Biology subjects

Costello, J.

Publications and source records attributed to Costello, J..

16 recordsLinked to original sources

bioRxiv2026

An AI-Powered Trisomy 21 Research Assistant

Down syndrome, caused by trisomy 21, increases the risk of diverse co-occurring conditions. With more than 34,000 related publications indexed in PubMed as of early 2026, keeping pace with this expanding literature is challenging. While general-purpose large language models are widely used for information retrieval, they often rely on broad training data rather than specific evidence. Retrieval-augmented generation (RAG) improves rigor and reliability of responses by linking model outputs to source texts. In research, source texts are peer-reviewed articles. Standard implementations treat all manuscript sections equally, allowing background text to rank as highly as experimental results. To focus model outputs on experimentally supported responses, we developed the T21 Research Assistant, a section-aware RAG system that prioritizes Results sections to ground responses in primary experimental evidence. The system draws exclusively from 1,789 open-access Down syndrome publications from PubMed Central, including 327 NIH INCLUDE-funded studies, and uses a multistage pipeline for query validation, retrieval, reranking, synthesis, and citation verification. Built on NVIDIA Nemotron models, it generates structured, cited responses. Evaluation using expert-curated questions demonstrated strong performance, achieving a BERTScore F1 of 0.712 and recall of 0.758, comparable to or exceeding leading proprietary and open-source models. T21 Research Assistant is available at: https://bioinformatics.cuanschutz.edu/t21-res-assi/

bioinformatics↗

bioRxiv2026

Estradiol Reprograms Microglia to Create an Immune-Suppressed Niche Permissive to Breast Cancer Brain Metastasis

BackgroundYoung age is an independent risk factor for the development of breast cancer brain metastases (BM). Prior work showed that 17{beta}-estradiol (E2), the predominant premenopausal hormone, promotes BM of tumors intrinsically unresponsive to E2, in part through modulating estrogen receptor-alpha expressing (ER) glial cells. However, how E2 reshapes the brain tumor microenvironment (TME), particularly microglia-mediated immunity, and its impact to BM progression remains unclear. MethodsscRNA sequencing and multiparametric flow cytometry were used to define the impact of E2 and E2-suppression on brain immune-cell populations across different stages of BM progression using spontaneous and experimental models of BM. Depletion of microglia and T cell co-cultures were used to study microglias role in E2-induced BM. The effects of E2-suppression alone or in combination with whole brain radiotherapy were tested in preclinical models mimicking late-stage BM. ResultsE2 repressed immune surveillance and immune activation programs in microglia from early to late stages of brain metastatic progression, suppressing recruitment of effector immune cells to BM. Estrogen suppression, in turn reactivated anti-tumoral signaling in microglia and increased recruitment of effector immune cells to the brain. Microglia from E2-stimulated BM-bearing mice showed decreased ability to induce interferon cytotoxic function and expansion of activated T cells. Conversely, E2-suppression reactivated an effective anti-tumoral response and synergized with RT to significantly decrease BM progression. ConclusionThese findings reveal a previously unrecognized mechanism by which E2 accelerates BC-BM progression through microglial immunosuppression and support evaluation of endocrine therapies as adjunct treatments for ER- brain metastases. Importance of the StudyStandard of care for BM includes stereotactic radiosurgery (SRS) alone or in combination with surgery, systemic chemotherapy or targeted therapies. Our studies show that ovariectomy (which eliminates ovarian E2) and aromatase inhibitors (AIs, which eliminate peripheral E2 synthesis) reduce progression of BM when used in combination with WBRT and in immuno-competent models. We demonstrate E2 promotes an immunosuppressive brain microenvironment from early stages of metastatic progression, in part through modulation of myeloid cells and repression of recruitment of effector T cells to the brain. Thus, these studies suggest that FDA-approved E2-depletion therapies (aromatase inhibitors and selective-estrogen modulators) could be used in combination with brain irradiation to decrease BM progression.

