Biology subjects

Avery, L.

Publications and source records attributed to Avery, L..

5 recordsLinked to original sources

bioRxiv2026

pH-dependent anti-TfR1 NANOBODY(R) molecules deliver efficacious oligonucleotide payloads to muscle and CNS tissues

The blood-brain barrier (BBB) is a highly selective, semi-permeable border of endothelial cells that prevents solutes and therapeutic agents in systemic circulation from passively crossing into the central nervous system (CNS) parenchyma. The Transferrin receptor 1 (TfR1) endocytosis pathway for iron homeostasis is one of the most well-characterized strategies for therapeutic delivery across the BBB. The work presented here showcases the discovery of novel anti-TfR1 NANOBODY(R) shuttles. The identified anti-TfR1 NANOBODY(R) molecules display cross-reactivity and pH-dependent binding to human, cynomolgus (cyno), and mouse TfR1. Structural data further explain and support the underlying mechanism of this pH-dependent binding. These anti-TfR1 NANOBODY(R) molecules were successfully conjugated to both short-interfering RNA (siRNA) and antisense oligonucleotide (ASO) tool payloads. anti-TfR1 NANOBODY(R)-siRNA conjugates can induce up to 60% knockdown of the target mRNA transcript in skeletal muscle up to two weeks post a single IV dose in mice and up to 35-40% at four weeks post dose. Furthermore, extending the half-life of the anti-TfR1 NANOBODY(R)-ASO shuttles enhances heart, sciatic nerve, and brain exposure and enables up to 30-60% target knockdown in different CNS cell types. Altogether, these results highlight important features for the development of anti-TfR1 shuttles for the purpose of downregulating target mRNA transcripts in muscle and CNS for a variety of neurologic and neuromuscular indications.

neuroscience↗

bioRxiv2024

Enhancing reproducibility and decentralization in single cell research with biocytometry

Biomedicine today is experiencing a shift towards decentralized data collection, which promises enhanced reproducibility and collaboration across diverse laboratory environments. This inter-laboratory study evaluates the performance of biocytometry, a method utilizing engineered bioparticles for enumerating cells based on their surface antigen patterns. In a decentralized framework, spanning 78 assays conducted by 30 users across 12 distinct laboratories, biocytometry consistently demonstrated significant statistical power in discriminating numbers of target cells at varying concentrations as low as 1 cell per 100,000 background cells. User skill levels varied from expert to beginner capturing a range of proficiencies. Measurement was performed in a decentralized environment without any instrument cross-calibration or advanced user training outside of a basic instruction manual. The results affirm biocytometry to be a viable solution for immunophenotyping applications demanding sensitivity as well as scalability and reproducibility and paves the way for decentralized analysis of rare cells in heterogeneous samples.

cell biology↗

bioRxiv2021

A Keller-Segel model for C elegans L1 aggregation

We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh-2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh-2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type. Author summaryAmong the most complex of animal behaviors are collective behaviors, in which animals interact with each other so as to produce large-scale organization. Starved first-stage larvae of the nematode Caenorhabditis elegans exhibit such a behavior: they come together to form aggregates of several hundred worms. How and why they do this are unknown. To address these questions, we developed a mathematical model of starved L1 aggregation. This model reproduced the main features of the behavior.

animal behavior and cognition↗

bioRxiv2019

Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species

A quantitative understanding of organism-level behavior requires predictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the motile behavior of nematodes at the level of their translational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioral repertoire by measuring motile trajectories of the canonical lab strain C. elegans N2 as well as wild strains and distant species. We focus on trajectory dynamics over timescales spanning the transition from ballistic (straight) to diffusive (random) movement and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bearing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioral control and a trade-off between exploration and exploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies considerably across strains, suggesting that these nematode lineages employ contrasting \"bet-hedging\" strategies for foraging.

biophysics↗

bioRxiv2017

Tim-3 co-stimulation promotes short-term effector T cells, restricts memory precursors and is dispensable for T cell exhaustion

Tim-3 is highly expressed on a subset of T cells during T cell exhaustion, in settings of chronic viral infection and tumors (1, 2). Using LCMV Clone-13, a model for chronic infection, we have found that Tim-3 is neither necessary nor sufficient for the development of T cell exhaustion. Nonetheless, expression of Tim-3 was sufficient to drive resistance to PD-L1 blockade therapy during chronic infection. Strikingly, expression of Tim-3 promoted development of short-term effector T cells, at the expense of memory precursor development, after acute LCMV infection. These effects were accompanied by increased Akt/mTOR signaling in T cells expressing endogenous or ectopic Tim-3. Conversely, Akt/mTOR signaling was reduced in effector T cells from Tim-3 deficient mice. Thus, Tim-3 is essential for optimal effector T cell responses, but may also contribute to exhaustion, by restricting development of long-lived memory T cells, including PD-1int \"stem-like\" exhausted T cells that expand during PD-1 pathway blockade. Taken together, our results suggest that Tim-3 is actually more similar to co-stimulatory receptors that are upregulated after T cell activation, rather than a dominant inhibitory protein like PD-1. These findings have significant implications for the development of anti-Tim-3 antibodies as therapeutic agents.\n\nSignificanceDuring a chronic viral infection, prolonged exposure to viral antigens leads to dysfunction or \"exhaustion\" of T cells specific to the virus, a condition also observed in T cells that infiltrate tumors. The exhausted state is associated with expression of specific cell-surface proteins, some of which may inhibit T cell activation. Expression of Tim-3 is associated with acquisition of T cell exhaustion, although it is also expressed transiently during acute infection. Here we provide evidence that a major function of Tim-3 is to enhance T cell activation, during either acute or chronic viral infection. However, Tim-3 is not required for development of exhaustion. Thus, we propose that Tim-3 would be better described as a stimulatory, rather than inhibitory, protein.

immunology↗