Biology subjects

Duncan, G.

Publications and source records attributed to Duncan, G..

24 records · Page 2Linked to original sources

bioRxiv2022

A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus

Non-coding RNAs (ncRNAs) play important roles in host-pathogen interactions; oncogenic viruses like Kaposi sarcoma herpesvirus (KSHV) employ ncRNAs to establish a latent reservoir and persist for the life of the host. We previously reported that KSHV infection alters a novel class of RNA, circular RNAs (circRNAs). CircRNAs are alternative splicing isoforms and regulate gene expression but, their importance in infection is largely unknown. Here, we showed that a human circRNA, hsa_circ_0001400, is induced by various pathogenic viruses, namely KSHV, Epstein-Barr virus, and human cytomegalovirus. The induction of circRNAs including circ_0001400 by KSHV is co-transcriptionally regulated, likely at splicing. Consistently, screening for circ_0001400-interacting proteins identified a splicing factor, PNISR. Functional studies using infected primary endothelial cells revealed that circ_0001400 inhibits KSHV lytic transcription and virus production. Simultaneously, the circRNA promoted cell cycle, inhibited apoptosis, and induced immune genes. RNA-pulldown assays identified transcripts interacting with circ_0001400, including TTI1, which is a component of the pro-growth mTOR complexes. We thus identified a circRNA that is pro-growth and anti-lytic replication. These results support a model in which KSHV induces circ_0001400 expression to maintain latency. Since circ_0001400 is induced by multiple viruses, this novel viral strategy may be widely employed by other viruses. AUTHOR SUMMARYCircular RNAs (circRNAs) are single-stranded, closed-circular RNAs. They coincide with linear mRNAs as alternative splice isoforms. CircRNAs binds to other RNAs or proteins to regulate their abundance or functions. We previously showed that specific human circRNAs are differentials regulated upon infection with an oncogenic DNA virus, Kaposis sarcoma herpesvirus (KSHV). Functions of such circRNAs for virus infections were largely elusive. Here, we identified that one of circRNAs, hsa_circ_0001400 controls both viral and human gene expression so that infected human cells have less virus production but better cell growth. KSHV, like other herpesviruses, has two phases: latent and lytic cycle. The functions of circ_0001400 suggest it biases the cells to latent cycle during which, unlike lytic phase, viruses express only limited number of genes to survive and new viruses are not produced. Since oncogenic viruses like KSHV mainly stay at latent phase for the life of the host, our results suggest that the virus utilized circRNAs to switch to latent phase after the infection. Infection of other pathogenic viruses like Epstein-Barr virus and human cytomegalovirus were also found to induce circ_0001400. The circRNA may be thus controlling infection of various viruses.

microbiology↗

bioRxiv2022

Machine Learning Informed Predictions of Nanoparticle Mobility and Fate in the Mucus Barrier

Diffusion and transport of nanomaterials through mucus, is of critical importance to many basic and applied areas of research such as drug delivery and infectious disease. However, it is often challenging to interpret the dynamics of nanoparticles within the mucus gel due to its inherently heterogeneous microstructure and biochemistry. In this study, we measured the diffusion of densely PEGylated nanoparticles (NP) in human airway mucus ex vivo using multiple particle tracking and utilized machine learning to classify NP movement as either traditional Brownian motion (BM) or one of two different models of anomalous diffusion, fractional Brownian motion (FBM) and continuous time random walk (CTRW). Specifically, we employed a physics-based neural network model to predict the modes of diffusion experienced by individual NP in human airway mucus. We observed rapidly diffusing NP primarily exhibit BM whereas CTRW and FBM exhibited lower diffusion rates. Given the use of muco-inert nanoparticles, the observed transition from diffusive (BM) to sub-diffusive (CTRW/FBM) motion is likely a result of patient-to-patient variation in mucus network pore size. Using mathematic models that account for the mode of NP diffusion, we predicted the percentage of nanoparticles that would cross the mucus barrier over time in human airway mucus with varied total solids concentration. We also applied this approach to explore the transport modes and predicted fate of influenza A virus within human mucus. These results provide new tools to evaluate the extent of synthetic and viral nanoparticle penetration through mucus in the lung and other tissues.

