Biology subjects

McFarland, J.

Publications and source records attributed to McFarland, J..

8 recordsLinked to original sources

bioRxiv2026

Fpk1 regulates Cdr1 expression and ergosterol homeostasis in Nakaseomyces glabratus (Candida glabrata) during azole exposure

Azoles remain the most common antifungal therapy worldwide. However, Nakaseomyces glabratus (previously named Candida glabrata) has a high intrinsic tolerance against azole drugs. The organism can also accrue additional chromosomal mutations to elevate its resistant level during treatment. These genetic alterations often result in overexpression of the ABC transmembrane transporter Cdr1, which has been shown to directly transport drugs out of the fungal cells. Another resistant mechanism is the upregulation of the ergosterol biosynthesis pathway, which is the direct target of azoles. Although the mechanisms of azole resistance in N. glabratus are well defined, knowledge of their regulation remains limited. Here, we show that the protein kinase Fpk1 is required for optimal azole response in vitro and in an in vivo mouse infection model. Loss of Fpk1 gene or its kinase function significantly enhances azole sensitivity in both azole-susceptible and -resistant clinical isolates. Fpk1 function is required for optimal expression of Cdr1 upon azole challenge. It also influences the intracellular trafficking of ergosterol, without affecting its biosynthesis. Together, our data demonstrates the important role of Fpk1 function in the N. glabratus azole response and characterizes it as a new regulator of the efflux pump and ergosterol biosynthesis pathways. IMPORTANCEAntifungal treatment against life-threatening bloodstream Candida infection remains limited to azoles, echinocandins, and polyenes. Among them, azoles are the most prescribed therapy worldwide. However, the pathogenic yeast Nakaseomyces glabrataus has a high level of resistance against azoles (> 10%) (1). This often complicates treatment and increases mortality and morbidity rates. Therefore, understanding the mechanism of azole resistance would reinforce the treatment strategy and bolster future therapy development. Here, we identify the protein kinase Fpk1 as an important regulator of the drug efflux plump and ergosterol biosynthesis pathways. Disruption of the Fpk1 function significantly enhances the azole efficacy in vitro and in a mouse model of Candida systemic infection. Protein kinases are druggable targets, and our data presents Fpk1 as a viable candidate for future antifungal development.

microbiology↗

bioRxiv2022

The Free Association Sessions: Perspectives on a Novel Teaching Platform by Final Year Medical Students and Basic Specialist Trainees in Psychiatry.

IntroductionNotwithstanding the many advantages of outcomes-based education within Psychiatry placements in Medical School and Basic Specialist Training within the College of Psychiatry of Ireland, there is limited protected time for broad Reflective Practice that appreciates the complexity of working in the Mental Health setting. Furthermore, there are limitations to the current model of restricting Reflective Practice sessions to the Balint Group Format. MethodsA novel programme of structured Reflective Practice was offered to students in the School of Medicine in The University of Limerick and trainees in the Mid-West Deanery. Six student and fourteen trainee participants were subsequently invited to provide perspectives on the programme via Focus Groups. The study employed an inductive latent phenomenological approach for analysis of qualitative data. ResultsFive major themes emerged: These related to the teaching environment, personal identity, complexity, awareness of cognitive dissonance and the structure of the sessions. There were a number of different perceptions, relating to the participants stage of training. ConclusionsThere was evidence that the structured reflective sessions created a comfortable environment, addressed hierarchy issues and facilitated wide-ranging opportunities for reflective practice, with an observed increased appreciation for complexity in Psychiatry. There was apparent tension between controlling content and facilitating the form of group process. Nonetheless, the structure appeared more approachable for medical students and those early in training.

scientific communication and education↗

bioRxiv2022

Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries

Reducing disparities is critical to promote equity of access to precision treatments for all patients with cancer. While socioenvironmental factors are a major driver behind such disparities, biological differences also are likely to contribute. The prioritization of cancer drug targets is foundational for drug discovery, yet whether ancestry-related signals in target discovery pipelines exist has not been systematically explored due to the absence of data at the appropriate scale. Here, we analyzed data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models as part of the Cancer Dependency Map to identify ancestry-associated genetic dependencies. Surprisingly, we found that most putative associations between ancestry and dependency arose from artifacts related to germline variants that are present at different frequencies across ancestry groups. In 2-5% of genes profiled in each cellular model, germline variants in sgRNA targeting sequences likely reduced cutting by the CRISPR/Cas9 nuclease. Unfortunately, this bias disproportionately affected cell models derived from individuals of recent African descent because their genomes tended to diverge more from the consensus genome typically used for CRISPR/Cas9 guide design. To help the scientific community begin to resolve this source of bias, we report three complementary methods for ancestry-agnostic CRISPR experiments. This report adds to a growing body of literature describing ways in which ancestry bias impacts cancer research in underappreciated ways.

cancer biology↗

bioRxiv2022

Evaluation of Postgraduate Educational Environment of Doctors Training in Psychiatry: a mixed method study

