Biology subjects

Lynch, S.

Publications and source records attributed to Lynch, S..

15 recordsLinked to original sources

bioRxiv2026

Avidity-controlled biotherapeutic delivery systems for the treatment of ischemia-reperfusion acute kidney injury

Regulatory T cells (Tregs) are key mediators of immune resolution and tissue repair following acute kidney injury (AKI), yet strategies to selectively enrich Tregs within the renal microenvironment remain limited. Interleukin-2 (IL-2) is essential for Treg survival and function, but systemic IL-2 delivery is constrained by a short half-life, narrow therapeutic window, and risk of off-target activation of cytotoxic T cells. Effective Treg-based immunomodulation may therefore require both localized cytokine signaling and targeted recruitment of precursor immune populations. Here, we present a sequential, biomaterial-based immunomodulatory strategy that integrates immune cell recruitment with sustained cytokine delivery. An injectable granular hydrogel physically encapsulating the chemokine CCL21 was used to initially recruit CD4+ T cells to the injured kidney. Subsequently, supramolecular guest-host interactions were leveraged to deliver IL-2 modified with the hydrophobic "guest" moiety adamantane, enabling prolonged local cytokine release over 28 days. In healthy mice, we observed early CD4+ T cell recruitment, followed by a pronounced increase in Treg frequency, consistent with immune reprogramming driven by our sequential delivery system. In a murine model of bilateral ischemia-reperfusion (BiAKI), this injectable biomaterial induced a local increase in the proportion of FOXP3-expressing Tregs and a concomitant decrease in the levels of AKI markers. This two-step immunomodulatory approach minimizes acute immune activation while promoting long-term enrichment of Tregs within the renal microenvironment. Together, these findings demonstrate that granular hydrogels with supramolecular host capability can orchestrate immune recruitment and differentiation in a spatiotemporally controlled manner, providing a versatile immunomodulatory platform for applicability in kidney disease.

bioengineering↗

bioRxiv2026

Relative Index of Chimeric Expression (RICE) Analysis: A Quantitative Approach for Chimeric RNAs Using FusionBlaster

Chimeric RNA molecules, which contain nucleotide sequences originating from multiple genes, are generated by chromosomal rearrangements, transcriptional read-throughs, or trans-splicing between separate parental transcripts. Chimeric RNAs have been functionally validated in both pathological and normal healthy physiological contexts indicating the biological significance of chimeric RNA expression. There is, however, currently no standard for computationally quantifying chimeric RNA expression and only limited benchmarking data available for the few chimeric RNA detection software that attempt to measure the abundance of the predicted chimeras. Here, we develop the relative index of chimeric expression, RICE, that is calculated based on the relative expression of chimeric transcripts compared to the respective parental WT transcripts. We evaluate three different methods for generating this measurement from simulated RNA sequencing data with known transcript abundances. Our BLAST-based approach outperforms STAR and Kallisto based approaches when considering both accuracy and consistency between simulated data of different read lengths and sequencing depths. We further demonstrate that RICE values can be validated using qPCR and are sensitive to dynamic conditions using siRNA targeting chimeric RNA expression. Finally, we apply our RICE analysis pipeline to clinical prostate cancer data. We quantify over 1200 chimeric RNAs in primary prostate cancer, metastatic prostate cancer, and non-cancer tissue samples from GTEx. Our differential RICE analysis revealed a clustering of prostate cancer tissue samples from three different sequencing cohorts distinct from their associated tissue type noncancer GTEx clusters. Our pipeline is publicly available on github and can be run on a personal laptop with computational resources and processing time dependent on the number of quantified chimeras.

