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Burke, D.

Publications and source records attributed to Burke, D..

10 recordsLinked to original sources

The Influence of Macrophages within the Tumor Microenvironment on Ovarian Cancer Growth and Response to Therapies

While the majority of ovarian cancer (OC) patients respond to front-line carboplatin/paclitaxel chemotherapy and surgical debulking, nearly all patients will develop platinum-resistance and recur. Our study investigates how tumor-associated macrophages (TAMs) within the tumor microenvironment (TME) affect chemotherapy outcomes using OC patient-derived organoids and humanized patient-derived xenografts (huPDX). In vitro macrophage migration assays demonstrate the selective recruitment of M2 polarized macrophages to OC organoids. M2 macrophages, but not M1 macrophages, increase OC organoid viability and reduce their sensitivity to paclitaxel in co-culture assays. Furthermore, we identified BMS777607, a receptor tyrosine kinase inhibitor, that is capable of repolarizing M2 macrophages in vitro and reduces organoid viability by a macrophage-dependent mechanism. In a platinum-sensitive humanized patient-derived xenograft (huPDX) model, the presence of human immune cells increased between-mouse variability in response to paclitaxel with two of four mice demonstrating tumor regrowth after two weeks of treatment. A TAM-targeted CSF-1R inhibitor, BLZ945 significantly reduced the total number of human immune cells within the ascites fluid of huPDX3 mice, but did not reduce tumor burden. However BLZ945 in combination with paclitaxel reduced tumor burden with no sign of regrowth. Our study demonstrates that patient-derived OC organoids and huPDX, are useful for evaluating the immunomodulatory effects of therapies and the influence of TAMs on response. huPDX models could serve as a robust platform for preclinical testing of novel anti-cancer treatments, providing insights into the complex interplay between immune cells and cancer therapeutics.

cancer biology↗

A genome-scale single cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines

Population-scale resources of genetic, molecular, and cellular information form the basis for understanding human genomes, charting the heritable basis of disease, and tracing the effects of mutations. Pooled perturbation assays applied to cellular models, probing the effect of many perturbations coupled with an scRNA-seq readout (Perturb-seq), are especially potent references for interpreting disease-linked mutations or gene expression changes. However, the utility of existing maps has been limited by the comprehensiveness of perturbations possible, and the relevance of their cell line context. Here, we present the first genome-scale CRISPR interference (CRISPRi) perturbation map with single-cell RNA sequencing readout across many human genetic backgrounds in human pluripotent cells. To do so, we establish large-scale CRISPRi screening in human induced pluripotent stem cells from healthy donors, using over 20,000 guide RNAs to target 7,226 genes across 34 cell lines from 26 genetic backgrounds, and gather expression data from nearly 2 million cells. We comprehensively map trans expression changes induced by the target knockdowns, which complement co-expression patterns in unperturbed cells and facilitate the functional annotation of target genes to biological processes and complexes. Consistency of targeting protein complex members point to protein complexes as a nexus for aggregating transcriptional variation, revealing novel interaction partners. We characterise variation in perturbation effects across donors, with expression quantitative trait loci linked to higher genetic modulation of perturbation effects but overall low replication of trans effects due to knockdown of their corresponding cis regulators. This study pioneers population-scale CRISPR perturbations with single cell readouts that will fuel foundation models for the future of effective modulation of cellular disease phenotypes.

genetics↗

Organoid Models Derived from Primary Tumors and Patient-Derive Xenograft Tumors Reflect Platinum Sensitivity of Ovarian Cancer Patients

