Biology subjects

Lim, E. L.

Publications and source records attributed to Lim, E. L..

6 recordsLinked to original sources

bioRxiv2025

Woodsmoke and Diesel Exhaust: Distinct Transcriptomic Profiles in the Human Airway Epithelium

Climate change is increasing the frequency and severity of wildfires globally, causing significant woodsmoke (WS) emissions. Vehicles emit sizable amounts of toxic traffic-related air pollution (TRAP), for which diesel exhaust (DE) is a model. Both WS and DE contain particulate matter <2.5 microns (PM2.5) which deeply penetrates the lungs, causing respiratory epithelial inflammation that drives health effects. Regulations focus on PM2.5 concentration, despite emerging research that highlights how composition mediates health effects. As WS and DE are compositionally distinct, we conducted the first head-to-head comparison of effects on the transcriptomes of air-liquid interface cultured primary human bronchial epithelial cells (HBEC). Differentiated donor-matched HBEC transwells were exposed for 2-hours to filtered air (FA; control), or WS (furnace tube burning pine) or DE (Hatz 1B30E generator) both diluted to 300 {micro}g/m3 of PM2.5. WS had higher ultrafine PM, whereas DE exposure contained significantly higher NO2, CO, and O3. RNA sequencing showed that WS exposure resulted in 119 ({uparrow}41, {downarrow}78) differentially expressed genes, while DE modulated 399 ({uparrow}255, {downarrow}144) compared to FA exposure. WS was associated with small ribosomal subunit and cytochrome complex related genes, while DE exposure was associated with HIF-1 signaling, respiratory chain complex and interferon alpha/beta signaling/ISG15-protein conjugation, suggesting how TRAP exposure may enhance infection risk. We also analyzed exposure effects on protein immune-mediators. We demonstrate that two major air pollution sources modulate different genes and pathways in HBECs, with minimal overlap. This informs the debate regarding the regulatory focus on concentration and assumptions that similar concentrations of air pollution have indistinct effects. HighlightsO_LILung health effects of diesel exhaust (DE) and wood smoke (WS) are underexplored C_LIO_LIRNAseq of DE and WS-exposed primary lung epithelial cells revealed larger DE effects C_LIO_LIDE showed greater repression of host antiviral response-associated genes than WS C_LIO_LIA regulatory focus on PM concentration may miss composition-specific lung effects C_LI

bioinformatics↗

bioRxiv2024

Loss of PI3Kδ activity drives autoimmune colitis by impairing extrathymic Treg differentiation

Peripherally-derived regulatory T cells (pTregs) have a prominent role in maintaining intestinal immune homeostasis. In cases of phosphoinositide-3-kinase {delta} (PI3K{delta}) inactivation, such as in patients receiving PI3K{delta} inhibitor idelalisib as a cancer treatment, breakdown of intestinal immune tolerance occurs frequently in the form of diarrhoea and colon inflammation. In a mouse model of systemic PI3K{delta} inactivation, both enhancement of anti-tumor immunity and colitis have been described, as a result of Treg impairment. However, in view of the critical role for Tregs in the prevention of systemic autoimmunity, the basis for such tissue-restricted breach of immune tolerance upon loss of PI3K{delta} function is not yet understood. We report here that mice lacking PI3K{delta} activity do not suffer a general defect in Treg immunosuppression, but specifically fail to develop Helios- pTregs in the colon. We demonstrate reduced extrathymic Treg induction, in vitro and in vivo, from naive CD4+ T cells with inactive PI3K{delta}, along with dysregulation of a tissue-resident phenotype. These results suggest a non-redundant role for PI3K{delta}-dependent pTreg differentiation in maintaining tolerance to commensal microbial antigens in the gut.

immunology↗

bioRxiv2024

Th17 cells with a pathogenic signature in joints of ZAP-70 mutant arthritic mice harbor unique TCR repertoires that share features with WT Tregs