bioinformatics↗

bioRxiv2026

Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing

The D4Z4 macrosatellite repeat encompasses some of the most difficult-to-resolve disease-related variations in the human genome. D4Z4 has a repeat unit of 3.3 kb (encoding the DUX4 gene) that is present in up to 100 copies on two chromosomes (4 and 10), while DUX4 can only be expressed in somatic cells from the permissive A haplotype that usually occurs on chromosome 4. Facioscapulohumeral muscular dystrophy (FSHD) is caused by chromatin relaxation and ectopic expression of DUX4 in skeletal muscle, mediated by contraction of D4Z4 to 1-10 copies (FSHD1, 95% of FSHD cases) or mutations in chromatin factor genes such as SMCHD1 (FSHD2, 5% of FSHD cases). Due to its large size, disease specific haplotypes and sequence homology between chromosomes, D4Z4 is challenging to resolve by current sequencing technologies. We report a computational tool, Kivvi, to genotype D4Z4 using PacBio whole-genome long-read sequence data. Kivvi detects all D4Z4 alleles in a sample, reporting the repeat size, chromosome (4 vs. 10), distal haplotype (A vs. non-permissive haplotypes) and the methylation level of each allele. We validated Kivvi against gold standard assays for FSHD diagnostics, detecting 100% of contracted alleles and correctly classifying 90% of noncontracted alleles. We showed differential methylation signals between FSHD1 and candidate FSHD2 samples. We profiled D4Z4 across 601 individuals from five ancestral populations, revealing extensive genetic diversity. We identified common haplotypes of D4Z4 alleles and characterized hybrid repeat units, hybrid repeat arrays, and translocation alleles. Combined with HiFi long reads, Kivvi enables the consolidation of multiple FSHD assays into a single workflow and facilitates the discovery of novel genetic modifiers of FSHD through population-scale studies.

genetics↗

bioRxiv2026

Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1R206H-driven heterotopic ossification

Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1R206H mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfr-Cre/Acvr1R206H (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1{beta} blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions. One Sentence SummaryAntibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.

immunology↗

bioRxiv2026

Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains

DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their hosts modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.

microbiology↗

bioRxiv2026

Morphological characterization of moulting in the Atlantic horseshoecrab Limulus polyphemus: phylogenetic conservation amongchelicerates and evolutionary convergence of ecdysis linked to headshield patterns

Arthropods must periodically moult their exoskeleton to permit growth, a conserved developmental process whose morphological and behavioural execution varies widely among lineages. Horseshoe crabs (Limulidae) are members of Xiphosura, a chelicerate lineage with a fossil record extending as far back as the Ordovician and provide a valuable comparative framework for studying the evolution of moulting strategies in Arthropoda. Despite their importance, detailed morphological characterization of moulting in horseshoe crabs remains scarce, limiting developmental studies and broader comparative analyses. Here, we provide a detailed morphological characterization of the moulting process in the Atlantic horseshoe crab Limulus polyphemus. Morphological changes in specific anatomical structures, including the anterior margin of the prosoma, lateral spines and dorsal spinous process of the opisthosoma, were observed during the moulting process. By tracking these morphological markers, such as retraction of the epidermis from the cuticle and degree of corrugation of the epidermis, we were able to identify individuals in the early and late pre-moult stage, predict the onset of ecdysis, and distinguish post-moult and intermoult stages. We compare ecdysis patterns in L. polyphemus with other arthropod taxa, both extant and fossil. We find that, despite differences in behavioural execution, ecdysis in L. polyphemus shares features with other chelicerates, and that both phylogenetic signal and convergent patterns are evident across Arthropoda. This study offers a robust, non-invasive method for determining moult stages in juvenile horseshoe crabs and provides insights into the diversity and constraints of ecdysis in Arthropoda.

evolutionary biology↗

bioRxiv2025

Chlorotonils exhibit potent activity against Mycobacterium tuberculosis, while resistance is mediated by MmpR5-MmpL5

Treatment of Mycobacterium tuberculosis (Mtb) is challenging and requires administration of at least four different antibiotics. Unfortunately, multi-drug resistant Mtb strains continue to emerge, undermining the effectiveness of current treatment regimens and highlighting the urgent need for new therapeutics. In this study, we evaluated the potential of natural product-derived chlorotonils as anti-Mtb agents. We demonstrate that chlorotonils exhibit nanomolar potency against a range of attenuated and virulent Mtb strains. Mechanistic studies and resistance profiling in Mtb revealed that chlorotonils affect both lipid and energy metabolism. Through systems biology approaches, including the construction of an Mtb CRISPRi library specifically designed for chemical-genomic profiling, we identified MmpR5/MmpL5 as major driver of chlorotonil-resistance in Mtb leading also to cross-resistance with bedaquiline. Our findings highlight chlorotonils as valuable chemical tools to further dissect the role and function of the MmpS5-MmpL5 efflux pump in drug-resistant Mtb.