BackgroundOvarian cancer (OC) remains the deadliest gynecological cancer, primarily due to late-stage diagnosis and high rates of chemotherapy resistance and recurrence. Lack of representative preclinical models complicate the challenges of discovering effective therapies, especially for platinum-resistant OC. Patient-derived xenograft (PDX) models maintain the genetic characteristics of the original tumor and are ideal for testing candidate therapies in vivo, but their high cost limits their feasibility for high-throughput drug screening. Organoid models mimic the tumors 3D structure and preserve intra-tumoral heterogeneity. While organoids established directly from primary patient tumors are the optimal model for personalized drug response studies, the supply of primary tissue is often limited. Patient-derived xenograft tumors can be passaged in mice and provide a renewable source of cancer cells for organoids. This study aimed to determine if PDX-derived organoids (PDXOs) can reflect patient responses to chemotherapy similarly to primary patient-derived organoids (PDOs). Methods3D tumor organoid cultures were established from paired primary OC and PDX samples. Organoid viability after 72-hour treatment with paclitaxel (PTX), carboplatin (CBDCA), or their combination was compared between organoids derived directly from the patient or from the PDX models. The in vitro drug responses of PDXOs and PDOs were then compared to defined patient clinical responses: platinum-sensitive (initial response to standard platinum/taxol therapy lasting >6 months post-treatment), platinum-resistant (initial response to standard chemotherapy lasting < 6 months), or platinum-refractory (no initial response to standard chemotherapy). ResultsIn drug response assays, PDXOs and PDOs demonstrated similar sensitivity to standard chemotherapy and also reliably reflected patient responses based on the clinical designation of platinum sensitivity. While organoids derived from the ascites were smaller with a denser morphology, their drug response mirrored that of the organoids derived from solid tumor. Platinum-sensitive cases exhibited significant reductions (around 50% reduction) in organoid viability when treated with carboplatin, paclitaxel, or their combination. Platinum-resistant or refractory organoids showed little to no reduction in viability with carboplatin or paclitaxel monotherapy or the combination. Organoids derived from one platinum-resistant case did show a small but significant reduction in viability with single-agent paclitaxel, suggesting that organoid models might predict response to second-line paclitaxel therapy. ConclusionThis study demonstrates that PDXOs respond to drugs similarly to PDOs and confirms that both models effectively mirror patient response to standard chemotherapy. This highlights the potential of PDXOs as renewable models for screening novel therapies and developing personalized strategies in OC. SIMPLE SUMMARYOvarian cancer (OC) remains the most lethal gynecological cancer, largely due to its late diagnosis and resistance to chemotherapy. In order to identify novel therapies to treat ovarian cancer, we need better in vitro models that represent the genetic heterogeneity of the patient population. This study evaluates patient-derived organoid models established either directly from patient samples (PDOs) or from patient samples that were first passaged in mice and are referred to as patient-derived xenograft organoids (PDXOs). For each patient, organoid response to standard chemotherapy based on organoid viability assays was compared to the patients clinical designation of platinum sensitivity, which is categorized as platinum-sensitive, platinum-resistant, or platinum-refractory based on their response to standard chemotherapy. We demonstrated that both PDOs and PDXOs accurately reflect the patients clinical designation, suggesting their utility as effective models for testing new therapies and personalizing treatment. Importantly, by providing a renewable source of patient-derived cells, PDXOs extend the utility of each sample, making organoids essential tools for developing and refining personalized treatment strategies in oncology.

cancer biology↗

Predicted mechanistic impacts of human protein missense variants

Genome sequencing efforts have led to the discovery of tens of millions of protein missense variants found in the human population with the majority of these having no annotated role and some likely contributing to trait variation and disease. Sequence-based artificial intelligence approaches have become highly accurate at predicting variants that are detrimental to the function of proteins but they do not inform on mechanisms of disruption. Here we combined sequence and structure-based methods to perform proteome-wide prediction of deleterious variants with information on their impact on protein stability, protein-protein interactions and small-molecule binding pockets. AlphaFold2 structures were used to predict approximately 100,000 small-molecule binding pockets and stability changes for over 200 million variants. To inform on protein-protein interfaces we used AlphaFold2 to predict structures for nearly 500,000 protein complexes. We illustrate the value of mechanism-aware variant effect predictions to study the relation between protein stability and abundance and the structural properties of interfaces underlying trans protein quantitative trait loci (pQTLs). We characterised the distribution of mechanistic impacts of protein variants found in patients and experimentally studied example disease linked variants in FGFR1.

bioinformatics↗

CCQM-P199: Interlaboratory comparability study of HIV-1 RNA copy number quantification

