Biology subjects

West, M.

Publications and source records attributed to West, M..

11 recordsLinked to original sources

bioRxiv2026

Single-cell multi-ancestry regulatory map of systemic lupus erythematosus

Integrating genomic and single-cell transcriptomic profiles from patient cohorts can uncover regulatory effects underlying genetic associations with disease. Here we present SLEmap, a multi-ancestry single-cell expression quantitative trait locus (sc-eQTL) map generated from peripheral blood mononuclear cells from 281 patients with systemic lupus erythematosus (SLE). We identified 18,608 independent eQTLs in 5,656 genes, of which 149 signals in 66 genes colocalized with SLE GWAS loci. Nearly half of these colocalizations were detected exclusively through cell type-level analyses, highlighting the importance of cellular context for interpreting disease-associated genetic variation. Multi-ancestry data identified regulatory signals robust across diverse ancestral backgrounds and improved signal resolution. Most colocalizations were undetectable in sc-eQTLs from a healthy cohort (OneK1K), with novel SLE colocalizations highlighting disease-relevant regulatory mechanisms across distinct cell types, including the NF-{kappa}B pathway. These findings demonstrate the value of disease-specific, multi-ancestry single-cell regulatory maps for resolving the genes and cellular mechanisms underlying disease-associated genetic variation.

genetics↗

bioRxiv2025

Wbm0152, an outer membrane lipoprotein of the Wolbachia endosymbiont of Brugia malayi, inhibits yeast ESCRT complex activity

Human pathogenic filarial nematodes of the family Onchocercidae, including Brugia malayi and Onchocerca volvulus, cause debilitating filarial diseases such as lymphatic filariasis and river blindness. These mosquito-borne pathogens are obligately colonized by the gram-negative intracellular alphaproteobacterium, Wolbachia pipientis, which is essential for nematode sexual reproduction, long-term survival, and pathogenicity in the mammalian host. Like many intracellular bacteria, Wolbachia likely uses numerous surface-exposed and secreted effector proteins to regulate its ability to persist and replicate within nematode host cells. However, due to the inability to cultivate Wolbachia in the laboratory and the genetic intractability of both filarial nematodes and the bacterium, the molecular underpinnings that define the bacterium:nematode relationship are almost completely unknown. In this work, we show that the expression of a Wolbachia outer membrane lipoprotein, wBm0152, in Saccharomyces cerevisiae inhibits the activity of the conserved Endosomal Sorting Complex Required for Transport (ESCRT) complex and strongly disrupts endosomal maturation, leading to defects in ubiquitylated protein turnover. Using in vivo bimolecular fluorescence complementation, we find that Wbm0152 interacts with the Vps2p subunit of the ESCRT-III subcomplex as well as the Vps2p ortholog (BmVps2, Bm6583b) from a Wolbachia host nematode, Brugia malayi. These data suggest a novel role of ESCRT in Wolbachia persistence providing insight into the elusive relationship between these two organisms. AUTHOR SUMMARYFilarial diseases of mammals, including lymphatic filariasis and canine heartworm, are caused by vector-borne filarial nematodes of the family Onchocercidae. Many of the nematodes in this family are obligately colonized by an intracellular bacterium, Wolbachia pipientis, which is essential for the nematodes long-term survival, reproduction, and pathogenicity. Therefore, understanding the mechanisms used by Wolbachia to persist and replicate within host cells could provide new molecular targets for treating filarial infections. Due to the genetic intractability of both nematode and bacterium, however, significant progress on characterizing these interactions have proven difficult. In this work, we show that a predicted outer membrane lipoprotein, Wbm0152, of the Wolbachia endosymbiont of Brugia malayi inhibits yeast Endosomal Sorting Complex Required for Transport (ESCRT) complex activity in vivo. Wbm0152 interacts with a core subunit of the yeast ESCRT-III complex, as well as with the orthologous ESCRT-III protein from Brugia. ESCRTs are conserved across eukaryotes and are important for diverse cellular processes such as endosomal maturation, autophagy, and cellular division. As Wolbachia persists within a membrane-bound compartment within Brugia and must avoid host autophagic pathways, this study presents a potential mechanism by which Wolbachia may regulate Brugia membrane trafficking pathways to ensure its intracellular survival.

microbiology↗

bioRxiv2025

Variation in social organization and supergene control along a latitudinal gradient