Mutations in the ZAP-70 gene that cause moderate attenuation of T cell receptor (TCR) signaling in mice can result in autoimmune manifestations. One explanation for this pathology is a shift in the regulatory-conventional (Treg-Tconv) T cell repertoire composition. To test this hypothesis, we characterized the single-cell gene expression profiles and TCR repertoires of Tconv and Treg CD4+ T cells of arthritic (ZAC), poised (SKG) ZAP-70 mutant, and wild-type (WT) mice. We identified a group of Th17 cells which exhibited a pathogenic signature and occurred exclusively in inflamed joints of ZAC mice. Such pathogenic signature was uniquely detected in CD4+ T cells obtained from inflamed joints of RA patients. Overall, the Tconv repertoires of ZAP-70 mutant mice were increasingly similar to the repertoires of WT Tregs, and this effect was most notable in the subset of pathogenic Th17 cells. Our results support a model where, upon moderate ZAP-70-mediated signal weakening, T cells that would normally develop into Tregs, instead develop into self-reactive Tconvs, resulting in a breakdown in self-tolerance and susceptibility to autoimmune arthritis.

immunology↗

bioRxiv2023

Endosome dysfunction leads to gain-of-function TLR7 and human lupus

Hyperactive Toll-like receptor (TLR) 7 signaling has long been appreciated as a driver of autoimmune disease by breaking tolerance to self-nucleic acids in mouse models1-5. Recently, mutations in TLR7 or its associated regulator UNC93B16, 7, were identified as monogenic causes of human lupus; the unifying feature of these mutations being TLR7 gain-of-function. TLR7 is an intracellular transmembrane receptor, sensing RNA breakdown products within late endosomes8, 9. Hence, its function depends on intricate transport mechanisms and membrane interactions within the endomembrane network. Whether perturbations of any of these endosome-related processes can give rise to TLR7 gain-of-function and facilitate self-reactivity has not been investigated. Here, we show that a dysregulated endosomal compartment leads to unrestricted TLR7 signaling and human lupus. The late endosomal BLOC-1-related protein complex (BORC) together with the small Arf1-like GTPase Arl8b controls TLR7 protein levels, and a direct interaction between Arl8b and Unc93b1 is required to regulate TLR7 turnover. We identified an amino acid insertion in UNC93B1 in a patient with childhood-onset lupus, which reduces the interaction with the BORC-Arl8b complex and leads to endosomal TLR7 accumulation. Therefore, a failure to control the proper progression of TLR7 through its endocytic life cycle is sufficient to break immunological tolerance to nucleic acids in humans. Our results highlight the importance of an intact endomembrane system to prevent autoimmune disease. As the cellular mechanisms restricting TLR7 signaling can be manifold, identifying and stratifying lupus patients based on a TLR7-driven pathogenesis could be a viable strategy towards a targeted therapy.

immunology↗

bioRxiv2022

Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity

Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patients disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample reference phasing. We demonstrate Refphases ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.

bioinformatics↗

bioRxiv2017

Comprehensive characterization of pediatric acute myeloid leukemia reveals novel molecular features and age-specific interactions

We present the molecular landscape of pediatric acute myeloid leukemia (AML), characterizing nearly 1,000 participants in Childrens Oncology Group (COG) AML trials. The COG/NCI TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA, miRNA sequencing and CpG methylation profiling. Validated DNA variants revealed diverse, infrequent mutations with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including novel gene fusions and focal MBNL1, ZEB2, and ELF1 deletions, were disproportionately prevalent in young as compared to adult patients. Conversely, DNMT3A and TP53 mutations, common in adults, are conspicuously absent from virtually all pediatric cases. Novel GATA2, FLT3, and CBL mutations, recurrent MYC-ITD, NRAS, KRAS, and WT1 mutations are frequent in pediatric AML. Deletions, mutations, and promoter DNA hypermethylation convergently impact Wnt signaling, Polycomb repression, innate immune cell interactions, and a cluster of zinc finger genes associated with KMT2A rearrangements. These results highlight the need for, and facilitate the development of age-tailored targeted therapies for the treatment of pediatric AML.

cancer biology↗