Infection with human immunodeficiency virus (HIV)-1 leads to acquired immunodeficiency syndrome (AIDS) if left untreated. According to UN figures, approximately 39 million people globally were living with HIV in 2022, with 76% of those individuals accessing antiretroviral therapy. Measurement of plasma viral RNA load using calibrated nucleic acid amplification tests (like reverse transcription quantitative PCR, RT-qPCR) is routinely performed to monitor response to treatment and ultimately prevent viral transmission. RNA quantities measured by commercial tests can vary over many orders of magnitude, from trace single copy levels to, in cases, over 109 /mL of plasma, presenting an analytical challenge for calibrating across a broad measurement range. Interlaboratory study CCQM-P199 "HIV-1 RNA copy number quantification" (April to September 2019) was conducted under the auspices of the Consultative Committee for Amount of Substance (CCQM) Nucleic Acid analysis Working Group (NAWG), with the aims of supporting national metrology institutes (NMIs) and designated institutes (DIs) development of the capacity and evaluating candidate reference measurement procedures for applied viral nucleic acid measurements. Thirteen laboratories participated in CCQM-P199 and were requested to report the RNA copy number concentration, expressed in copies per microliter, of the HIV-1 group specific antigen (gag) gene of in vitro transcribed RNA molecules at low ({approx} 103 /L) and high concentration ({approx} 109 /L) (Study Materials 1 and 2, linked by gravimetric dilution) and purified genomic RNA from cultured virus (Study Material 3). Study Materials 1 and 3 were measured by participants using one-step reverse transcription digital PCR (RT-dPCR) (Bio-Rad reagents) and/or two-step RT-dPCR with alternative cDNA synthesis reagents. Study Material 2 was measured by both RT-dPCR (one-step) (n = 4) and orthogonal methods: single molecule flow cytometric counting (n = 2), high performance liquid chromatograph (HPLC) (n = 1) and isotype dilution-mass spectrometry (ID-MS) (n = 1). Interlaboratory reproducibilities (expressed as %CV) were 21.4 %, 15.3 % and 22.0 % for Study Materials 1, 2 and 3 respectively. Analysis of overdispersion showed that the interlaboratory variation for all three Study Materials was not accounted for in their reported uncertainties, indicating uncharacterized sources of variation remain. Although the mean values of RT-dPCR and orthogonal method results were not statistically significantly different (p = 0.46), the extrapolated mean Study Material 2 results were higher than mean Study Material 1 results (1196 vs. 808 /L; p < 0.05). Follow-up analysis of Study Material 2 purity by ultra-performance liquid chromatography (UPLC) indicated higher molecular weight (MW) impurities constituted 16.6 % of the molecules, which are hypothesised to be the cause of the HPLC and ID-MS results being higher than the majority of Study Material 1 and 2 results. This study demonstrates that reproducible measurement of RNA templates was achieved by metrology laboratories, illustrating the potential of RT-dPCR combined with complimentary orthogonal approaches to support traceability and precision of contemporary methods for RNA quantification. This study also highlighted that detailed characterization of RNA materials and sources of bias affecting measurements such as RT efficiency is needed to further establish RT-dPCR as a primary reference measurement procedure for RNA copy number quantification.

molecular biology↗

TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

Transposable elements (TEs) replicate within genomes and are an active source of genetic variability in many species. Their role in immunity and domestication underscores their biological significance. However, analyzing TEs, especially within lesser-studied and wild populations, poses considerable challenges. To address this, we introduce TEPEAK, a simple and efficient approach to identify and characterize TEs in populations without any prior sequence or loci information. In addition to processing user-submitted genomes, TEPEAK integrates with the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) to increase cohort sizes or incorporate proximate species. Our application of TEPEAK to 256 horse genomes spanning 11 groups reaffirmed established genetic histories and highlighted disruptions in crucial genes. Some identified TEs were also detectable in species closely related to horses. TEPEAK paves the way for comprehensive genetic variation analysis in traditionally understudied populations by simplifying TE studies. TEPEAK is open-source and freely available at https://github.com/mrburke00/TEPEAK.

bioinformatics↗

Standardisation of cell-free DNA measurements: An International Study on Comparability of Low Concentration DNA Measurements using cancer variants