Widespread species often experience vastly different environmental conditions across their range. In species with polymorphic traits under strong genetic control, we can investigate how environmental variation influences the distribution of traits and whether the strength of genetic control is consistent across environmental gradients. Here, we investigate the distribution of phenotypic and genetic variation in the ant Formica podzolica across 30{degrees} of latitude. This species shares a supergene that is associated with colony queen number and colony sex ratio with other congeners, but we detect a surprising six common supergene variants. Colonies with a single queen are more abundant in the north compared to those with multiple queens, although the queen number polymorphism is present throughout the range. In parallel, the frequency of supergene haplotypes also varies with latitude. Of the 170 colonies examined, 10.6% contained supergene haplotypes that did not match the queen number phenotype. The highest concentration of these mismatched colonies occurred in one site, raising the possibility that the environmental conditions there override supergene function. While the supergene system in F. podzolica is complex, this species holds promise for understanding how an ancient supergene system evolves in a single species experiencing highly variable environmental conditions.

evolutionary biology↗

bioRxiv2024

Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions

Upon infection, human papillomavirus (HPV) manipulates host cell gene expression to create an environment that is supportive of a productive and persistent infection. The virus-induced changes to the host cells transcriptome are thought to contribute to carcinogenesis. Here, we show by RNA-sequencing that oncogenic HPV18 episome replication in primary human foreskin keratinocytes (HFKs) drives host transcriptional changes that are consistent between multiple HFK donors. We have previously shown that HPV18 episome replication in HFKs results in post-transcriptional stabilisation of the host chromatin insulation protein CTCF. Since CTCF is an important regulator of host cell transcription via coordination of epigenetic boundaries and long-range chromosomal interactions, we hypothesised that HPV18-induced stabilisation of CTCF may contribute to host transcription reprogramming. Analysis of CTCF binding in the host cell genome by ChIP-Seq revealed that while the total number of CTCF binding sites is not altered by the virus, there are a sub-set of CTCF binding sites that are either enriched or depleted of CTCF. Many of these altered sites are clustered within regulatory elements of differentially expressed genes, including the tumour suppressor gene cell adhesion molecule 1 (CADM1), which supresses epithelial cell growth and invasion. We show that HPV18 establishment results in reduced CTCF binding at the CADM1 promoter and upstream enhancer. Loss of CTCF binding is coincident with epigenetic repression of CADM1, in the absence of CpG hypermethylation, while adjacent genes including the transcriptional regulator ZBTB16 are activated. These data indicate that the CADM1 locus is subject to topological rearrangement following HPV18 establishment. We tested this hypothesis using 4C-Seq (circular chromosome confirmation capture-sequencing) and show that HPV18 establishment causes a loss of long-range chromosomal interactions between the CADM1 transcriptional start site and the upstream transcriptional enhancer. These data show that HPV18 manipulates host cell promoter-enhancer interactions to drive transcriptional reprogramming that may contribute to HPV-induced disease progression. AUTHOR SUMMARYInfection with oncogenic HPV is the cause of numerous cancer types, which generally arise after persistent HPV infection. Upon infection, HPV alters the gene expression profile of infected cells to facilitate virus replication and persistence. Multiple mechanisms of HPV-induced host cell reprogramming have been previously suggested. Here, we show that HPV infection induces rearrangement of specific genomic loci by altering the chromatin binding of the host cell protein CTCF, an important regulator of chromatin architecture. Loss of CTCF binding to a cluster of binding sites at the CADM1 locus on chromosome 11 is coincident with epigenetic reprogramming and disruption of long-range chromatin interactions, resulting in transcriptional repression of CADM1. Our data show that repression of CADM1 is an early event in HPV-driven disease, preceding hypermethylation of the CADM1 transcriptional promoter that is frequently observed in HPV-driven cancers, demonstrating a novel mechanism of HPV-induced host cell transcriptional reprogramming.

microbiology↗

bioRxiv2023

A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting

Endosomes are specialized organelles that function in the secretory and endocytic protein sorting pathways. Endocytosed cell surface receptors and transporters destined for lysosomal degradation are sorted into intralumenal vesicles (ILVs) at endosomes by Endosomal Sorting Complex Required for Transport (ESCRT) proteins. The endosomes (multivesicular bodies, MVBs) then fuse with the lysosome. During endosomal maturation, the number of ILVs increases, but the size of endosomes does not decrease despite consumption of the limiting membrane during ILV formation. Vesicle-mediated trafficking is thought to provide lipids to support MVB biogenesis. However, we have uncovered an unexpected contribution of a large bridge-like lipid transfer protein, Vps13, in this process. Here, we reveal that Vps13-mediated lipid transfer at ER-endosome contact sites is required for the ESCRT pathway. We propose that Vps13 may play a critical role in supplying lipids to the endosome, ensuring continuous ESCRT-mediated sorting during MVB formation.