microbiology↗

bioRxiv2025

Disentangling the role of chromosome inversions in the structure of flat oyster (Ostrea edulis): origin, adaptation and phylogeography

Chromosomal inversions are large-scale structural variants that disrupt recombination and contribute to population differentiation and local adaptation. In this study, we characterized the genomic features, frequency, and evolutionary significance of chromosomal inversions in the European flat oyster (Ostrea edulis), a species of ecological and commercial relevance. Using a low-density SNP array ([~]5K), we obtained confident genotyping data across the native European distribution of the species. The breakpoints of the inversions at chromosome (C) 2, C5 and C8, spanning 27, 7 and 35 Mb, respectively, were precisely mapped by combining linkage disequilibrium in a large sample and long-read sequencing. This enabled us to identify the SNPs and genes within the inversions for comparative population genomics and functional evaluation. A north to south cline was observed for the three inversions, although with low-moderate correlation between them. Strong signals for divergent selection were detected for the three inversions, although with specific profiles suggestive of adaptive peaks around highly divergent SNPs across the inversion length. The three inversions seem to be old considering genetic diversity and differentiation between arrangements. Phylogeographic events and adaptation to the current environment seem underlying the structural pattern observed. Gene content and enrichment analyses within inversions suggest that these polymorphisms may play a role in the immune system and response to different stressors including parasite resistance. Our results provide new insights into the genomic architecture of adaptation in O. edulis and highlight the potential of structural variants as targets for conservation and selective breeding.

genomics↗

bioRxiv2024

Contrasting dynamics of two incursions of low pathogenicity avian influenza virus into Australia

The current panzootic of high pathogenicity avian influenza virus H5N1 demonstrates how viral incursions can have major ramifications for wildlife and domestic animals. Herein, we describe the recent incursion into Australia of two low pathogenicity avian influenza virus subtypes, H4 and H10, that exhibited contrasting evolutionary dynamics. Viruses detected from national surveillance and disease investigations between 2020-2022 revealed 27 genomes, 24 of which have at least one segment more closely related to Eurasian or North American avian influenza lineages than those already circulating in Australia. Phylogenetic analysis revealed that H4 viruses circulating in shorebirds represent a recent incursion from Asia that is distinct from those circulating concurrently in Australian waterfowl. Analysis of the internal segments further demonstrates exclusive, persistent circulation in shorebirds. This contrasts with H10, where a novel lineage has emerged in wild waterfowl, poultry and captive birds across Australia, and has likely replaced previously circulating H10 lineages through competitive exclusion. Elucidating different dynamics for avian influenza incursions supports effective disease risk identification and communication that better informs disease preparedness and response.

microbiology↗

bioRxiv2023

Neural representation of phonological wordform in bilateral posterior temporal cortex

While the neural bases of the earliest stages of speech categorization have been widely explored using neural decoding methods, there is still a lack of consensus on questions as basic as how wordforms are represented and in what way this word-level representation influences downstream processing in the brain. Isolating and localizing the neural representations of wordform is challenging because spoken words evoke activation of a variety of representations (e.g., segmental, semantic, articulatory) in addition to form-based representations. We addressed these challenges through a novel integrated neural decoding and effective connectivity design using region of interest (ROI)-based, source reconstructed magnetoencephalography/electroencephalography (MEG/EEG) data collected during a lexical decision task. To localize wordform representations, we trained classifiers on words and nonwords from different phonological neighborhoods and then tested the classifiers ability to discriminate between untrained target words that overlapped phonologically with the trained items. Training with either word or nonword neighbors supported decoding in many brain regions during an early analysis window (100-400 ms) reflecting primarily incremental phonological processing. Training with word neighbors, but not nonword neighbors, supported decoding in a bilateral set of temporal lobe ROIs, in a later time window (400-600 ms) reflecting activation related to word recognition. These ROIs included bilateral posterior temporal regions implicated in wordform representation. Effective connectivity analyses among regions within this subset indicated that word-evoked activity influenced the decoding accuracy more than nonword-evoked activity did. Taken together, these results evidence functional representation of wordforms in bilateral temporal lobes isolated from phonemic or semantic representations.

