Biology subjects

Harrison, L.

Publications and source records attributed to Harrison, L..

8 recordsLinked to original sources

bioRxiv2026

Allosteric capsid inhibitors and their escape mutants drive HIV-1 sensing

Small-molecule capsid inhibitors suppress HIV-1 infectivity by binding to capsid at the same site as FG motif-bearing host cofactors Sec24C, NUP153, CPSF6 and disordered nucleoporins residing in the nuclear pore complex central channel. We have used rational design to develop inhibitors called "allosteres" that target this pocket and inhibit HIV-1 infectivity. X-ray crystal structures of capsid/inhibitor complexes, reveal allosteric shifts upon inhibitor binding in the capsid C-terminal domain which impact the capsid lattice three-fold symmetry axis. Consistent with an uncoating mechanism, we find that allosteres cause HIV-1 to trigger innate immune response dependent on viral DNA and DNA sensor cGAS. Allosteres exhibit a similar loss of potency against clinically induced Lenacapavir resistance mutants but, strikingly, we find that HIV-1 bearing key resistance mutations induces innate immune activation in the absence of inhibitor. We hypothesise that resistant mutant sensitivity to cGAS contributes to reduction of HIV-1 transmission during Lenacapavir use in prophylaxis. Our work expands the physicochemical space and scaffold range for HIV capsid targeting inhibitors, provides mechanistic details of inhibition and facilitates improved inhibitor design.

microbiology↗

bioRxiv2026

Validation of tissue-specific RNAi systems in C. elegans reveals a converging role for polyubiquitin UBQ-1/UBC in vitellogenin metabolism and lifespan

Numerous studies in C. elegans have taken advantage of gene silencing RNAi libraries and tissue-specific RNAi systems to temporally and spatially understand gene function. Tissue-specific RNAi strains were created via tissue-specific functional expression of a key gene in the RNAi system in a presumably RNAi insensitive correspondingly mutated background. Here, we tested the level of RNAi insensitivity across different commonly used RNAi-defective mutants (rde-1 and sid-1) using lifespan analyses. Remarkably, while we found similarly important lifespan shortening in wild-type animals by silencing the polyubiquitin gene ubq-1 (UBC) at both 20{degrees}C and 25{degrees}C, we found wide and temperature-sensitive variations in RNAi sensitivity across different rde-1 and sid-1 strains from substantial sensitivity to complete insensitivity. This riveting finding warrants a re-evaluation of the tissue-specific interpretations in numerous tissue-specific RNAi studies in C. elegans. Using validated tissue-specific RNAi systems, we determined that proteasomal burden largely differs between the germline and the soma. Notably, gonadally accumulating vitellogenin proteins substantially contributed to the total polyubiquitinated proteins observed during aging. Interestingly, we found that UBQ-1 was essential to maintain the transcription of highly expressed genes, including vitellogenins, supporting a broad and key role for polyubiquitin beyond proteostasis. Altogether, we authenticated commonly used tissue-specific RNAi systems and uncovered a new approach to improve RNAi insensitivity in RNAi-defective strains. With validated tissue-specific RNAi strains, we spatially analyzed proteasomal function and age-related polyubiquitinated protein accumulation and revealed a converging regulatory link between UBQ-1, vitellogenin metabolism and lifespan in C. elegans.

genetics↗

bioRxiv2026

Lysosomal abundance in young and aged mouse hearts assessed by In Vivo Imaging Systems (IVIS) Lysotracker imaging and autophagy-related gene expression