cell biology↗

bioRxiv2023

Mitochondrial-Derived Compartments are Multilamellar Domains that Encase Membrane Cargo and Cytosol

Preserving the health of the mitochondrial network is critical to cell viability and longevity. To do so, mitochondria employ several membrane remodeling mechanisms, including the formation of mitochondrial-derived vesicles (MDVs) and compartments (MDCs) to selectively remove portions of the organelle. In contrast to well-characterized MDVs, the distinguishing features of MDC formation and composition remain unclear. Here we used electron tomography to observe that MDCs form as large, multilamellar domains that generate concentric spherical compartments emerging from mitochondrial tubules at ER-mitochondria contact sites. Time-lapse fluorescence microscopy of MDC biogenesis revealed that mitochondrial membrane extensions repeatedly elongate, coalesce, and invaginate to form these compartments that encase multiple layers of membrane. As such, MDCs strongly sequester portions of the outer mitochondrial membrane, securing membrane cargo into a protected domain, while also enclosing cytosolic material within the MDC lumen. Collectively, our results provide a model for MDC formation and describe key features that distinguish MDCs from other previously identified mitochondrial structures and cargo-sorting domains. SUMMARYWilson and colleagues use electron tomography and time-lapse fluorescence microscopy to observe that mitochondrial-derived compartments (MDCs) are generated from outer mitochondrial membrane extensions that repeatedly elongate, coalesce, and invaginate to secure membrane cargo and cytosol within a distinct, protected domain.

cell biology↗

bioRxiv2021

Lateral Preoptic Area Neurons Signal Cocaine Self-Administration Behaviors

The lateral preoptic area is implicated in numerous aspects of substance use disorder. In particular, the lateral preoptic area is highly sensitive to the pharmacological properties of psychomotor stimulants, and its activity promotes drug-seeking in the face of punishment and reinstatement during abstinence. Despite the lateral preoptic areas complicity in substance use disorder, how precisely lateral preoptic area neurons encode the individual components of drug self-administration has not been ascertained. To bridge this gap, we examined how the firing of single lateral preoptic area neurons correlates with three discrete elements of cocaine self-administration: 1) drug-seeking (pre-response), 2) drug-taking (response), and 3) receipt of the cocaine infusion. A significant subset of lateral preoptic area neurons responded to each component with a mix of increases and decreases in firing-rate. A majority of these neurons encoded the operant response with increases in spiking, though responses during the drug-seeking, taking, and reciept windows were highly correlated.

neuroscience↗

bioRxiv2021

de novo variant calling identifies cancer mutation profiles in the 1000 Genomes Project

Detection of de novo variants (DNVs) is critical for studies of disease-related variation and mutation rates. We developed a GPU-based workflow to rapidly call DNVs (HAT) and demonstrated its effectiveness by applying it to 4,216 Simons Simplex Collection (SSC) whole-genome sequenced parent-child trios from DNA derived from blood. In our SSC DNV data, we identified 78 {+/-} 15 DNVs per individual, 18% {+/-} 5% at CpG sites, 75% {+/-} 9% phased to the paternal chromosome of origin, and an average allele balance of 0.49. These calculations are all in line with DNV expectations. We sought to build a control DNV dataset by running HAT on 602 whole-genome sequenced parent-child trios from DNA derived from lymphoblastoid cell lines (LCLs) from the publicly available 1000 Genomes Project (1000G). In our 1000G DNV data, we identified 740 {+/-} 967 DNVs per individual, 14% {+/-} 4% at CpG sites, 61% {+/-} 11% phased to the paternal chromosome of origin, and an average allele balance of 0.41. Of the 602 trios, 80% had > 100 DNVs and we hypothesized the excess DNVs were cell line artifacts. Several lines of evidence in our data suggest that this is true and that 1000G does not appear to be a static reference. By mutation profile analysis, we tested whether these cell line artifacts were random and found that 40% of individuals in 1000G did not have random DNV profiles; rather they had DNV profiles matching B-cell lymphoma. Furthermore, we saw significant excess of protein-coding DNVs in 1000G in the gene IGLL5 that has already been implicated in this cancer. As a result of cell line artifacts, 1000G has variants present in DNA repair genes and at Clinvar pathogenic or likely-pathogenic sites. Our study elucidates important implications of the use of sequencing data from LCLs for both reference building projects as well as disease-related projects whereby these data are used in variant filtering steps.