neuroscience↗

bioRxiv2023

RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data

Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor (https://github.com/sandybioteck/RTCpredictor) has less memory requirements and faster execution time.

genomics↗

bioRxiv2022

Urban population structure and local movement ecology of a native Australian mosquito involved in disease transmission

Dispersal is a critical factor in designing successful pest control measures as it determines the rate of movement across target control areas and influences the risk of human exposure to the species and its pathogens. Here we used a fine scale spatial population genomic approach to investigate the dispersal ecology and population structure of Aedes notoscriptus, an important disease transmitting mosquito, on the Mornington Peninsula near Melbourne, Australia. The species is suspected to be involved in the transmission of Mycobacterium ulcerans, the bacterium that causes Buruli ulcer, in this area. We sampled and reared Ae. notoscriptus eggs at two time points from 170 traps up to 5 km apart and generated genomic data from 240 individuals. We also produced a draft genome assembly from a laboratory colony established from mosquitoes sampled near the study area. We found low genetic structure (Fst) and high coancestry throughout the study region. Using genetic data to identify close kin dyads, we found that mosquitoes had moved distances of >1km within a generation, which is further than previously described for this species. A spatial autocorrelation analysis of genetic distances indicated genetic dissimilarity at >4 km separation, a fourfold higher distance than for a comparable population of the dengue mosquito, Ae. aegypti, from Cairns, Australia. These findings point to high mobility of Ae. notoscriptus, highlighting the challenges of localized intervention strategies targeting this species. Further sampling within the same area at two time points 6 and 12 months after initial sampling showed that egg counts were relatively consistent across time, and that spatial variation in egg counts covaried with spatial variation in Wrights neighbourhood size (NS). As NS increases linearly with population density, egg counts may be useful for estimating relative density in Ae. notoscriptus. The results highlight the importance of acquiring species-specific data when planning control measures.

ecology↗

bioRxiv2021

DNA-dependent binding of nargenicin to DnaE1 inhibits replication in Mycobacterium tuberculosis

Natural products provide a rich source of potential antimicrobials for use in treating infectious diseases for which drug resistance has emerged. Foremost among these is tuberculosis. Assessment of the antimycobacterial activity of nargenicin, a natural product that targets the replicative DNA polymerase of Staphylococcus aureus, revealed that it is a bactericidal genotoxin that induces a DNA damage response in Mycobacterium tuberculosis (Mtb) and inhibits growth by blocking the replicative DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding of nargenicin to Mtb DnaE1 requires the DNA substrate such that nargenicin is wedged between the terminal base pair and the polymerase and occupies the position of both the incoming nucleotide and templating base. Comparative analysis across three bacterial species suggests that the activity of nargenicin is partly attributable to the DNA binding affinity of the replicative polymerase. This work has laid the foundation for target-led drug discovery efforts focused on Mtb DnaE1.

