reduce the efficacy of current COVID-19 vaccines is a major threat to pandemic control. We evaluate a SARS-CoV-2 Spike receptor-binding domain ferritin nanoparticle protein vaccine (RFN) in a nonhuman primate challenge model that addresses the need for a next-generation, efficacious vaccine with increased pan-SARS breadth of coverage. RFN, adjuvanted with a liposomal-QS21 formulation (ALFQ), elicits humoral and cellular immune responses exceeding those of current vaccines in terms of breadth and potency and protects against high-dose respiratory tract challenge. Neutralization activity against the B.1.351 VOC within two-fold of wild-type virus and against SARS-CoV-1 indicate exceptional breadth. Our results support consideration of RFN for SARS-like betacoronavirus vaccine development.
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http://dx.doi.org/10.1101/2021.04.09.439166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043445PMC
April 2021

Normal tissue architecture determines the evolutionary course of cancer.

Nat Commun 2021 04 6;12(1):2060. Epub 2021 Apr 6.

Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.

Cancer growth can be described as a caricature of the renewal process of the tissue of origin, where the tissue architecture has a strong influence on the evolutionary dynamics within the tumor. Using a classic, well-studied model of tumor evolution (a passenger-driver mutation model) we systematically alter spatial constraints and cell mixing rates to show how tissue structure influences functional (driver) mutations and genetic heterogeneity over time. This approach explores a key mechanism behind both inter-patient and intratumoral tumor heterogeneity: competition for space. Time-varying competition leads to an emergent transition from Darwinian premalignant growth to subsequent invasive neutral tumor growth. Initial spatial constraints determine the emergent mode of evolution (Darwinian to neutral) without a change in cell-specific mutation rate or fitness effects. Driver acquisition during the Darwinian precancerous stage may be modulated en route to neutral evolution by the combination of two factors: spatial constraints and limited cellular mixing. These two factors occur naturally in ductal carcinomas, where the branching topology of the ductal network dictates spatial constraints and mixing rates.
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http://dx.doi.org/10.1038/s41467-021-22123-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8024392PMC
April 2021

Design of Alphavirus Virus-Like Particles Presenting Circumsporozoite Junctional Epitopes That Elicit Protection against Malaria.

Vaccines (Basel) 2021 Mar 18;9(3). Epub 2021 Mar 18.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

The most advanced malaria vaccine, RTS,S, includes the central repeat and C-terminal domains of the circumsporozoite protein (PfCSP). We have recently isolated human antibodies that target the junctional region between the N-terminal and repeat domains that are not included in RTS,S. Due to the fact that these antibodies protect against malaria challenge in mice, their epitopes could be effective vaccine targets. Here, we developed immunogens displaying PfCSP junctional epitopes by genetic fusion to either the N-terminus or B domain loop of the E2 protein from chikungunya (CHIK) alphavirus and produced CHIK virus-like particles (CHIK-VLPs). The structural integrity of these junctional-epitope-CHIK-VLP immunogens was confirmed by negative-stain electron microscopy. Immunization of these CHIK-VLP immunogens reduced parasite liver load by up to 95% in a mouse model of malaria infection and elicited better protection than when displayed on keyhole limpet hemocyanin, a commonly used immunogenic carrier. Protection correlated with PfCSP serum titer. Of note, different junctional sequences elicited qualitatively different reactivities to overlapping PfCSP peptides. Overall, these results show that the junctional epitopes of PfCSP can induce protective responses when displayed on CHIK-VLP immunogens and provide a basis for the development of a next generation malaria vaccine to expand the breadth of anti-PfCSP immunity.
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http://dx.doi.org/10.3390/vaccines9030272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003078PMC
March 2021

Efficacy of a Broadly Neutralizing SARS-CoV-2 Ferritin Nanoparticle Vaccine in Nonhuman Primates.

bioRxiv 2021 Mar 25. Epub 2021 Mar 25.

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants stresses the continued need for next-generation vaccines that confer broad protection against coronavirus disease 2019 (COVID-19). We developed and evaluated an adjuvanted SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine in nonhuman primates (NHPs). High-dose (50 g) SpFN vaccine, given twice within a 28 day interval, induced a Th1-biased CD4 T cell helper response and a peak neutralizing antibody geometric mean titer of 52,773 against wild-type virus, with activity against SARS-CoV-1 and minimal decrement against variants of concern. Vaccinated animals mounted an anamnestic response upon high-dose SARS-CoV-2 respiratory challenge that translated into rapid elimination of replicating virus in their upper and lower airways and lung parenchyma. SpFN's potent and broad immunogenicity profile and resulting efficacy in NHPs supports its utility as a candidate platform for SARS-like betacoronaviruses.