bioengineering↗

bioRxiv2021

Natal and adult dispersal among four elephant seal colonies

Dispersal plays a key role fostering recovery of endangered species because reoccupying a former range can only happen via dispersal. The northern elephant seal (Mirounga angustirostris) is a large, marine predator that was nearly exterminated in the 19th century by over-hunting. Once they were afforded protection from harvest, the species spread from a single remnant colony to reoccupy its former range. As colonies in central California were reestablished during the 1960s-1990s, tagged seals documented northward dispersal from southern California. The central California colonies are now large and well-established, and tagging programs at the four northernmost colonies allowed us to quantify the extent and direction of dispersal. Natal dispersal by females was highest from the southernmost colony at Piedras Blancas, where 61% of surviving females emigrated to breed. Dispersal from the other three colonies was much lower, 5.6% from SE Farallon Island, 10.3% from Ano Nuevo, and 16.6% from Point Reyes. Adult dispersal of females, after breeding, was rare, with an annual rate < 2%. Juvenile dispersal is thus frequent in elephant seals, highest northward but also occurring southward, suggesting that continued expansion to new colonies throughout the west coast is probable.

ecology↗

bioRxiv2020

Influenza A virus diffusion through mucus gel networks

In this study, influenza A virus (IAV) and nanoparticle diffusion in human airway mucus was quantified using fluorescent video microscopy and multiple particle tracking. In previous work, it was determined that mucin-associated sialic acid acts as a decoy receptor for IAV hemagglutinin binding, and that virus passage through the mucus gel layer is facilitated through the sialic-acid cleaving enzyme, neuraminidase (NA), also present on the IAV envelope. However, our data suggests the mobility of IAV in mucus is significantly influenced by the mesh structure of the gel, as measured by nanoparticle probes, and NA activity is not required to facilitate virus passage through mucus gels. Using newly developed analyses, the binding affinity of IAV to the 3D mucus meshwork was estimated for individual virions with dissociation constants in the mM range, indicative of weak and reversible IAV-mucus interactions. We also found IAV diffusion significantly increased in mucus when treated with a mucolytic agent to break mucin-mucin disulfide bonds. In addition, IAV diffusion was significantly limited in a synthetic mucus model as crosslink density was systematically increased and network pore size was reduced. The results of this work provide important insights on how the balance of adhesive and physical barrier properties of mucus influence the dissemination of IAV within the lung microenvironment.

biophysics↗

bioRxiv2019

Disulfide disruption reverses mucus dysfunction in allergic airway disease

Airway mucus is essential for healthy lung defense1, but excessive mucus in asthma obstructs airflow, leading to severe and potentially fatal outcomes2-5. Current asthma therapies reduce allergic inflammation and relax airway smooth muscle, but treatments are often inadequate due to their minimal effects on mucus obstruction6,7. The lack of efficacious mucus-targeted treatments stems from a poor understanding of healthy mucus function and pathological mucus dysfunction at a molecular level. The chief macromolecules in mucus, polymeric mucins, are massive glycoproteins whose sizes and biophysical properties are dictated in part by covalent disulfide bonds that link mucin molecules into assemblies of 10 or more subunits8. Once secreted, mucin glycopolymers can aggregate to form plugs that block airflow. Here we show that reducing mucin disulfide bonds depolymerizes mucus in human asthma and reverses pathological effects of mucus hypersecretion in a mouse allergic asthma model. In mice challenged with a fungal allergen, inhaled mucolytic treatment acutely loosened mucus mesh, enhanced mucociliary clearance (MCC), and abolished airway hyperreactivity (AHR) to the bronchoprovocative agent methacholine. AHR reversal was directly related to reduced mucus plugging. Furthermore, protection in mucolytic treated mice was identical to prevention observed in mice lacking Muc5ac, the polymeric mucin required for allergic AHR in murine models9. These findings establish grounds for developing novel fast-acting agents to treat mucus hypersecretion in asthma10,11. Efficacious mucolytic therapies could be used to directly improve airflow, help resolve inflammation, and enhance the effects of inhaled treatments for asthma and other respiratory conditions11,12.

physiology↗

bioRxiv2019

Designing viscoelastic mucin-based hydrogels

We report the design of a mucin hydrogel created using a thiol-based cross-linking strategy. By using a cross-linking reagent capable of forming disulfide linkages between mucins, the mucin-based hydrogels possess viscoelastic properties comparable to native mucus as measured by bulk rheology. We confirmed disulfide cross-links mediate gel formation in our system using chemical treatments to block and reduce cysteines where we found mucin hydrogel network formation was inhibited and disrupted, respectively. Particle tracking microrheology was used to investigate the kinetics and evolution of microstructure and viscoelasticity within the hydrogel as it formed. We found that the rate of gel formation could be tuned by varying the mucin to crosslinker ratio, producing network pore sizes in the range measured previously in human mucus. The results of this work provide a new, simple method for creating mucin hydrogels with physiologically relevant properties using readily available reagents.

bioengineering↗