genomics↗

bioRxiv2020

Bro1 directly stimulates Vps4 activity to promote Intralumenal Vesicle Formation during Multivesicular Body biogenesis

Endosomal sorting complexes required for transport (ESCRT-0, -I, -II, -III) execute cargo sorting and intralumenal vesicle (ILV) formation during conversion of endosomes to multivesicular bodies (MVBs). The AAA-ATPase Vps4 regulates the ESCRT-III polymer to facilitate membrane remodeling and ILV scission during MVB biogenesis. Here we show that the conserved V domain of ESCRT-associated protein Bro1 (the yeast homolog of mammalian proteins ALIX and HD-PTP) directly stimulates Vps4. This activity is required for MVB cargo sorting. Furthermore, the Bro1 V domain alone supports Vps4/ESCRT-driven ILV formation in vivo without efficient MVB cargo sorting. These results reveal a novel activity of the V domains of Bro1 homologs in licensing ESCRT-III-dependent ILV formation and suggest a role in coordinating cargo sorting with membrane remodeling during MVB sorting. Moreover, ubiquitin binding enhances V domain stimulation of Vps4 to promote ILV formation via the Bro1/Vps4/ESCRT-III axis, uncovering a novel role for ubiquitin during MVB biogenesis in addition to facilitating cargo recognition. SummaryCargo sorting is coordinated with intralumenal vesicle budding during ESCRT-mediated multivesicular body biogenesis. Bro1 V domain stimulates Vps4 to promote ESCRT-III-driven intralumenal vesicle formation in a manner required for this coordinated process.

cell biology↗

bioRxiv2018

Maintenance of active chromatin states by Hmgn1 and Hmgn2 is required for stem cell identity

Chromatin plasticity is thought to be fundamental to the pluripotency of embryonic stem cells. Hmgn proteins modulate chromatin structure and are highly expressed during early development and in neural stem/progenitor cells of the developing and adult brain. Here, we show that loss of Hmgn1 or Hmgn2 in pluripotent embryonal carcinoma cells leads to increased levels of spontaneous neuronal differentiation. This is accompanied by the loss of pluripotency markers and increased expression of the pro-neural transcription factors Neurog1 and Ascl1. Neural stem cells derived from these Hmgn-knockout lines also show increased spontaneous neuronal differentiation and Neurog1 expression. The loss of Hmgn2 is associated with the disruption of active chromatin states at specific classes of gene. The levels of H3K4me3, H3K9ac, H3K27ac and H3K122ac are considerably reduced at the pluripotency genes Nanog and Oct4, which impacts transcription. At endodermal/mesodermal lineage-specific genes, the loss of Hmgn2 leads to a switch from a bivalent to a repressive chromatin configuration. However, at the neuronal lineage genes Neurog1 and Ascl1, no epigenetic changes are observed and their bivalent states are retained. We conclude that Hmgn proteins play important roles in maintaining chromatin plasticity in stem cells, and are essential for maintaining stem cell identity and pluripotency.

molecular biology↗

bioRxiv2018

Development of a genetically encoded sensor for endogenous CaMKII activity

CaMKII is a crucial oligomeric enzyme in neuronal and cardiac signaling, fertilization and immunity. Here, we report the construction of a novel, substrate-based, genetically-encoded sensor for CaMKII activity, FRESCA (FRET-based Sensor for CaMKII Activity). Currently, there is one biosensor for CaMKII activity, Camui, which contains CaMKII. FRESCA allows us to measure all endogenous CaMKII variants, while Camui can track a single variant. Since there are ~40 CaMKII variants, using FRESCA to measure aggregate activity allows a fresh perspective on CaMKII activity. We show, using live-cell imaging, FRESCA response is concurrent with Ca2+ rises in HEK293T cells and mouse eggs. In eggs, we stimulate oscillatory patterns of Ca2+ and observe the differential responses of FRESCA and Camui. Our results implicate an important role for the variable linker region in CaMKII, which tunes its activation. FRESCA will be a transformative tool for studies in neurons, cardiomyocytes and other CaMKII-containing cells.

biochemistry↗