One-sentence Summary: A SARS-CoV-2 Spike protein ferritin nanoparticle vaccine, co-formulated with a liposomal adjuvant, elicits broad neutralizing antibody responses that exceed those observed for other major vaccines and rapidly protects against respiratory infection and disease in the upper and lower airways and lung tissue of nonhuman primates.
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http://dx.doi.org/10.1101/2021.03.24.436523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010721PMC
March 2021

Observation of the rotational Doppler shift with spatially incoherent light.

Opt Express 2021 Feb;29(3):4058-4066

The rotational Doppler shift (RDS) is typically measured by illuminating a rotating target with a laser prepared in a simple, known orbital angular momentum (OAM) superposition. We establish theoretically and experimentally that detecting the rotational Doppler shift does not require the incident light to have a well-defined OAM spectrum but instead requires well-defined correlations within the OAM spectrum. We demonstrate measurement of the rotational Doppler shift using spatially incoherent light.
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http://dx.doi.org/10.1364/OE.415580DOI Listing
February 2021

Adaptive Therapy for Metastatic Melanoma: Predictions from Patient Calibrated Mathematical Models.

Cancers (Basel) 2021 Feb 16;13(4). Epub 2021 Feb 16.

Integrated Mathematical Oncology, H. Lee Moffitt Cancer and Research Institute, Tampa, FL 33612, USA.

Adaptive therapy is an evolution-based treatment approach that aims to maintain tumor volume by employing minimum effective drug doses or timed drug holidays. For successful adaptive therapy outcomes, it is critical to find the optimal timing of treatment switch points in a patient-specific manner. Here we develop a combination of mathematical models that examine interactions between drug-sensitive and resistant cells to facilitate melanoma adaptive therapy dosing and switch time points. The first model assumes genetically fixed drug-sensitive and -resistant popul tions that compete for limited resources. The second model considers phenotypic switching between drug-sensitive and -resistant cells. We calibrated each model to fit melanoma patient biomarker changes over time and predicted patient-specific adaptive therapy schedules. Overall, the models predict that adaptive therapy would have delayed time to progression by 6-25 months compared to continuous therapy with dose rates of 6-74% relative to continuous therapy. We identified predictive factors driving the clinical time gained by adaptive therapy, such as the number of initial sensitive cells, competitive effect, switching rate from resistant to sensitive cells, and sensitive cell growth rate. This study highlights that there is a range of potential patient-specific benefits of adaptive therapy and identifies parameters that modulate this benefit.
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http://dx.doi.org/10.3390/cancers13040823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7920057PMC
February 2021

IgA transcytosis and antigen recognition govern ovarian cancer immunity.

Nature 2021 Mar 3;591(7850):464-470. Epub 2021 Feb 3.

Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.

Most ovarian cancers are infiltrated by prognostically relevant activated T cells, yet exhibit low response rates to immune checkpoint inhibitors. Memory B cell and plasma cell infiltrates have previously been associated with better outcomes in ovarian cancer, but the nature and functional relevance of these responses are controversial. Here, using 3 independent cohorts that in total comprise 534 patients with high-grade serous ovarian cancer, we show that robust, protective humoral responses are dominated by the production of polyclonal IgA, which binds to polymeric IgA receptors that are universally expressed on ovarian cancer cells. Notably, tumour B-cell-derived IgA redirects myeloid cells against extracellular oncogenic drivers, which causes tumour cell death. In addition, IgA transcytosis through malignant epithelial cells elicits transcriptional changes that antagonize the RAS pathway and sensitize tumour cells to cytolytic killing by T cells, which also contributes to hindering malignant progression. Thus, tumour-antigen-specific and -antigen-independent IgA responses antagonize the growth of ovarian cancer by governing coordinated tumour cell, T cell and B cell responses. These findings provide a platform for identifying targets that are spontaneously recognized by intratumoural B-cell-derived antibodies, and suggest that immunotherapies that augment B cell responses may be more effective than approaches that focus on T cells, particularly for malignancies that are resistant to checkpoint inhibitors.
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http://dx.doi.org/10.1038/s41586-020-03144-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7969354PMC
March 2021

The harsh microenvironment in early breast cancer selects for a Warburg phenotype.