IntroductionEducational Environment (EE) is of paramount importance in Medical Education, but can be intangible and hard to clearly determine. Professional satisfaction and patient care improve in a pleasant learning environment; where postgraduate physicians are encouraged, suitably supervised, and fostered. A negative learning environment can be detrimental to trainees and teams morale and can jeopardize the multidisciplinary working relationship. ObjectivesThe objective of this study was to measure the Educational Environment (EE) of Psychiatry postgraduate training in the Midwest of Ireland training Deanery; what aspects of training are working well and what areas are seen as not optimal. MethodsThis study took place between April and June 2021. A mixed methods approach was adopted, using the Postgraduate Hospital Educational Environment Measure (PHEEM) and semi-structured one-to-one interviews. ResultsResponse rate was 88% (n=22). The total PHEEM score was 105.64{+/-}23.52, indicating a postgraduate EE with more positive than negative aspects, but with room for improvement. There were no differences in overall PHEEM and subscale scores between trainees gender, training grades or years of working experience. Three themes were identified that contribute to trainees perception of EE: the commitment of the trainees supervisors to the role they play in trainees overall development, the clinical workload of the trainee, and the day-to-day working conditions of the trainee. Definite disparities between work placements were evident in the collected data across these three themes. ConclusionsAlthough the training program had an overall positive EE, specific answers and interview themes indicated some areas of weakness that may contribute to trainee dissatisfaction and possible burnout. Planned interventions targeting these areas and tracking changes in EE and burnout rates over time may be useful measures going forward. Declaration of InterestNone

scientific communication and education↗

bioRxiv2021

Chronos: a CRISPR cell population dynamics model

CRISPR loss of function screens are a powerful tool to interrogate cancer biology but are known to exhibit a number of biases and artifacts that can confound the results, such as DNA cutting toxicity, incomplete phenotype penetrance and screen quality bias. Computational methods that more faithfully model the CRISPR biological experiment could more effectively extract the biology of interest than typical current methods. Here we introduce Chronos, an algorithm for inferring gene knockout fitness effects based on an explicit model of the dynamics of cell proliferation after CRISPR gene knockout. Chronos is able to exploit longitudinal CRISPR data for improved inference. Additionally, it accounts for multiple sources of bias and can effectively share information across screens when jointly analyzing large datasets such as Project Achilles and Score. We show that Chronos outperforms competing methods across a range of performance metrics in multiple types of experiments.

bioinformatics↗

bioRxiv2020

Post-perturbational transcriptional signatures of cancer cell line vulnerabilities

While chemical and genetic viability screens in cancer cell lines have identified many promising cancer vulnerabilities, simple univariate readouts of cell proliferation fail to capture the complex cellular responses to perturbations. Complementarily, gene expression profiling offers an information-rich measure of cell state that can provide a more detailed account of cellular responses to perturbations. Relatively little is known, however, about the relationship between transcriptional responses to per-turbations and the long-term cell viability effects of those perturbations. To address this question, we integrated thousands of post-perturbational transcriptional profiles from the Connectivity Map with large-scale screens of cancer cell lines viability response to genetic and chemical perturbations. This analysis revealed a generalized transcriptional signature associated with reduced viability across perturbations, which was consistent across post-perturbation time-points, perturbation types, and viability datasets. At a more granular level, we lay out the landscape of treatment-specific expression-viability relationships across a broad panel of drugs and genetic reagents, and we demonstrate that these post-perturbational expression signatures can be used to infer long-term viability. Together, these results help unmask the transcriptional changes that are associated with perturbation-induced viability loss in cancer cell lines.

bioinformatics↗

bioRxiv2020

Gene expression has more power for predicting in vitro cancer cell vulnerabilities than genomics

Achieving precision oncology requires accurate identification of targetable cancer vulnerabilities in patients. Generally, genomic features are regarded as the state-of-the-art method for stratifying patients for targeted therapies. In this work, we conduct the first rigorous comparison of DNA- and expression-based predictive models for viability across five datasets encompassing chemical and genetic perturbations. We find that expression consistently outperforms DNA for predicting vulnerabilities, including many currently stratified by canonical DNA markers. Contrary to their perception in the literature, the most accurate expression-based models depend on few features and are amenable to biological interpretation. This work points to the importance of exploring more comprehensive expression profiling in clinical settings.

cancer biology↗

bioRxiv2018

WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers

Summary paragraphSynthetic lethality, an interaction whereby the co-occurrence of two or more genetic events lead to cell death but one event alone does not, can be exploited to develop novel cancer therapeutics1. DNA repair processes represent attractive synthetic lethal targets since many cancers exhibit an impaired DNA repair pathway, which can lead these cells to become dependent on specific repair proteins2. The success of poly (ADP-ribose) polymerase 1 (PARP-1) inhibitors in homologous recombination-deficient cancers highlights the potential of this approach in clinical oncology3,4. Hypothesizing that other DNA repair defects would give rise to alternative synthetic lethal relationships, we asked if there are specific dependencies in cancers with microsatellite instability (MSI), which results from impaired DNA mismatch repair (MMR). Here we analyzed data from large-scale CRISPR/Cas9 knockout and RNA interference (RNAi) silencing screens and found that the RecQ DNA helicase WRN was selectively essential in MSI cell lines, yet dispensable in microsatellite stable (MSS) cell lines. WRN depletion induced double-strand DNA breaks and promoted apoptosis and cell cycle arrest selectively in MSI models. MSI cancer models specifically required the helicase activity, but not the exonuclease activity of WRN. These findings expose WRN as a synthetic lethal vulnerability and promising drug target in MSI cancers.

cancer biology↗