Biology subjects

Coyle, K. M.

Publications and source records attributed to Coyle, K. M..

5 recordsLinked to original sources

bioRxiv2025

LCR-modules: a collection of workflows for cancer genome analysis

The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10,800 samples.

bioinformatics↗

bioRxiv2025

Natural killer cell TGF- signaling regulates senolytic activity and vascular patterning in the postnatal lung

BackgroundBronchopulmonary dysplasia (BPD) is a disease of neonatal lung development that is linked to impaired pulmonary vascularization, dysregulated transforming growth factor-{beta} (TGF-{beta}) signaling and the accumulation of senescent cells. Despite the established role for TGF-{beta} signaling in promoting vascular remodeling and suppressing the senolytic activity of natural killer (NK) cells, the contribution of NK cell TGF-{beta} signaling to postnatal lung patterning and the pathogenesis of BPD remains unclear. MethodsMice bearing an NK cell-selective deletion of the type-II TGF-{beta} receptor (Tgfbr2NK-/-) were analyzed for vascular and alveolar structure, lung NK cell infiltration, senescence markers and lung function testing across neonatal and adult timepoints. Single-cell RNA sequencing of lung tissue from both neonatal mice and human infants with BPD was performed. The effect of enhanced NK cell activity in a hyperoxia-induced model of BPD was assessed in Tgfbr2NK-/-neonates, as well as pharmacologically, using the TGF-{beta} ligand trap/IL-15 superagonist, HCW9218. ResultsNeonatal Tgfbr2NK-/- mice exhibited a baseline reduction in distal arteriolar density, impaired alveolarization, and sex-specific deficits in long-term lung function. Single-cell RNA sequencing identified the excessive clearance of senescent endothelial cells by TGF-{beta} insensitive NK cells in the lungs of Tgfbr2NK-/- neonates, which served as a contributor of the BPD-like phenotype observed in naive animals. Tgfbr2NK-/- mice were protected from impaired lung development in the hyperoxia model. Sequencing from lung tissue from infants with BPD confirmed excessive TGF-{beta} signaling and cytotoxic impairment in NK cells. Treatment with HCW9218 prevented senescent cell accumulation and rescued lung development in the hyperoxia mouse model. ConclusionsThese findings identify TGF-{beta} as a tunable regulator of NK cell senolytic activity that is essential to normal postnatal lung development. Excessive NK cell TGF-{beta} signaling contributes to impaired lung development following exposure to neonatal hyperoxia and may serve as a viable therapeutic target for human BPD.

developmental biology↗

bioRxiv2021

Shared and distinct genetic features in human and canine B-cell lymphomas

Animal models of human cancers are an important tool for the development and preclinical evaluation of therapeutics. Canine B-cell lymphoma (cBCL) is an appealing model for human mature B-cell neoplasms due to the high sequence similarity in cancer genes to humans and inactive telomerase in adult tissues. We performed targeted sequencing on 86 canine patients from the Canine Comparative Oncology Genomic Consortium, with 61 confirmed as B-cell lymphomas. We confirmed a high frequency of mutations in TRAF3 (45%) and FBXW7 (20%) as has been reported by our group and others. We also note a higher frequency of DDX3X (20%) and MYC (13%) mutations in our canine cohort. We compared the pattern and incidence of mutations in cBCL to human diffuse large B-cell lymphoma (hDLBCL) and human Burkitt lymphoma (hBL). Canine MYC mutations displayed a focal pattern with 80% of mutations affecting the conserved phosphodegron sequence in MYC box 1, which are known to stabilize MYC protein. We also note that MYC and FBXW7 mutations do not co-occur in our cBCL cohort, leading to the hypothesis that these mutations represent alternative approaches to stabilize MYC in canine lymphoma. We observed striking differences in the pattern of DDX3X mutations in canine lymphoma as compared to hBL and uncovered a sex-specific pattern of DDX3X mutations in hBL that is not consistent with those identified in canine lymphomas. In sum, we describe key differences between cBCL and human mature B-cell lymphomas which may indicate differences in the biology of these cancers. This should be considered in future studies of cBCL as a model of human lymphomas.

cancer biology↗

bioRxiv2020

Human-specific GAPDH RT-qPCR is an accurate and sensitive method of xenograft metastasis quantification

Metastasis is the primary cause of cancer-related mortality. Having experimental models that accurately reflect changes in the metastatic burden is imperative for developing improved treatments and a better understanding of the disease. The murine xenograft tumor model mimics the human scenario and provides a platform for in vivo and ex vivo metastasis quantification analyses. Histological analysis of hematoxylin and eosin (H&E) stained thin sections has been the gold standard for quantifying metastasis ex vivo but gaining favor for its ease and accuracy is reverse transcription-qualitative polymerase chain reaction (RT-qPCR). Herein we directly compare histological and RT-qPCR-based methods for quantifying lung metastasis in a murine xenograft tumor model. Furthermore, we have introduced a variation of the RT-qPCR method; human-specific glyceraldehyde 3-phosphate dehydrogenase (GAPDH) RT-qPCR, which allows quantification of metastasis in xenograft models, without the requirement of overexpression of exogenous genes. Human-specific GAPDH RT-qPCR detected increased lung metastasis resulting from aldehyde dehydrogenase 1A3 (ALDH1A3) expression in MDA-MB-231 breast cancer cells orthotopically implanted in NOD/SCID mice. Further, in the xenograft tumor model, human-specific GAPDH RT-qPCR was more sensitive and cost-effective than quantification of lung metastasis by histological analysis of H&E stained fixed thin sections. The two assays were highly correlative in terms of determining relative metastatic burden, suggesting that the human-specific GAPDH RT-qPCR method could be used as a standard method for quantification of disseminated human cells in murine xenograft models.

cancer biology↗

bioRxiv2019

Coding and regulatory drivers of mantle cell lymphoma identified through exome and genome sequencing

Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established and the features known to contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes alongside previously published exome cohorts. To confirm our findings, we re-sequenced the genes identified in the exome cohort in 212 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations and further nominate two additional genes, EWSR1 and MEF2B, whose mutation respectively associated with poor and good outcome. Our sequencing revealed novel recurrent mutations including a unique missense hot spot in MEF2B and a pattern of non-coding mutations surrounding a single exon of the HNRNPH1 gene. We sequenced the whole genomes of 34 MCLs to confirm the focal nature of HNRNPH1 mutations. Using RNA-seq data from 110 of these cases, we identified a functional role for recurrent non-coding HNRNPH1 mutations in disrupting an auto-regulatory feedback mechanism. Overall, we identified three novel MCL-related genes with roles in RNA trafficking or splicing, namely DAZAP1, EWSR1, and HNRNPH1. Taken together, these data strongly implicate a role for aberrant regulation of splicing in MCL pathobiology.\n\nKey pointsO_LIRNA-binding proteins with roles in regulating alternative splicing, DAZAP1, EWSR1, HNRNPH1, are frequently mutated in MCL\nC_LIO_LIThe majority of recurrent somatic HNRNPH1 mutations are intronic and HNRNPH1 exhibits self-regulation through alternative splicing\nC_LI

genomics↗