Proc Natl Acad Sci U S A 2021 01;118(3)

Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL 33612;

The harsh microenvironment of ductal carcinoma in situ (DCIS) exerts strong evolutionary selection pressures on cancer cells. We hypothesize that the poor metabolic conditions near the ductal center foment the emergence of a Warburg Effect (WE) phenotype, wherein cells rapidly ferment glucose to lactic acid, even in normoxia. To test this hypothesis, we subjected low-glycolytic breast cancer cells to different microenvironmental selection pressures using combinations of hypoxia, acidosis, low glucose, and starvation for many months and isolated single clones for metabolic and transcriptomic profiling. The two harshest conditions selected for constitutively expressed WE phenotypes. RNA sequencing analysis of WE clones identified the transcription factor KLF4 as potential inducer of the WE phenotype. In stained DCIS samples, KLF4 expression was enriched in the area with the harshest microenvironmental conditions. We simulated in vivo DCIS phenotypic evolution using a mathematical model calibrated from the in vitro results. The WE phenotype emerged in the poor metabolic conditions near the necrotic core. We propose that harsh microenvironments within DCIS select for a WE phenotype through constitutive transcriptional reprogramming, thus conferring a survival advantage and facilitating further growth and invasion.
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http://dx.doi.org/10.1073/pnas.2011342118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826394PMC
January 2021

O-acetylation controls the glycosylation of bacterial serine-rich repeat glycoproteins.

J Biol Chem 2021 Jan-Jun;296:100249. Epub 2021 Jan 9.

Department of Medicine, Division of Infectious Diseases, San Francisco Veteran Affairs Medical Center, and the Department of Medicine, University of California, San Francisco, California, USA. Electronic address:

The serine-rich repeat (SRR) glycoproteins of gram-positive bacteria are a family of adhesins that bind to a wide range of host ligands, and expression of SRR glycoproteins is linked with enhanced bacterial virulence. The biogenesis of these surface glycoproteins involves their intracellular glycosylation and export via the accessory Sec system. Although all accessory Sec components are required for SRR glycoprotein export, Asp2 of Streptococcus gordonii also functions as an O-acetyltransferase that modifies GlcNAc residues on the SRR adhesin gordonii surface protein B (GspB). Because these GlcNAc residues can also be modified by the glycosyltransferases Nss and Gly, it has been unclear whether the post-translational modification of GspB is coordinated. We now report that acetylation modulates the glycosylation of exported GspB. Loss of O-acetylation due to aps2 mutagenesis led to the export of GspB glycoforms with increased glucosylation of the GlcNAc moieties. Linkage analysis of the GspB glycan revealed that both O-acetylation and glucosylation occurred at the same C6 position on GlcNAc residues and that O-acetylation prevented Glc deposition. Whereas streptococci expressing nonacetylated GspB with increased glucosylation were significantly reduced in their ability to bind human platelets in vitro, deletion of the glycosyltransferases nss and gly in the asp2 mutant restored platelet binding to WT levels. These findings demonstrate that GlcNAc O-acetylation controls GspB glycosylation, such that binding via this adhesin is optimized. Moreover, because O-acetylation has comparable effects on the glycosylation of other SRR adhesins, acetylation may represent a conserved regulatory mechanism for the post-translational modification of the SRR glycoprotein family.
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http://dx.doi.org/10.1074/jbc.RA120.016116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7948813PMC
August 2021

IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations.

Bioinformatics 2020 Dec 16. Epub 2020 Dec 16.

Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, 33612, Florida.

 : Evolutionary game theory describes frequency-dependent selection for fixed, heritable strategies in a population of competing individuals using a payoff matrix. We present a software package to aid in the construction, analysis, and visualization of three-strategy matrix games. The IsoMaTrix package computes the isoclines (lines of zero growth) of matrix games, and facilitates direct comparison of well-mixed dynamics to structured populations on a lattice grid. IsoMaTrix computes fixed points, phase flow, trajectories, (sub)velocities, and uncertainty quantification for stochastic effects in spatial matrix games. We describe a result obtained via IsoMaTrix's spatial games functionality, which shows that the timing of competitive release in a cancer model (under continuous treatment) critically depends on the initial spatial configuration of the tumor.

