Biology subjects

Parker, J. S.

Publications and source records attributed to Parker, J. S..

9 recordsLinked to original sources

bioRxiv2026

A single point mutation in the σ3 protein encoded by the reovirus S4 gene substantially attenuates the virulence of a highly myocarditic reassortant virus in neonatal mice

Viral myocarditis is a major cause of heart damage, sudden death, and heart failure. Some strains of Mammalian Orthoreoviruses (REOV) cause myocarditis in newborn mice. This study examines the role of the REOV {sigma}3 protein, encoded by the S4 gene, in modulating the virulence and myocarditic potential of a highly virulent T1L/T3DM2 reassortant virus that contains the M2 gene from the Type 3 Dearing (T3D) strain in the Type 1 Lang background. We introduced single-point mutations in the double-stranded RNA-binding region of {sigma}3 in the T1L/T3DM2 background. Our findings show that the K287T mutation in {sigma}3 prevents the myocarditic phenotype and significantly reduces the virulence of T1L/T3DM2. Unlike the parental reassortant virus and a control reassortant mutant S4(R296T), infection of neonatal mice with the T1L-S4(K287T)/T3DM2 virus resulted in 100% survival, lower viral titers, particularly in the heart and spleen, and no gross or severe histological signs of myocarditis. This attenuation, despite similar in vitro growth and in vivo dissemination, indicates a tissue-specific replication deficit and highlights a key role for {sigma}3 in the development of myocardial disease. The K287T mutation, unlike R296T, eliminates {sigma}3s capacity to inhibit protein kinase R (PKR) activation and to suppress NF-{kappa}B-driven transcription, leading to a strong innate immune response that likely controls viral replication and reduces cardiac damage. These results underscore the crucial role of the {sigma}3 protein in modulating host innate immune responses and in influencing the outcome of REOV infection and myocarditis development. IMPORTANCEViral myocarditis is a serious disease with life-threatening consequences, particularly in neonates and young animals. Infection of neonatal mice with certain strains of mammalian reovirus induces myocarditis. A reassortant virus containing the M2 gene from the Type 3 Dearing Strain in an otherwise Type 1 Lang background causes severe myocarditis in 100% of neonatal mice. Here, we show that a single point mutation in the S4 gene, which abolishes the capacity of the encoded {sigma}3 protein to inhibit protein kinase R (PKR) and to suppress transcription of NF-{kappa}B-dependent genes, significantly attenuates the lethality of the T1L/T3DM2 reassortant and significantly reduces the severity of myocarditis. These findings highlight the importance of viral innate immune suppression in the induction of myocarditis.

microbiology↗

bioRxiv2024

Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling

Annotation of the cis-regulatory elements that drive transcriptional dysregulation in cancer cells is critical to improving our understanding of tumor biology. Herein, we present a compendium of matched chromatin accessibility (scATAC-seq) and transcriptome (scRNA-seq) profiles at single-cell resolution from human breast tumors and healthy mammary tissues processed immediately following surgical resection. We identify the most likely cell-of-origin for luminal breast tumors and basal breast tumors and then introduce a novel methodology that implements linear mixed-effects models to systematically quantify associations between regions of chromatin accessibility (i.e. regulatory elements) and gene expression in malignant cells versus normal mammary epithelial cells. These data unveil regulatory elements with that switch from silencers of gene expression in normal cells to enhancers of gene expression in cancer cells, leading to the upregulation of clinically relevant oncogenes. To translate the utility of this dataset into tractable models, we generated matched scATAC-seq and scRNA-seq profiles for breast cancer cell lines, revealing, for each subtype, a conserved oncogenic gene expression program between in vitro and in vivo cells. Together, this work highlights the importance of non-coding regulatory mechanisms that underlie oncogenic processes and the ability of single-cell multi-omics to define the regulatory logic of BC cells at single-cell resolution.

genomics↗

bioRxiv2023

Calorie Restriction Outperforms Bariatric Surgery in a Murine Model of Obesity and Triple-Negative Breast Cancer

Obesity promotes triple-negative breast cancer (TNBC), and effective interventions are urgently needed to break the obesity-TNBC link. Epidemiologic studies indicate that bariatric surgery reduces TNBC risk, while evidence is limited or conflicted for weight loss via low-fat diet (LFD) or calorie restriction (CR). Using a murine model of obesity- driven TNBC, we compared the antitumor effects of vertical sleeve gastrectomy (VSG) with LFD, chronic CR, and intermittent CR. Each intervention generated weight and fat loss and suppressed tumor growth relative to obese mice (greatest suppression with CR). VSG and CR regimens exerted both similar and unique effects, as assessed using multi-omic approaches, in reversing obesity-associated transcriptional, epigenetic, secretome, and microbiota changes and restoring antitumor immunity. Thus, in a murine model of TNBC, bariatric surgery and CR each reverse obesity-driven tumor growth via shared and distinct antitumor mechanisms, and CR is superior to VSG in reversing obesitys procancer effects.

cancer biology↗

bioRxiv2023

Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1

Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.