For the impact of genomic testing from liquid biopsies to be maximized, mechanisms to ensure reproducible and comparable test performance will be required. This can be established and maintained through reference measurement procedures and materials with property values that are internationally comparable through traceability to a common standard. To achieve this objective, an interlaboratory study was organised to explore digital PCR (dPCR) for standardisation of cell-free DNA (cfDNA) quantification. Blinded samples of wild-type/variant mixtures of two DNA sequences (BRAF p.V600E single nucleotide variant or EGFR exon 19 deletion) were provided to 12 laboratories. Laboratories independently designed and applied dPCR assays to determine absolute and relative quantities, with no guidance provided to harmonise the approach. The mean and coefficient of variation (CV) of copy number concentrations for variant sequences were 18 copies/L (CV 7.2%) (BRAF variant sample) and 9 copies/L (CV 25%) (EGFR variant sample) while the mean variant allele frequencies (vAF) were 8.0% (CV 5.3%) and 0.080% (CV 29%) respectively. This study demonstrated that dPCR was capable of exceptional technical accuracy for variant copy number concentration and vAF, even when different assays and platforms were used. This implies that dPCR offers a unique analytical methodology that can be deployed globally in supporting comparability for cfDNA testing based on the existing framework of the International System of units of measurement.

genetics↗

Humanized NBSGW PDX Models of Disseminated Ovarian Cancer Recapitulate Key Aspects of the Tumor Immune Environment within the Peritoneal Cavity

The importance of the immune microenvironment in ovarian cancer progression, metastasis, and response to therapies has become increasingly clear, especially with the new emphasis on immunotherapies. In order to leverage the power of patient-derived xenograft (PDX) models within a humanized immune microenvironment, three ovarian cancer PDX were grown in humanized NBSGW mice engrafted with human CD34+ cord blood-derived hematopoietic stem cells. Analysis of cytokine levels in the ascites fluid and infiltrating immune cells in the tumors demonstrated that these humanized PDX (huPDX) established an immune tumor microenvironment similar to what has been reported for ovarian cancer patients. The lack of human myeloid cell differentiation has been a major setback for humanized mouse models, but our analysis shows that PDX engraftment increases the human myeloid population in the peripheral blood. Analysis of cytokines within the ascites fluid of huPDX revealed high levels of human M-CSF, a key myeloid differentiation factor as well as other elevated cytokines that have previously been identified in ovarian cancer patient ascites fluid including those involved in immune cell differentiation and recruitment. Human tumor-associated macrophages and tumor-infiltrating lymphocytes were detected within the tumors of humanized mice, demonstrating immune cell recruitment to tumors. Comparison of the three huPDX revealed certain differences in cytokine signatures and in the extent of immune cell recruitment. Our studies show that huNBSGW PDX models reconstitute important aspects of the ovarian cancer immune tumor microenvironment making this a superior approach for therapeutic trials.

cancer biology↗

A structural biology community assessment of AlphaFold 2 applications

Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods have led to protein structure predictions that have reached the accuracy of experimentally determined models. While this has been independently verified, the implementation of these methods across structural biology applications remains to be tested. Here, we evaluate the use of AlphaFold 2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modelling of interactions; and modelling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modelled when compared to homology modelling, identifying structural features rarely seen in the PDB. AF2-based predictions of protein disorder and protein complexes surpass state-of-the-art tools and AF2 models can be used across diverse applications equally well compared to experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life science research.

biophysics↗

Unaffected functional recovery after spinal cord contusions at different circadian times

The circadian rhythms of gene expression drive diurnal oscillations of physiological processes that determine the acute injury response including immunity, inflammation and hemostasis. While outcomes of various acute injuries are affected by the time of day at which the original insult occurred, such diurnal influences on recovery after spinal cord injury (SCI) are unknown. We report that several key regulators of circadian gene expression are differentially expressed in uninjured spinal cord tissue of naive mice at Zeitgeber time 1 (ZT1) or ZT12, where ZT0 or ZT12 are times when lights are turned on or off, respectively. However, mice that received moderate, T9 contusive SCI at ZT0 or ZT12 showed similar recovery of locomotion as determined using the ladder walking test and the Basso mouse scale (BMS) over a 6 week post-injury period. Consistent with those findings, terminal histological analysis revealed no significant differences in white matter sparing at the injury epicenter. Therefore, locomotor recovery after thoracic contusive SCI is not affected by the time of day at which the neurotrauma occurred at least when comparing the beginning to the end of the mouse active period.

neuroscience↗