Availability: The code is available at: https://github.com/mathonco/isomatrix.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa1025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016459PMC
December 2020

Mitochondrial protein import dysfunction: mitochondrial disease, neurodegenerative disease and cancer.

FEBS Lett 2021 04 28;595(8):1107-1131. Epub 2021 Jan 28.

Department of Biochemistry and Molecular Biology and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia.

The majority of proteins localised to mitochondria are encoded by the nuclear genome, with approximately 1500 proteins imported into mammalian mitochondria. Dysfunction in this fundamental cellular process is linked to a variety of pathologies including neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancer, demonstrating the importance of mitochondrial protein import machinery for cellular function. Correct import of proteins into mitochondria requires the co-ordinated activity of multimeric protein translocation and sorting machineries located in both the outer and inner mitochondrial membranes, directing the imported proteins to the destined mitochondrial compartment. This dynamic process maintains cellular homeostasis, and its dysregulation significantly affects cellular signalling pathways and metabolism. This review summarises current knowledge of the mammalian mitochondrial import machinery and the pathological consequences of mutation of its components. In addition, we will discuss the role of mitochondrial import in cancer, and our current understanding of the role of mitochondrial import in neurodegenerative diseases including Alzheimer's disease, Huntington's disease and Parkinson's disease.
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http://dx.doi.org/10.1002/1873-3468.14022DOI Listing
April 2021

Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ.

PLoS One 2020 2;15(12):e0242686. Epub 2020 Dec 2.

Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada.

Biofilms are community structures of bacteria enmeshed in a self-produced matrix of exopolysaccharides. The biofilm matrix serves numerous roles, including resilience and persistence, making biofilms a subject of research interest among persistent clinical pathogens of global health importance. Our current understanding of the underlying biochemical pathways responsible for biosynthesis of these exopolysaccharides is largely limited to Gram-negative bacteria. Clostridia are a class of Gram-positive, anaerobic and spore-forming bacteria and include the important human pathogens Clostridium perfringens, Clostridium botulinum and Clostridioides difficile, among numerous others. Several species of Clostridia have been reported to produce a biofilm matrix that contains an acetylated glucan linked to a series of hypothetical genes. Here, we propose a model for the function of these hypothetical genes, which, using homology modelling, we show plausibly encode a synthase complex responsible for polymerization, modification and export of an O-acetylated cellulose exopolysaccharide. Specifically, the cellulose synthase is homologous to that of the known exopolysaccharide synthases in Gram-negative bacteria. The remaining proteins represent a mosaic of evolutionary lineages that differ from the described Gram-negative cellulose exopolysaccharide synthases, but their predicted functions satisfy all criteria required for a functional cellulose synthase operon. Accordingly, we named these hypothetical genes ccsZABHI, for the Clostridial cellulose synthase (Ccs), in keeping with naming conventions for exopolysaccharide synthase subunits and to distinguish it from the Gram-negative Bcs locus with which it shares only a single one-to-one ortholog. To test our model and assess the identity of the exopolysaccharide, we subcloned the putative glycoside hydrolase encoded by ccsZ and solved the X-ray crystal structure of both apo- and product-bound CcsZ, which belongs to glycoside hydrolase family 5 (GH-5). Although not homologous to the Gram-negative cellulose synthase, which instead encodes the structurally distinct BcsZ belonging to GH-8, we show CcsZ displays specificity for cellulosic materials. This specificity of the synthase-associated glycosyl hydrolase validates our proposal that these hypothetical genes are responsible for biosynthesis of a cellulose exopolysaccharide. The data we present here allowed us to propose a model for Clostridial cellulose synthesis and serves as an entry point to an understanding of cellulose biofilm formation among class Clostridia.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0242686PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710045PMC
January 2021

Comparative study between discrete and continuum models for the evolution of competing phenotype-structured cell populations in dynamical environments.

Phys Rev E 2020 Oct;102(4-1):042404

Department of Mathematical Sciences "G. L. Lagrange", Dipartimento di Eccellenza 2018-2022, Politecnico di Torino, Italy.