cancer biology↗

bioRxiv2025

Loss of the Y chromosome drives cancer metabolic reprogramming

Metabolic reprogramming promotes cancer aggressiveness and an immune-suppressive tumor microenvironment. Loss of the Y chromosome (LOY) drives both phenotypes in bladder cancer (BC). We investigated the hypothesis that LOY leads to metabolic reprogramming using untargeted metabolomic profiling of human BC cells and analysis of pan-cancer transcriptomic datasets. This revealed that aerobic glycolysis is activated in LOY BC cells. Since prior work showed that expression of collagen receptor DDR2 drives BC progression and DDR2 is a regulator of tumor metabolism, we investigated if DDR2 is implicated in metabolic reprogramming of LOY-tumors. Analysis of scRNAseq data from 251 patients with 12 tumor types found that LOY and DDR2 expression promote aerobic glycolysis, and this was confirmed by metabolomics. Deletion of DDR2 in LOY BC cells reduced glycolytic flux, inhibited cell proliferation, reduced EMT and stemness features, and promoted apoptosis. Our data provide a rationale for using LOY as a tumor selection biomarker for DDR2 targeted therapeutics. TeaserLoss of the Y chromosome augments glycolytic metabolism in bladder cancer cells, and this is in part dependent on the collagen receptor DDR2.

cancer biology↗

bioRxiv2025

Tumor-initiating genetics and therapy drive divergent molecular evolution in IDH-mutant gliomas

Astrocytomas and oligodendrogliomas are slow-growing and treatment-sensitive IDH-mutant gliomas diagnosed at ages 30-50. Local tumor regrowth and treatment resistance is inevitable resulting in 3-10 year astrocytoma and up to >20 years oligodendroglioma survival. We sought to identify genetic changes associated with tumor evolution in response to therapy through multi-timepoint whole-genome/whole-exome sequencing of 206 IDH-mutant glioma patient samples collected through the Glioma Longitudinal Analysis (GLASS) Consortium. We validated known genomic markers of tumor progression, including hypermutation and CDKN2A homozygous deletion, and discovered novel genetic alterations that distinguish the response to treatment in astrocytomas compared to oligodendrogliomas. Point mutations in PIK3CA, PIK3R1, and NOTCH1 were newly acquired in recurrent oligodendrogliomas and associated with increased mutation rates. Focal oncogene amplifications, together with CDKN2A homozygous deletions, were associated with an increase in recurrence-specific chromosomal imbalances in astrocytomas. Mutational signature analysis revealed additional differences and detected enrichment for the SBS11, and SBS119 mutational signatures after temozolomide treatment in both IDH-glioma subtypes, whereas astrocytomas showed increased ID8 signatures after radiotherapy. These signatures suggest that the genomes of oligodendroglioma and astrocytoma adapt to the selective pressures of tumor progression and treatment in different ways. However, in both IDH-mutant glioma subtypes we observed a convergence of acquired driver gene alterations with genome-wide changes and worse patient outcomes, signaling selection of treatment-refractory clones. By identifying new prognostic markers and delineating the genomic divergence of oligodendrogliomas and astrocytomas after diagnosis, our results suggest that different DNA damage response mechanisms are engaged following chemo- and radiation therapy.

cancer biology↗

bioRxiv2024

Feeding Rates of Sessile and Motile Ciliates are Hydrodynamically Equivalent

Motility endows microorganisms with the ability to swim to nutrient-rich environments, but many species are sessile. Existing hydrodynamic arguments in support of either strategy, to swim or to attach and generate feeding currents, are often built on a limited set of experimental or modeling assumptions. Here, to assess the hydrodynamics of these "swim" or "stay" strategies, we propose a comprehensive methodology that combines mechanistic modeling with a survey of published shape and flow data in ciliates. Model predictions and empirical observations show small variations in feeding rates in favor of either motile or sessile cells. Case-specific variations notwithstanding, our overarching analysis shows that flow physics imposes no constraint on the feeding rates that are achievable by the swimming versus sessile strategies - they can both be equally competitive in transporting nutrients and wastes to and from the cell surface within flow regimes typically experienced by ciliates. Our findings help resolve a long-standing dilemma of which strategy is hydrodynamically optimal and explain patterns occurring in natural communities that alternate between free swimming and temporary attachments. Importantly, our findings indicate that the evolutionary pressures that shaped these strategies acted in concert with, not against, flow physics.

biophysics↗

bioRxiv2022

Zinc Finger MYND-Type Containing 8 (ZMYND8) is epigenetically regulated in mutant Isocitrate Dehydrogenase 1 (IDH1) glioma to promote radioresistance

Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. Establishment of glioma-specific methylation patterns by mIDH1 reprogramming drives oncogenic features of cancer metabolism, stemness and therapeutic resistance. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1. Treatment of glioma cells with mIDH1 specific inhibitor AGI-5198, upregulated gene networks involved in replication stress. Specifically, we found that the expression of ZMYND8, a regulator of DNA damage response was decreased in three patient-derived glioma cell cultures (GCC) after treatment with AGI-5198. ZMYND8 functions as a chromatin reader to modulate enhancer activity and recruit DNA repair machinery. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 knockout (KO) exhibit significant phosphorylation of ATM and sustained {gamma}H2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. The accumulation of DNA damage in ZMYND8 KO mIDH1 GCCs promoted the phosphorylation of cell cycle checkpoint proteins Chk1 and Chk2. In addition, the recruitment of ZMYND8 to sites of DNA damage has been shown to be PARP- dependent. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. Translational RelevanceOur understanding of radioresistance mechanisms in patient-derived glioma cell cultures (GCC) that endogenously express mIDH1-R132H are limited. We have uncovered a novel gene target Zinc Finger MYND-Type Containing 8 (ZMYND8) that is downregulated following treatment of human mIDH1 GCCs with mIDH1 specific inhibitors. We demonstrate that suppression of ZMYND8 expression by shRNA knockdown or genetic knockout reduces the cellular viability of mIDH1 GCCs to ionizing radiation (IR). Our findings reveal an epigenetic vulnerability of mIDH1 GCCs to ZMYND8 knockout (KO) which results in impaired resolution of IR-induced DNA damage and induction of cell cycle arrest. Additionally, ZMYND8 KO mIDH1 GCCs display increased radiosensitivity to inhibition of epigenetic regulators BRD4, HDAC, and PARP which could be mediated by enhanced replicative stress.

cancer biology↗

bioRxiv2022

The Voices of Medical Education Science: Describing the Published Landscape

IntroductionMedical education has been described as a dynamic and growing field, driven in part by its unique body of scholarship. The voices of authors who publish medical education literature have a powerful impact on the discourses of the community. While there have been numerous studies looking at aspects of this literature, there has been no comprehensive view of recent publications. MethodThe authors conducted a bibliometric analysis of all articles published in 24 medical education journals published between 2000-2020 to identify article characteristics, with an emphasis on author gender, geographic location, and institutional affiliation. This study replicates and greatly expands on two previous investigations by examining all articles published in these core medical education journals. ResultsThe journals published 37,263 articles with the majority of articles published in 2020 (n=3,957, 10.7%) and the least in 2000 (n=711, 1.9%) representing a 456.5% increase. The articles were authored by 139,325 authors of which 62,708 were unique. Males were more prevalent across all authorship positions (n=62,828; 55.7%) than females (n=49,975; 44.3%). Authors listed 154 country affiliations with the United States (n=42,236, 40.4%), United Kingdom (n=12,967, 12.4%), and Canada (n=10,481, 10.0%) most represented. Ninety-three countries (60.4%) were low- or middle-income countries accounting for 9,684 (9.3%) author positions. Few articles were written by multinational teams (n=3,765; 16.2%). Authors listed affiliations with 4,372 unique institutions. Across all author positions, 48,189 authors (46.1%) were affiliated with a top 200 institution, as ranked by the Times Higher Education ranking. DiscussionThere is a relative imbalance of author voices in medical education. If the field values a diversity of perspectives, there is considerable opportunity for improvement.

scientific communication and education↗

bioRxiv2021

Pan-cancer imaging of TERT expression using deuterium magnetic resonance spectroscopy-based assessment of pyruvate metabolism

Telomerase reverse transcriptase (TERT) expression is indispensable for tumor immortality. Non-invasive methods of imaging TERT can, therefore, report on tumor proliferation and response to therapy. Here, we show that TERT expression is associated with elevated levels of the redox metabolite NADH in multiple cancers, including glioblastoma, oligodendroglioma, melanoma, neuroblastoma, and hepatocellular carcinoma. Mechanistically, TERT acts via the metabolic regulator FOXO1 to upregulate nicotinamide phosphoribosyl transferase, which is the key enzyme for NADH biosynthesis. Importantly, deuterium magnetic resonance spectroscopy (2H-MRS), which is a novel, clinically translatable metabolic imaging modality, can be leveraged for imaging TERT-linked NADH in preclinical tumor models in vivo. Since NADH is essential for pyruvate flux to lactate, 2H-MRS following administration of 2H-labeled pyruvate non-invasively visualizes TERT expression and reports on early response to therapy. Collectively, our study provides insights into the mechanisms of TERT-linked metabolic reprogramming and, importantly, establishes 2H-MRS as a pan-cancer strategy for imaging tumor immortality.