microbiology↗

bioRxiv2019

Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy

BackgroundMicrobes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial communities are typically dominated by one or a few well adapted microbes, which are able to survive in a narrow pH range. In comparison to other human-associated microbes, vaginal microbes are adapted to live on host-derived carbon sources, likely sourced from glycogen and mucin present in the vaginal environment. MethodsUsing 16S rRNA and ITS amplicon sequencing, we characterized the cervicovaginal microbiomes of 18 healthy women throughout the three trimesters of pregnancy. Shotgun metagenomic sequencing permitted refinement of the taxonomy established by amplicon sequencing, and identification of functional genes. Additionally, we analyzed saliva and urine metabolomes using GC-TOF and LC-MS/MS lipidomics approaches for samples from mothers and their infants through the first year of life. ResultsAmplicon sequencing revealed most women had either a simple community with one highly abundant species of Lactobacillus or a more diverse community characterized by a high abundance of Gardnerella, as has also been previously described in several independent cohorts. Integrating GC-TOF and lipidomics data with amplicon sequencing, we found metabolites that distinctly associate with particular communities. For example, cervicovaginal microbial communities dominated by Lactobacillus crispatus also have high mannitol levels, which contradicts the basic characterization of L. crispatus as a homofermentative Lactobacillus species. It may be that fluctuations in which Lactobacillus dominate a particular vaginal microbiome are dictated by the availability of host sugars, such as fructose, which is the most likely substrate being converted to mannitol. Furthermore, indole-3-lactate (ILA) was also indicative of L. crispatus specifically. ILA has immunomodulatory properties through binding the human aryl hydrocarbon receptor (AhR), which may maintain the especially low diversity of L. crispatus dominated communities. ConclusionsOverall, using a multi- omic approach, we begin to address the genetic and molecular means by which a particular vaginal microbiome becomes vulnerable to large changes in composition.

microbiology↗

bioRxiv2019

Countries are out of step with international recommendations for tuberculosis testing, treatment, and care: Findings from a 29-country survey of policy adoption and implementation

BackgroundTuberculosis (TB) poses a global health crisis requiring robust international and country-level action. Adopting and implementing TB policies from the World Health Organization (WHO) is essential to meeting global targets for reducing TB burden. However, many high TB burden countries lag in implementing WHO recommendations. Assessing the progress of implementation at national level can identify key gaps that must be addressed to expand and improve TB care. MethodsIn 2016/2017, Medecins Sans Frontieres and the Stop TB Partnership conducted a survey on adoption and implementation of 47 WHO TB policies in the national TB programs of 29 countries. Here we analyze a subset of 23 key policies in diagnosis, models of care, treatment, prevention, and drug regulation to provide a snapshot of national TB policy adoption and implementation. We examine progress since an analogous 2015 survey of 23 of the same countries. ResultsAt the time of the survey, many countries had not yet aligned their national guidelines with all WHO recommendations, although some progress was seen since 2015. For diagnosis, about half of surveyed countries had adopted the WHO-recommended initial rapid test (Xpert MTB/RIF). A majority of countries had adopted decentralized models of care, although one-third of them still required hospitalization for drug-resistant (DR-)TB. Recommended use of the newer drugs bedaquiline (registered in only 6 high-burden TB countries) and delamanid (not registered in any high-burden country) was adopted by 23 and 18 countries, respectively, but short-course (9-month) and newer pediatric regimens by only 13 and 14 countries, respectively. Guidelines in all countries included preventive treatment of latent TB infection for child TB contacts and people living with HIV/AIDS, but only four extended this to adult contacts. ConclusionTo reach global TB targets, greater political will is needed to rapidly adopt and implement internationally recognized care guidelines. KEY MESSAGESO_ST_ABSWhat is already known?C_ST_ABSO_LICountries may be slow to adopt and implement updated World Health Organization (WHO) Tuberculosis (TB) testing, treatment, and prevention recommendations. C_LIO_LIImplementing updated TB guidelines from WHO is a fundamental first step to honoring international commitments, made through the United Nations (UN) Sustainable Development Goals (SDGs) and UN High-Level Meeting on TB Political Declaration, to end TB by 2030. C_LI What are the new findings?O_LIOf 29 mostly high TB burden countries, none had fully aligned their national guidelines with WHO recommendations, although some progress has been made since 2015. C_LIO_LIA lack of alignment with WHO recommendations was found across all policy areas surveyed, including prevention, diagnosis, treatment, models of care and drug regulation, particularly regarding uptake of newer, faster, more effective approaches. C_LI What do the new findings imply?O_LITo reach global TB targets, greater political will is needed to adopt and implement internationally recognized care guidelines more rapidly, and specifically, to keep up with the latest recommendations. C_LIO_LIPeriodic surveys of progress at the national level are a valuable way to identify specific areas where countries or regions have fallen behind and that require specific policy and/or programmatic attention. C_LI

epidemiology↗