Deterministic continuum models formulated as nonlocal partial differential equations for the evolutionary dynamics of populations structured by phenotypic traits have been used recently to address open questions concerning the adaptation of asexual species to periodically fluctuating environmental conditions. These models are usually defined on the basis of population-scale phenomenological assumptions and cannot capture adaptive phenomena that are driven by stochastic variability in the evolutionary paths of single individuals. In light of these considerations, in this paper we develop a stochastic individual-based model for the coevolution of two competing phenotype-structured cell populations that are exposed to time-varying nutrient levels and undergo spontaneous, heritable phenotypic changes with different probabilities. Here, the evolution of every cell is described by a set of rules that result in a discrete-time branching random walk on the space of phenotypic states, and nutrient levels are governed by a difference equation in which a sink term models nutrient consumption by the cells. We formally show that the deterministic continuum counterpart of this model comprises a system of nonlocal partial differential equations for the cell population density functions coupled with an ordinary differential equation for the nutrient concentration. We compare the individual-based model and its continuum analog, focusing on scenarios whereby the predictions of the two models differ. The results obtained clarify the conditions under which significant differences between the two models can emerge due to bottleneck effects that bring about both lower regularity of the density functions of the two populations and more pronounced demographic stochasticity. In particular, bottleneck effects emerge in the presence of lower probabilities of phenotypic variation and are more apparent when the two populations are characterized by lower fitness initial mean phenotypes and smaller initial levels of phenotypic heterogeneity. The emergence of these effects, and thus the agreement between the two modeling approaches, is also dependent on the initial proportions of the two populations. As an illustrative example, we demonstrate the implications of these results in the context of the mathematical modeling of the early stage of metastatic colonization of distant organs.
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http://dx.doi.org/10.1103/PhysRevE.102.042404DOI Listing
October 2020

Turnover Modulates the Need for a Cost of Resistance in Adaptive Therapy.

Cancer Res 2021 02 10;81(4):1135-1147. Epub 2020 Nov 10.

Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida.

Adaptive therapy seeks to exploit intratumoral competition to avoid, or at least delay, the emergence of therapy resistance in cancer. Motivated by promising results in prostate cancer, there is growing interest in extending this approach to other neoplasms. As such, it is urgent to understand the characteristics of a cancer that determine whether or not it will respond well to adaptive therapy. A plausible candidate for such a selection criterion is the fitness cost of resistance. In this article, we study a general, but simple, mathematical model to investigate whether the presence of a cost is necessary for adaptive therapy to extend the time to progression beyond that of a standard-of-care continuous therapy. Tumor cells were divided into sensitive and resistant populations and we model their competition using a system of two ordinary differential equations based on the Lotka-Volterra model. For tumors close to their environmental carrying capacity, a cost was not required. However, for tumors growing far from carrying capacity, a cost may be required to see meaningful gains. Notably, it is important to consider cell turnover in the tumor, and we discuss its role in modulating the impact of a resistance cost. To conclude, we present evidence for the predicted cost-turnover interplay in data from 67 patients with prostate cancer undergoing intermittent androgen deprivation therapy. Our work helps to clarify under which circumstances adaptive therapy may be beneficial and suggests that turnover may play an unexpectedly important role in the decision-making process. SIGNIFICANCE: Tumor cell turnover modulates the speed of selection against drug resistance by amplifying the effects of competition and resistance costs; as such, turnover is an important factor in resistance management via adaptive therapy..
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http://dx.doi.org/10.1158/0008-5472.CAN-20-0806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8455086PMC
February 2021

Education and Outreach in Physical Sciences in Oncology.

Trends Cancer 2021 01 7;7(1):3-9. Epub 2020 Nov 7.

Department of Biochemistry and Molecular Biology, Mayo Clinic, Jacksonville, FL, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Jacksonville, FL, USA; Department of Transplantation, Mayo Clinic, Jacksonville, FL, USA; Center for Immunotherapeutic Transport Oncophysics, Houston Methodist Research Institute, Houston, TX, USA. Electronic address:

Physical sciences are often overlooked in the field of cancer research. The Physical Sciences in Oncology Initiative was launched to integrate physics, mathematics, chemistry, and engineering with cancer research and clinical oncology through education, outreach, and collaboration. Here, we provide a framework for education and outreach in emerging transdisciplinary fields.
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http://dx.doi.org/10.1016/j.trecan.2020.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7895467PMC
January 2021

Centering a beam of light to the axis of rotation of a planar object.

Rev Sci Instrum 2020 Oct;91(10):105101

Department of Mechanical Engineering, University of Colorado, 427 UCB, 1111 Engineering Drive, Boulder, Colorado 80309, USA.