Lysosomal function is essential for cardiac proteostasis and cellular health, yet its regulation during ageing remains poorly defined. We hypothesised that ageing alters both the abundance of acidic organelles and the machinery supporting their acidification. Using fluorescence-based In Vivo Imaging Systems (IVIS) with Lysotracker Red in young (2-4 months) and aged (18 months) mouse hearts, we quantified whole-heart acidic-vesicle signals and assessed expression of lysosomal and autophagy-related genes (Lamp2, Atp6v1a, Sqstm1, Cd63, Atg12, Nfe2l2, M6pr) by RT-qPCR. Whole-heart labelled Lysotracker fluorescence did not differ significantly between age groups, indicating preservation of the total acidic-vesicle pool. No changes in Atp6v1a and Lamp2 expression suggest acidification capacity and structural stability are maintained, whereas the minor, upregulation of Sqstm1 might indicate increased autophagic demand and altered vesicle trafficking, which warrants further investigation. No statistical significant changes in M6pr, Atg12, or Nfe2l2 were detected, suggesting transcriptional stability in enzyme trafficking, core autophagy, and oxidative stress pathways. Regionally, atria showed higher Lysotracker signal than ventricles, consistent with known enrichment of acidic vesicular stores in atrial physiology. These findings highlight the utility of IVIS imaging of Lysotracker-labelled hearts, providing rapid whole-organ assessment of acidic vesicle distribution, albeit with limited depth resolution. Complementary techniques such as RT-qPCR analysis is essential to interpret IVIS findings, enabling insight into underlying molecular changes in lysosomal and autophagy pathways during cardiac ageing.

physiology↗

bioRxiv2025

Developmental candidate GHP-88310/EIDD-3608 with high tolerability and oral efficacy in measles and respiratory paramyxovirus models

Orthoparamyxoviruses such as human parainfluenza virus type-3 (HPIV3) and measles virus (MeV), are a major health threat. We discovered an orally efficacious broad-spectrum inhibitor of orthoparamyxovirus polymerases. However, here we found that tolerability in higher mammals was limited. We report development of clinical candidate analog GHP-88310 (EIDD-3608), which combines improved oral efficacy with favorable tolerability in non-rodents (ferrets and dogs). GHP-88310 was active against HPIV3, Sendai virus (SeV), MeV, and related canine distemper virus (CDV). In 7-day tolerability studies, daily doses of 2,000 mg/kg were well tolerated. Pharmacokinetic analysis revealed altered plasma exposure of GHP-88310 compared to the original hit. In HPIV3-infected cotton rats, GHP-88310 lowered respiratory tract viral load. Dosing of ferrets infected with CDV, causing lethal measles-like disease, resulted in complete survival, reduction of viremia and shed viral load, and alleviated lymphocytopenia. Once-daily GHP-88310 was efficacious in the CDV-ferret and HPIV3-cotton rat models. The compound was sterilizing against HPIV3 at physiological concentrations in human airway epithelium organoids.

microbiology↗

bioRxiv2024

Evolutionary insights into the emergence of virulent Leptospira spirochetes

Pathogenic Leptospira are spirochete bacteria which cause leptospirosis, a re-emerging zoonotic disease of global importance. Here, we use a recently described lineage of environmental-adapted leptospires, which are evolutionarily the closest relatives of the highly virulent Leptospira species, to explore the key phenotypic traits and genetic determinants of Leptospira virulence. Through a comprehensive approach integrating phylogenomic comparisons with in vitro and in vivo phenotyping studies, we show that the evolution towards pathogenicity is associated with both a decrease of the ability to survive in the environment and the acquisition of strategies that enable successful host colonization. This includes the evasion of the human complement system and the adaptations to avoid activation of the innate immune cells. Moreover, our analysis reveals specific genetic determinants that have undergone positive selection during the course of evolution in Leptospira, contributing directly to virulence and host adaptation as demonstrated by gain-of-function and knock-down studies. Taken together, our findings define a new vision on Leptospira pathogenicity, identifying virulence attributes associated with clinically relevant species, and provide insights into the evolution and emergence of these life-threatening pathogens. AUTHOR SUMMARYLeptospira is a highly heterogeneous bacterial genus and leptospires are ubiquitous bacteria found as free-living saprophytes or as pathogens that can cause disseminated infections, from asymptomatic carriage in rats to lethal acute infection in both humans and animals. Leptospirosis is thus causing over one million cases and nearly 60,000 deaths annually. Despite leptospirosis being a re-emerging zoonosis, little is known about the ability of the etiologic agent to adapt to different hosts and cause disease. Here, combining genome analysis and phenotyping studies of representative species and mutant strains, we show that only a small group of species have the ability to evade the host immune system and cause disease. In addition, our findings provide key insight into the emergence of pathogens from a saprophytic ancestor through events of gene gain and genome reduction.

microbiology↗

bioRxiv2022

Urban ecological connectivity as a planning tool for different animal species.