microbiology↗

bioRxiv2022

A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer

The human genome contains regulatory elements, such as enhancers, that are often rewired by cancer cells for the activation of genes that promote tumorigenesis and resistance to therapy. This is especially true for cancers that have little or no known driver mutations within protein coding genes, such as ovarian cancer. Herein, we have utilized an integrated set of genomic and epigenomic datasets to identify clinically relevant super-enhancers that are preferentially amplified in ovarian cancer patients. We have systematically probed the top 86 super-enhancers, using CRISPR-interference and CRISPR-deletion assays coupled to RNA-sequencing, to nominate two salient super-enhancers that drive proliferation and migration of cancer cells. Utilizing Hi-C, we constructed chromatin interaction maps that enabled the annotation of direct target genes for these super-enhancers and later confirmed their activity specifically within the cancer cell compartment of human tumors using single-cell genomics data. Together, our multi-omic approach has examined a number of fundamental questions about how regulatory information encoded into super-enhancers drives gene expression networks that underlie the biology of ovarian cancer.

cancer biology↗

bioRxiv2020

FastPG: Fast clustering of millions of single cells

Current single-cell experiments can produce datasets with millions of cells. Unsupervised clustering can be used to identify cell populations in single-cell analysis but often leads to interminable computation time at this scale. This problem has previously been mitigated by subsampling cells, which greatly reduces accuracy. We built on the graph-based algorithm PhenoGraph and developed FastPG which has the same cell assignment accuracy but is on average 27x faster in our tests. FastPG also has higher cell assignment accuracy than two other fast clustering methods, FlowSOM and PARC. AvailabilityFastPG is available here: https://github.com/sararselitsky/FastPG

bioinformatics↗

bioRxiv2020

CRTC1-MAML2 Establishes a PGC1α-IGF1 Circuit that Confers Vulnerability to PPARγ Inhibition

Mucoepidermoid carcinoma (MEC) is a life-threatening salivary gland cancer that is driven primarily by the transcriptional co-activator fusion CRTC1-MAML2. The mechanisms by which the chimeric CRTC1-MAML2 oncoprotein rewires gene expression programs that promote tumorigenesis remain poorly understood. Here, we show that CRTC1-MAML2 induces transcriptional activation of the non-canonical PGC-1 splice variant PGC-14, which regulates PPAR{gamma}-dependent IGF-1 expression. This mitogenic transcriptional circuitry is consistent across cell lines and primary tumors. CRTC1-MAML2 positive tumors are dominated by IGF-1 pathway activation and small molecule drug screens reveal that tumor cells harboring the fusion gene are selectively sensitive to IGF-1R inhibition. Furthermore, this dependence on autocrine regulation of IGF-1 transcription renders MEC cells susceptible to PPAR{gamma}inhibition with inverse agonists. These results yield insights into the aberrant co-regulatory functions of CRTC1-MAML2 and identify a specific vulnerability that can be exploited for precision therapy.

cancer biology↗

bioRxiv2020

A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels

BackgroundPan-cancer genomic analyses based on the magnitude of pathway activity are currently lacking. Focusing on the cell cycle, we examined the DNA mutations and chromosome arm-level aneuploidy within tumours with low, intermediate and high cell cycle activity. Patients and methodsMatching mRNA, gene mutational status, chromosomal arm-level aberrations and clinico-pathological data was assembled from pan-cancer studies of 9,515 patients with 32 different cancers. Cell cycle activity was estimated from mRNA data using the cell cycle score (CCS) signature. Barplots were used to visualise mutation and chromosomal aberration frequency within CCS subgroups. Kaplan-Meier and multivariable Cox-regression analyses were used to determine survival differences between CCS subgroups. ResultsCell cycle activity varied broadly across and within all cancers. TP53 and PIK3CA mutations were common in all CCS subgroups but with increasing frequency as cell cycle activity levels increased (P < 0.001). Mutations in BRAF and gains in 16p were less frequent CCS high tumours (P < 0.001). In Kaplan-Meier analysis, patients whose tumours were CCS Low had a longer PFI relative to intermediate or high (P < 0.001) and this significance remained in multivariable analysis (CCS intermediate: HR = 1.37; 95% CI 1.17 - 1.60, CCS high: 1.54; 1.29 - 1.84, CCS Low = Ref). ConclusionsCell cycle activity varies across and within cancers and whilst similar DNA alterations can be found at all activity levels, some notable exceptions exist. These data also demonstrate that independent prognostic information can be derived on a pan-cancer level from a simple measure of cell cycle activity.

genomics↗

bioRxiv2018

An Integrative Boosting Approach for Predicting Survival Time With Multiple Genomics Platforms

Recent technological advances have made it possible to collect multiple types of genomics data on the same set of patients. It is of great interest to integrate multiple genomics data types together for predicting disease outcomes. We propose a variable selection method, termed Integrative Boosting (I-Boost), that makes proper use of all available clinical and genomics data in predicting individual patient survival time. Through simulation studies and applications to data sets from The Cancer Genome Atlas, we demonstrate that I-Boost provides substantially higher prediction accuracy than existing variable selection methods. Using I-Boost, we show that (1) the integration of multiple genomics platforms with clinical variables significantly improves the prediction accuracy for survival time over the use of clinical variables alone; (2) gene expression values are typically more prognostic of survival time than other genomics data types; and (3) gene modules/signatures are at least as prognostic as the collection of individual gene expression data.

bioinformatics↗