cancer biology↗

bioRxiv2020

From amazing work to I beg to differ - analysis of bioRxiv preprints that received one public comment till September 2019

While early commenting on studies is seen as one of the advantages of preprints, the nature of such comments, and the people who post them, have not been systematically explored. We analysed comments posted between 21 May 2015 and 9 September 2019 for 1,983 bioRxiv preprints that received only one comment. Sixty-nine percent of comments were posted by non-authors (n=1,366), and 31% by preprint authors (n=617). Twelve percent of non-author comments (n=168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (n=577, 42%), suggestions (n=399, 29%), or criticisms (n=226, 17%). Authors comments most commonly contained publication status updates (n=354, 57%), additional study information (n=158, 26%), or solicited feedback for the preprints (n=65, 11%). Our study points to the value of preprint commenting, but further studies are needed to determine the role that comments play in shaping preprint versions and eventual journal publications.

scientific communication and education↗

bioRxiv2020

Scoping reviews in medical education: A scoping review

PurposeThe purpose of this study was to characterize the extent, range, and nature of scoping reviews published in core medical education journals. In so doing, the authors identify areas for improvement in the conduct and reporting of scoping reviews, and highlight opportunities for future research. MethodThe authors searched PubMed for scoping reviews published between 1999 through April 2020 in 14 medical education journals. From each review, the authors extracted and summarized key bibliometric data, the rationales given for conducting a scoping review, the research questions, and key reporting elements as described in the PRISMA-ScR reporting guidelines. Rationales and research questions were mapped to the reasons for conducting a scoping review, as described by Arksey and OMalley. ResultsOne hundred and one scoping reviews were included. On average 10.1 scoping reviews (MED=4, SD=13.08) were published annually with the most reviews published in 2019 (n=42) in 13 of the included 14 journals reviewed. Academic Medicine published the most scoping reviews (n=28) overall. Authors described multiple reasons for undertaking scoping reviews, including to: summarize and disseminate research findings (n=77); examine the extent, range, and nature of research activity in a given area (n=74); and to analyze an emerging topic or heterogenous literature base (n=46). In 11 reviews there was alignment between the rationales for the scoping review and the stated research questions. No review addressed all elements of the PRISMA-ScR, with only a minority of authors publishing a protocol (n=2) or including stakeholders (n=20). Authors identified several shortcomings of scoping review methodology, including being unable to critically assess the included studies. ConclusionsMedical educators are increasingly conducting scoping reviews with a desire to characterize the literature on a topic. There is room for improvement in the reporting of scoping reviews, including the alignment of research questions, the creation and publishing of protocols, and the inclusion of external stakeholders in published works.

scientific communication and education↗

bioRxiv2020

Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding

Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of -synuclein, a dynamic protein linked to Parkinsons disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of -synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to -synuclein biology and pathobiology. We found that the conformation of -synuclein previously shown to drive yeast toxicity--an extended, membrane-bound helix--is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress -synuclein toxicity. Moreover, we find that sequence determinants of -synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that -synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.

biochemistry↗

bioRxiv2020

Brain capillary pericytes exert a substantial but slow influence on blood flow

The majority of the brains vasculature is comprised of intricate capillary networks lined by capillary pericytes. However, it remains unclear whether capillary pericytes contribute to blood flow control. Using two-photon microscopy to observe and manipulate single capillary pericytes in vivo, we find their optogenetic stimulation decreases lumen diameter and blood flow, but with slower kinetics than mural cells of upstream pial and pre-capillary arterioles. This slow, optogenetically-induced vasoconstriction was inhibited by the clinically-used vasodilator fasudil, a Rho kinase inhibitor that blocks contractile machinery. Capillary pericytes were also slower to constrict back to baseline following hypercapnia-induced dilation, and relax towards baseline following optogenetically-induced vasoconstriction. In a complementary approach, optical ablation of single capillary pericytes led to sustained local dilation and a doubling of blood cell flux in capillaries lacking pericyte contact. Altogether these data indicate that capillary pericytes contribute to basal blood flow resistance and slow modulation of blood flow throughout the capillary bed.