We detail an experimentally simple approach for centering a beam of light to the axis of a rotating surface. This technique can be understood as a rotating analog to knife-edge profilometry, a common experimental technique wherein the intensity (or power) of various masked portions of a beam is used to ascertain the transverse intensity profile of the beam. Instead of collecting the light transmitted through a mask, we give the surface a variable reflectivity (such as with a strip of retro-reflective tape) and sample the light scattered from the surface as it rotates. We co-align the transverse position (not the tilt) of the axis of rotation and the beam centroid by minimizing the modulation amplitude of this scattered light. In a controlled experiment, we compare the centroid found using this approach to the centroid found using the canonical knife-edge approach in two directions. We find our results to be accurate to within the uncertainty of the benchmark measurement, ±0.03 mm (±2.9% of the beam waist). Using simulations that mimic the experiments, we estimate that the uncertainty of the technique is much smaller than that of the benchmark measurement, ±0.01 mm (±1% of the beam waist), limited here by the size of the components used in these experiments. We expect this centering technique to find applications in experimental and industrial fabrication and processing settings where alignment involving rotating surfaces is critical.
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http://dx.doi.org/10.1063/5.0010160DOI Listing
October 2020

Sex differences in health and disease: A review of biological sex differences relevant to cancer with a spotlight on glioma.

Cancer Lett 2021 02 29;498:178-187. Epub 2020 Oct 29.

Mathematical NeuroOncology Laboratory, Precision Neurotherapeutics Innovation Program, Mayo Clinic, Phoenix, AZ, USA; Department of Neurological Surgery, Mayo Clinic, Phoenix, AZ, USA; School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA. Electronic address:

The influence of biological sex differences on human health and disease, while being increasingly recognized, has long been underappreciated and underexplored. While humans of all sexes are more alike than different, there is evidence for sex differences in the most basic aspects of human biology and these differences have consequences for the etiology and pathophysiology of many diseases. In a disease like cancer, these consequences manifest in the sex biases in incidence and outcome of many cancer types. The ability to deliver precise, targeted therapies to complex cancer cases is limited by our current understanding of the underlying sex differences. Gaining a better understanding of the implications and interplay of sex differences in diseases like cancer will thus be informative for clinical practice and biological research. Here we review the evidence for a broad array of biological sex differences in humans and discuss how these differences may relate to observed sex differences in various diseases, including many cancers and specifically glioblastoma. We focus on areas of human biology that play vital roles in healthy and disease states, including metabolism, development, hormones, and the immune system, and emphasize that the intersection of sex differences in these areas should not go overlooked. We further propose that mathematical approaches can be useful for exploring the extent to which sex differences affect disease outcomes and accounting for those in the development of therapeutic strategies.
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http://dx.doi.org/10.1016/j.canlet.2020.07.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8409250PMC
February 2021

Searching for Goldilocks: How Evolution and Ecology Can Help Uncover More Effective Patient-Specific Chemotherapies.

Cancer Res 2020 12 15;80(23):5147-5154. Epub 2020 Sep 15.

Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.

Deaths from cancer are mostly due to metastatic disease that becomes resistant to therapy. A mainstay treatment for many cancers is chemotherapy, for which the dosing strategy is primarily limited by patient toxicity. While this MTD approach builds upon the intuitively appealing principle that maximum therapeutic benefit is achieved by killing the largest possible number of cancer cells, there is increasing evidence that moderation might allow host-specific features to contribute to success. We believe that a "Goldilocks Window" of submaximal chemotherapy will yield improved overall outcomes. This window combines the complex interplay of cancer cell death, immune activity, emergence of chemoresistance, and metastatic dissemination. These multiple activities driven by chemotherapy have tradeoffs that depend on the specific agents used as well as their dosing levels and schedule. Here we present evidence supporting the idea that MTD may not always be the best approach and offer suggestions toward a more personalized treatment regime that integrates insights into patient-specific eco-evolutionary dynamics.
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http://dx.doi.org/10.1158/0008-5472.CAN-19-3981DOI Listing
December 2020

Evolutionary dynamics of neoantigens in growing tumors.

Nat Genet 2020 10 14;52(10):1057-1066. Epub 2020 Sep 14.

Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.

Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of neoantigens in a growing cancer by constructing a mathematical model of neoantigen evolution. The model predicts that, without immune escape, tumor neoantigens are either clonal or at low frequency; hypermutated tumors can only establish after the evolution of immune escape. Moreover, the site frequency spectrum of somatic variants under negative selection appears more neutral as the strength of negative selection increases, which is consistent with classical neutral theory. These predictions are corroborated by the analysis of neoantigen frequencies and immune escape in exome and RNA sequencing data from 879 colon, stomach and endometrial cancers.
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http://dx.doi.org/10.1038/s41588-020-0687-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610467PMC
October 2020

Histoecology: Applying Ecological Principles and Approaches to Describe and Predict Tumor Ecosystem Dynamics Across Space and Time.

Cancer Control 2020 Jul-Aug;27(3):1073274820946804

Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.

Cancer cells exist within a complex spatially structured ecosystem composed of resources and different cell types. As the selective pressures imposed by this environment determine the fate of cancer cells, an improved understanding of how this ecosystem evolves will better elucidate how tumors grow and respond to therapy. State of the art imaging methods can now provide highly resolved descriptions of the microenvironment, yielding the data required for a thorough study of its role in tumor growth and treatment resistance. The field of landscape ecology has been studying such species-environment relationship for decades, and offers many tools and perspectives that cancer researchers could greatly benefit from. Here, we discuss one such tool, species distribution modeling (SDM), that has the potential to, among other things, identify critical environmental factors that drive tumor evolution and predict response to therapy. SDMs only scratch the surface of how ecological theory and methods can be applied to cancer, and we believe further integration will take cancer research in exciting new and productive directions. Here we describe how species distribution modeling can be used to quantitatively describe the complex relationship between tumor cells and their microenvironment. Such a description facilitates a deeper understanding of cancers eco-evolutionary dynamics, which in turn sheds light on the factors that drive tumor growth and response to treatment.
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http://dx.doi.org/10.1177/1073274820946804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710396PMC
April 2021

High-acuity vision from retinal image motion.

J Vis 2020 07;20(7):34

School of Optometry, Helen Wills Neuroscience Institute, and Redwood Center for Theoretical Neuroscience, University of California, Berkeley, Berkeley, CA, USA.

A mathematical model and a possible neural mechanism are proposed to account for how fixational drift motion in the retina confers a benefit for the discrimination of high-acuity targets. We show that by simultaneously estimating object shape and eye motion, neurons in visual cortex can compute a higher quality representation of an object by averaging out non-uniformities in the retinal sampling lattice. The model proposes that this is accomplished by two separate populations of cortical neurons - one providing a representation of object shape and another representing eye position or motion - which are coupled through specific multiplicative connections. Combined with recent experimental findings, our model suggests that the visual system may utilize principles not unlike those used in computational imaging for achieving "super-resolution" via camera motion.
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http://dx.doi.org/10.1167/jov.20.7.34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424138PMC
July 2020

Biophysical characterization of polydisperse liposomal adjuvant formulations.

Biochem Biophys Res Commun 2020 08 1;529(2):362-365. Epub 2020 Jul 1.

U.S. Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD, 20817, USA. Electronic address:

Army Liposome Formulations (ALF) are potent adjuvants, of which there are two primary forms, lyophilized ALF (ALFlyo) containing monophosphoryl lipid A (MPLA) and ALF containing MPLA and QS21 (ALFQ). ALFlyo and ALFQ adjuvants are essential constituents of candidate vaccines for bacterial, viral, and parasitic diseases. They have been widely used in preclinical immunogenicity studies in small animals and non-human primates and are progressing to phase I/IIa clinical trials. ALFQ was prepared by adding saponin QS21 to small unilamellar liposome vesicles (SUVs) of ALF55 that contain 55 mol% cholesterol, whereas ALFlyo was created by reconstituting lyophilized SUVs of ALF43, consisting of 43 mol% cholesterol, in aqueous buffer solution. These formulations display heterogenous particle size distribution. Since biophysical characteristics of liposomes may impact their adjuvant potential, we characterized the particle size distribution and lamellarity of the individual liposome particles in ALFlyo and ALFQ formulations using cryo-electron microscopy and a newly developed MANTA technology. ALFlyo and ALFQ exhibited similar particle size distributions with liposomes ranging from 50 nm to several μm. However, fundamental differences were observed in the lamellar structures of the liposomes. ALFlyo displayed a greater number of multilamellar and multivesicular liposome particles, as compared to that in ALFQ, which was predominately unilamellar.
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http://dx.doi.org/10.1016/j.bbrc.2020.05.156DOI Listing
August 2020
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