Biology subjects

Brown, K. L.

Publications and source records attributed to Brown, K. L..

10 recordsLinked to original sources

bioRxiv2025

α-Parvin regulation of cell re-arrangement is critical for ureteric bud branching morphogenesis

All branched tubular structures, including the kidney collecting system, are formed by branching morphogenesis, a process that includes tip branching and trunk narrowing. Tight control of cell movement and rearrangements is a prerequisite for branching morphogenesis. The role of integrin-associated adhesion proteins in coordinating actin dynamics and cell rearrangements during branching morphogenesis is poorly understood. Here we used 3D live imaging of mouse ureteric bud branching to show that -parvin, a component of the integrin binding ILK-PINCH-Parvin (IPP) complex, regulates tip branching and tubule thinning by inhibiting excessive cell adhesion and actin polymerization. Mechanistically, -parvin promotes actin turnover by inhibiting activation of the small GTPases RhoA and Cdc42, which in turn enhances the severing function of the actin regulatory protein, cofilin. These results underscore the importance of adhesion protein-regulated actin dynamics in the critical process of cell rearrangement, which is required for branching morphogenesis. TeaserScaffold protein -parvin limits cell adhesion and actin polymerization, enabling cell rearrangements that drive kidney branching

developmental biology↗

bioRxiv2024

Optimized phenotype definitions boost GWAS power

AO_SCPLOWBSTRACTC_SCPLOWComplex diseases are among the central challenges facing the world, and genetics underlie a large fraction of the risk. Observational data, such as electronic health records (EHR), offer numerous advantages in the study of complex disease genetics. These include their large scale, cost-effectiveness, information on many different conditions, and future scalability with the widespread adoption of EHRs. Observational data, however, are challenging for research as they reflect various factors including the healthcare process and access to care, as well as broader societal effects like systemic biases. Here, we introduce MaxGCP, a novel phenotyping method designed to purify the genetic signal in observational data. Our approach optimizes a phenotype definition to maximize its coheritability with the complex trait of interest. We validated the method in simulations and applied it to real data analyses of stroke and Alzheimers disease. We found that MaxGCP improves genomewide association study (GWAS) power compared to conventional, single-code phenotype definitions. MaxGCP is a powerful tool for genetic discovery in observational data, and we anticipate that it will be broadly useful for studying complex diseases using observational data.

bioinformatics↗

bioRxiv2023

Phenotype projections accelerate biobank-scale GWAS

Understanding the genetic basis of complex disease is a critical research goal due to the immense, worldwide burden of these diseases. Pan-biobank genome-wide association studies (GWAS) provide a powerful resource in complex disease genetics, generating shareable summary statistics on thousands of phenotypes. Biobank-scale GWAS have two notable limitations: they are resource-intensive to compute and do not inform about hand-crafted phenotype definitions, which are often more relevant to study. Here we present Indirect GWAS, a summary-statistic-based method that addresses these limitations. Indirect GWAS computes GWAS statistics for any phenotype defined as a linear combination of other phenotypes. Our method can reduce runtime by an order of magnitude for large pan-biobank GWAS, and it enables ultra-rapid (roughly one minute) GWAS on hand-crafted phenotype definitions using only summary statistics. Overall, this method advances complex disease research by facilitating more accessible and cost-effective genetic studies using large observational data.

genetics↗

bioRxiv2023

Notch signaling regulates immunosuppressive tumor-associated macrophage function in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDA) continues to have a dismal prognosis. The poor survival of patients with PDA has been attributed to a high rate of early metastasis and low efficacy of current therapies, which partly result from its complex immunosuppressive tumor microenvironment. Previous studies from our group and others have shown that tumor-associated macrophages (TAMs) are instrumental in maintaining immunosuppression in PDA. Here, we explored the role of Notch signaling, a key regulator of immune response, within the PDA microenvironment. We identified Notch pathway components in multiple immune cell types within human and mouse pancreatic cancer. TAMs, the most abundant immune cell population in the tumor microenvironment, express high levels of Notch receptors with cognate ligands such as JAG1 expressed on tumor epithelial cells, endothelial cells and fibroblasts. TAMs with activated Notch signaling expressed higher levels of immunosuppressive mediators including arginase 1 (Arg1) suggesting that Notch signaling plays a role in macrophage polarization within the PDA microenvironment. Combination of Notch inhibition with PD-1 blockade resulted in increased cytotoxic T cell infiltration, tumor cell apoptosis, and smaller tumor size. Our work implicates macrophage Notch signaling in the establishment of immunosuppression and indicates that targeting the Notch pathway may improve the efficacy of immune-based therapies in PDA patients.

cancer biology↗

bioRxiv2022

Wildlife exposure to SARS-CoV-2 across a human use gradient

Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to captive animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections to date are found in a single species, the white-tailed deer. The extent of SARS-CoV-2 exposure among wildlife species and the factors that influence wildlife transmission risk remain unknown. We sampled 23 wildlife species for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We detected SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.

ecology↗

bioRxiv2022

Rieske FeS overexpression in tobacco provides increased abundance and activity of Cytochrome b6f