neuroscience↗

bioRxiv2019

Measuring chromosome conformation by fluorescence microscopy

Measurement of in-vivo chromosome conformations (structures) in single cells is a major technological goal of structural biology. If one could identify many genetic loci in a microscope image despite the limited palette of fluorescent colors used to label them, then the conformation could be solved at some resolution by connecting the dots. Computational tools for making this reconstruction are expected to produce near-perfect reconstructions when the number of fluorescent colors is high enough, irrespective of the number of loci assayed. Here we report the first experimental test of the performance of these reconstruction algorithms and check their ability to reconstruct experimentally-measured conformations. We also demonstrate the experimental metrics needed to assess reconstruction quality. Our results indicate that current sequential FISH experiments may be close to the point where the reconstructions are nearly flawless at some distance scales.

genomics↗

bioRxiv2019

GSEA-InContext Explorer: An interactive visualization tool for putting gene set enrichment analysis results into biological context.

SummaryGSEA-InContext Explorer is a Shiny app that allows users to perform two methods of gene set enrichment analysis (GSEA). The first, GSEAPreranked, applies the GSEA algorithm in which statistical significance is estimated from a null distribution of enrichment scores generated for randomly permuted gene sets. The second, GSEA-InContext, incorporates a user-defined set of background experiments to define the null distribution and calculate statistical significance. GSEA-InContext Explorer allows the user to build custom background sets from a compendium of over 5,700 curated experiments, run both GSEAPreranked and GSEA-InContext on their own uploaded experiment, and explore the results using an interactive interface. This tool will allow researchers to visualize gene sets that are commonly enriched across experiments and identify gene sets that are uniquely significant in their experiment, thus complementing current methods for interpreting gene set enrichment results.\n\nAvailability and implementationThe code for GSEA-InContext Explorer is available at: https://github.com/CostelloLab/GSEA-InContext_Explorer and the interactive tool is at: http://gsea-incontext_explorer.ngrok.io

bioinformatics↗

bioRxiv2018

GSEA-InContext: Identifying novel and common patterns in expression experiments

MotivationGene Set Enrichment Analysis (GSEA) is routinely used to analyze and interpret coordinate changes in transcriptomics experiments. For an experiment where less than seven samples per condition are compared, GSEA employs a competitive null hypothesis to test significance. A gene set enrichment score is tested against a null distribution of enrichment scores generated from permuted gene sets, where genes are randomly selected from the input experiment. Looking across a variety of biological conditions, however, genes are not randomly distributed with many showing consistent patterns of up- or down-regulation. As a result, common patterns of positively and negatively enriched gene sets are observed across experiments. Placing a single experiment into the context of a relevant set of background experiments allows us to identify both the common and experiment-specific patterns of gene set enrichment.\n\nResultsWe compiled a compendium of 442 small molecule transcriptomic experiments and used GSEA to characterize common patterns of positively and negatively enriched gene sets. To identify experiment-specific gene set enrichment, we developed the GSEA-InContext method that accounts for gene expression patterns within a user-defined background set of experiments to identify statistically significantly enriched gene sets. We evaluated GSEA-InContext on experiments using small molecules with known targets and show that it successfully prioritizes gene sets that are specific to each experiment, thus providing valuable insights that complement standard GSEA analysis.\n\nAvailability and ImplementationGSEA-InContext is implemented in Python. Code, the background expression compendium, and results are available at: https://github.com/CostelloLab/GSEA-InContext

bioinformatics↗

bioRxiv2017

Modeling heterogeneous populations using Boolean networks

Certain biological processes such as cancer development and immune activation are controlled by rare cellular events that are difficult to capture computationally through simulations of individual cells. Here we show that when cellular states are described using a Boolean network model, one can exactly simulate the dynamics of non-interacting, highly heterogeneous populations directly, without having to model the various subpopulations. This strategy captures even the rarest outcomes of the model with no sampling error. Our method can incorporate heterogeneity in both cell state and, by augmenting the model, the underlying rules of the network as well (i.e. mutations). We demonstrate our method by using it to simulate a heterogeneous population of Boolean networks modeling the T-cell receptor, spanning ~ 1020 distinct cellular states and mutational profiles.

systems biology↗