Biology subjects

Morgan, R. A.

Publications and source records attributed to Morgan, R. A..

5 recordsLinked to original sources

bioRxiv2025

A computational strategy to uncover fusion genes in prostate cancer cell lines

Fusion genes, chimeric transcripts formed by the merging of two distinct genes due to chromosomal structural changes (e.g., inversions or trans/cis-splicing), are established cancer drivers. Advances in genomic technologies, particularly RNA sequencing and improved fusion gene prediction algorithms, have significantly expanded our understanding of fusion genes in cancer. This chapter explores computational methods for identifying fusion genes through RNA sequencing data, using the TMPRSS2::ERG fusion in prostate cancer cell lines as a case study, and includes analysis of both fusion-positive and fusion-negative cell lines. To achieve high-confidence detection, three open-source fusion prediction tools, STAR-Fusion, FusionCatcher, and JAFFA are investigated. These tools were selected for their accessibility, active maintenance, and strong performance in benchmarking studies. Their sensitivity and accuracy in detecting TMPRSS2::ERG is systematically evaluated and validated, ensuring robust and high-resolution detection of fusion events.

bioinformatics↗

bioRxiv2025

A Precision Gene Engineered B Cell Medicine Producing Sustained Levels of Active Factor IX for Hemophilia B Therapy

Hemophilia B gene therapy treatments currently have not addressed the need for predictable, durable, active, and redosable factor IX (FIX). Unlike conventional gene therapy, engineered B Cell Medicines (BCMs) are durable, redosable, and titratable, and thus have the potential to address significant unmet needs in the Hemophilia B treatment paradigm. BE-101 is an autologous BCM comprised of expanded and differentiated B lymphocyte lineage cells genetically engineered ex vivo to secrete FIX-Padua. CRISPR/Cas9 mediated gene editing at the C-C chemokine receptor type 5 locus was used to facilitate transgene insertion of an AAV6-encoded DNA template via homology-directed repair. Transgene insertion did not alter B cell biology, viability, or differentiation into plasma cells. Appreciable levels of BE-101-derived FIX-Padua were detected within 1 day after IV administration in mouse and steady state was reached within 2 weeks and persisted for over 184 days. Redosing produced an increase in FIX-Padua production close to linear dose proportionality. Comprehensive genotoxicity analysis found no off-target issues of concern. No safety signals were observed in animal tolerability and GLP toxicology studies. In conclusion, BE-101 produces sustained levels of active FIX-Padua with the ability to engraft without host preconditioning and with the potential for redosing and titratability.

pharmacology and toxicology↗

bioRxiv2024

In vivo tracking of ex vivo generated 89Zr-oxine labeled plasma cells by PET in a non-human primate model

B cells are an attractive platform for engineering to produce protein-based biologics absent in genetic disorders, and potentially for the treatment of metabolic diseases and cancer. As part of pre-clinical development of B cell medicines, we demonstrate a method to collect, ex vivo expand, differentiate, radioactively label, and track adoptively transferred non-human primate (NHP) B cells. These cells underwent 10- to 15-fold expansion, initiated IgG class switching, and differentiated into antibody secreting cells. Zirconium-89-oxine labeled cells were infused into autologous donors without any preconditioning and tracked by PET/CT imaging. Within 24 hours of infusion, 20% of the initial dose homed to the bone marrow and spleen and distributed stably and equally between the two. Interestingly, approximately half of the dose homed to the liver. Image analysis of the bone marrow demonstrated inhomogeneous distribution of the cells. The subjects experienced no clinically significant side effects or laboratory abnormalities. A second infusion of B cells into one of the subjects resulted in an almost identical distribution of cells, suggesting a non-limiting engraftment niche and feasibility of repeated infusions. This work supports the NHP as a valuable model to assess the potential of B cell medicines as potential treatment for human diseases.

bioengineering↗

bioRxiv2024

ATP-Binding Cassette Family C member 1 constrains metabolic responses to high-fat diet in male mice

Glucocorticoids modulate glucose homeostasis, acting on metabolically active tissues such as liver, skeletal muscle, and adipose tissue. Intra-cellular regulation of glucocorticoid action in adipose tissue impacts metabolic responses to obesity. ATP-Binding Cassette Family C member 1 (ABCC1) is a transmembrane glucocorticoid transporter known to limit the accumulation of exogenously administered corticosterone in adipose tissue. However, the role of ABCC1 in the regulation of endogenous glucocorticoid action and its impact on fuel metabolism has not been studied. Here, we investigate the impact of Abcc1 deficiency on glucocorticoid action and high fat-diet (HFD)-induced obesity. In lean mice, deficiency of Abcc1 increased endogenous corticosterone levels in skeletal muscle and adipose tissue but did not impact insulin sensitivity. In contrast, Abcc1-deficient mice on HFD displayed impaired glucose and insulin tolerance, and fasting hyperinsulinemia, without alterations in tissue corticosterone levels. Proteomics and bulk RNA sequencing in adipose tissue and skeletal muscle revealed that Abcc1 deficiency amplified the transcriptional response to an obesogenic diet in adipose tissue. Moreover, the Abcc1 deficiency impairs key signalling pathways related to glucose metabolism in both skeletal muscle and adipose tissue, in particular those related to OXPHOS machinery and Glut4. Together, our results highlight a role for ABCC1 in regulating glucose homeostasis, demonstrating diet-dependent effects that are not associated with altered tissue glucocorticoid concentrations.

physiology↗

bioRxiv2023

Gene networks driven by genetic variation for plasma cortisol in hepatic and adipose tissues implicate corticosteroid binding globulin in modulating tissue glucocorticoid action and cardiovascular risk

Genome wide association meta-analyses (GWAMA) by the CORtisol NETwork (CORNET) consortium identified genetic variants spanning the SERPINA6/ SERPINA1 locus on chromosome 14 associated with morning plasma cortisol, cardiovascular disease (CVD), and SERPINA6 mRNA expression encoding corticosteroid binding globulin (CBG) in liver. These and other findings indicate that higher plasma cortisol levels are causally associated with cardiovascular disease, however, the mechanisms by which variations in CBG lead to CVD are undetermined. Using genomic and transcriptomic data from The Stockholm Tartu Atherosclerosis Reverse Networks Engineering Task (STARNET) study, we identified plasma cortisol linked Single Nucleotide Polymorphisms (SNPs) that are trans-associated with genes from 7 different vascular and metabolic tissues, finding the highest representation of transgenes in liver, subcutaneous adipose and visceral abdominal adipose tissue (FDR = 15%). We identified a sub-set of cortisol-associated trans-genes that are putatively regulated by the Glucocorticoid Receptor (GR), the primary transcription factor activated by cortisol. Using causal inference, we identified GR-regulated trans-genes that are responsible for the regulation of tissue specific gene networks. Cis-expression Quantitative Trait Loci (eQTLs) were used as genetic instruments for identification of pairwise causal relationships from which gene networks could be reconstructed. Gene networks were identified in liver, subcutaneous fat and visceral abdominal fat, including a high confidence gene network specific to subcutaneous adipose (FDR = 10%) under the regulation of the interferon regulatory transcription factor, IRF2. These data identify a plausible pathway through which variation in liver CBG production perturbs cortisol-regulated gene networks in peripheral tissues and thereby promote CVD.

genetics↗