Photosynthesis is fundamental for plant growth and yield. The Cytochrome b6f complex catalyses a rate-limiting step in thylakoid electron transport and therefore represents an important point of regulation of photosynthesis. Here we show that overexpression of a single core subunit of Cytochrome b6f, the Rieske FeS protein, led to up to a 40% increase in the abundance of the complex in Nicotiana tabacum (tobacco) and was accompanied by an enhanced in vitro Cytochrome f activity, indicating a full functionality of the complex. Analysis of transgenic plants overexpressing Rieske FeS by the light-induced fluorescence transients technique revealed a more oxidised primary quinone acceptor of Photosystem II (QA) and plastoquinone pool and a faster electron transport from the plastoquinone pool to Photosystem I upon changes in irradiance, compared to control plants. A faster establishing of qE, the energy-dependent component of non-photochemical quenching, in transgenic plants suggested a more rapid build-up of the transmembrane proton gradient, also supporting the increased in vivo Cytochrome b6f activity. However, there was no consistent increase in steady-state rates of electron transport or CO2 assimilation in plants overexpressing Rieske FeS grown in either laboratory conditions or in field trials, suggesting that the in vivo activity of the complex was only transiently increased upon changes in irradiance. Our results show that overexpression of Rieske FeS in tobacco enhances abundance of functional Cytochrome b6f and electron transport capacity and may have a potential to increase plant productivity if combined with other traits. One-sentence summaryIncreased abundance of Cytochrome b6f complex leads to transient increases in photosynthetic electron transport rate in tobacco.

plant biology↗

bioRxiv2021

Extrinsic KRAS signaling shapes the pancreatic microenvironment through fibroblast reprogramming.

Oncogenic KRAS is the hallmark mutation of human pancreatic cancer and a driver of tumorigenesis in genetically engineered mouse models of the disease. While the tumor cell-intrinsic effects of oncogenic Kras expression have been widely studied, its role in regulating the extensive pancreatic tumor microenvironment is less understood. Using a genetically engineered mouse model of inducible and reversible oncogenic Kras expression and a combination of approaches that include mass cytometry and single cell RNA sequencing, we have discovered that non-cell autonomous (i.e., extrinsic) oncogenic KRAS signaling reprograms pancreatic fibroblasts, activating an inflammatory gene expression program. As a result, fibroblasts become a hub of extracellular signaling, mediating the polarization and function of pro-tumorigenic myeloid cells while also preventing tissue repair. Our study provides fundamental new knowledge on the mechanisms underlying the formation of the fibroinflammatory stroma in pancreatic cancer and highlights stromal pathways with the potential to be exploited therapeutically.

cancer biology↗

bioRxiv2021

Latent gammaherpesvirus exacerbates arthritis and requires age-associated B cells

Epstein-Barr virus (EBV) infection is associated with rheumatoid arthritis (RA) in adults, though the nature of the relationship remains unknown. Herein, we examine the contribution of viral infection to the severity of arthritis in mice. We provide the first evidence that latent gammaherpesvirus infection enhances clinical arthritis, modeling EBVs role in RA. Mice latently infected with a murine analog of EBV, gammaherpesvirus 68 ({gamma}HV68), develop more severe collagen-induced arthritis and a Th1-skewed immune profile reminiscent of human disease. We demonstrate that disease enhancement requires viral latency and is not due to active virus stimulation of the immune response. Age-associated B cells (ABCs) are associated with several human autoimmune diseases, including arthritis, though their contribution to disease is not well understood. Using ABC knockout mice, we provide the first evidence that ABCs are mechanistically required for viral enhancement of disease, thereby establishing that latent gammaherpesvirus infection stimulates ABCs to provoke arthritis. Conflict of interest statementThe authors have declared that no conflict of interest exists.

immunology↗

bioRxiv2021

Transcriptome variation in human tissues revealed by long-read sequencing

Regulation of transcript structure generates transcript diversity and plays an important role in human disease. The advent of long-read sequencing technologies offers the opportunity to study the role of genetic variation in transcript structure. In this paper, we present a large human long-read RNA-seq dataset using the Oxford Nanopore Technologies platform from 88 samples from GTEx tissues and cell lines, complementing the GTEx resource. We identified just under 100,000 new transcripts for annotated genes, and validated the protein expression of a similar proportion of novel and annotated transcripts. We developed a new computational package, LORALS, to analyze genetic effects of rare and common variants on the transcriptome via allele-specific analysis of long reads. We called allele-specific expression and transcript structure events, providing novel insights into the specific transcript alterations caused by common and rare genetic variants and highlighting the resolution gained from long-read data. We were able to perturb transcript structure upon knockdown of PTBP1, an RNA binding protein that mediates splicing, thereby finding genetic regulatory effects that are modified by the cellular environment. Finally, we use this dataset to enhance variant interpretation and study rare variants leading to aberrant splicing patterns.

genomics↗

bioRxiv2020

Simultaneous stimulation of RuBP regeneration and electron transport increases productivity and water use efficiency under field conditions

Previous studies have demonstrated that independent stimulation of either electron transport or RuBP regeneration can increase the rate of photosynthetic carbon assimilation and plant biomass. In this paper, we present evidence that a multi-gene approach to simultaneously manipulate these two processes provides a further stimulation of photosynthesis. We report on the introduction of the cyanobacterial bifunctional enzyme fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase or overexpression of the plant enzyme sedoheptulose-1,7-bisphosphatase, together with expression of the red algal protein cytochrome c6, and show that a further increase in biomass accumulation under both glasshouse and field conditions can be achieved. Furthermore, we provide evidence that the simultaneous stimulation of electron transport and RuBP regeneration can lead to enhanced intrinsic water use efficiency under field conditions. One sentence summarySimultaneous stimulation of RuBP regeneration and electron transport results in improvements in biomass yield in glasshouse and field grown tobacco.

plant biology↗