The application of ecological theory to urban planning is becoming more important as land managers focus on increasing urban biodiversity as a way to improve human welfare. City authorities must decide not only what types of biodiversity-focused infrastructure should be prioritized, but also where new resources should be positioned and existing resources protected or enhanced. Careful spatial planning can contribute to the successful return and conservation of urban nature by maximizing the contribution of green infrastructure to landscape connectivity. By using ecological connectivity theory as a planning tool, governments can quantify the effect of different interventions on the ease with which wildlife can move across the landscape. Here we outline an approach to a) quantify ecological connectivity for different urban wildlife species and b) use this to test different urban planning scenarios using QGIS. We demonstrate four extensions to the work by Deslaurier et al. (2018) and Spanowicz & Jaeger (2019) which improve the application of this method as a planning tool for local government: O_LIA step-by-step method for calculating effective mesh size using the open-source software QGIS. C_LIO_LIConversion of the effective mesh size value (meff) to a "probability of connectedness" (Pc, for easier interpretation by local government and comparisons between planning scenarios). C_LIO_LIGuidance for measuring species-specific connectivity, including how to decide what spatial information should be included and which types of species might be most responsive to connectivity planning. C_LIO_LIAdvice for using the method to measure the outcome of different urban planning scenarios on ecological connectivity. C_LI

ecology↗

bioRxiv2020

Parallel cortical-brainstem pathways to attentional analgesia

Pain perception is diminished when attention is diverted. Our previous human fMRI study, using a 2x2 factorial design with thermal stimuli and concurrent visual attention task, linked the brainstem triad of locus coeruleus (LC), rostroventromedial medulla (RVM) and periaqueductal grey (PAG) to attentional analgesia. This study was repeated with a larger cohort, replicating our earlier findings. Pain intensity was encoded by the RVM, whilst activity in the contralateral LC correlated with the magnitude of attentional analgesia. Psycho-Physiological Interaction analysis informed subsequent Dynamic Causal Modelling and identified two parallel paths between forebrain and the brainstem regions involved in analgesia. These cortico-brainstem connections were modulated by attentional demand: a bidirectional anterior cingulate cortex (ACC) - right-LC loop, and a top-down influence of task on ACC-PAG-RVM. Under conditions of competing attentional demands the ACC recruits discrete brainstem circuits to modulate nociceptive input.

neuroscience↗

bioRxiv2019

Disrupting HIV-1 capsid formation causes cGAS sensing of viral DNA

Detection of viral DNA by cyclic GMP-AMP synthase (cGAS) is a first line of defence leading to the production of type-I interferon (IFN). As HIV-1 is not a strong inducer of IFN we have hypothesised that its capsid cloaks viral DNA from cGAS. To test this we generated defective viral particles by treatment with HIV-1 protease inhibitors or by genetic manipulation of gag. These viruses had defective Gag cleavage, reduced infectivity and diminished capacity to saturate TRIM5. Importantly, unlike wild-type HIV-1, infection with cleavage defective HIV-1 triggered an IFN response in THP-1 cells and primary human macrophages that was dependent on viral DNA and cGAS. Infection in the presence of the capsid destabilising small molecule PF-74 also induced a cGAS-dependent IFN response. These data demonstrate a protective role for capsid and suggest that antiviral activity of capsid- and protease-targeting antivirals may benefit from enhanced innate and adaptive immunity in vivo.

microbiology↗