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Higgins, G.

Publications and source records attributed to Higgins, G..

3 recordsLinked to original sources

Pseudomonas aeruginosa PA5oct jumbo phage reduces planktonic and biofilm population and impacts its host virulence through a pseudolysogeny event

In this work we analyzed the impact of jumbo phage PA5oct on the planktonic, cell line adhered, and biofilm population of P. aeruginosa. PA5oct has a broad host-range, able to infect up to 40% of our clinical P. aeruginosa Cystic Fibrosis (CF) collection. In the airway surface liquid (ASL) model, the infection of PA5oct effectively reduced the bacterial population both adhered to epithelial cells, mucus entrapped, and dispersed. The explanation for its infectivity can also be linked to the sensitization of infected bacteria to the innate immune mechanisms and pro-inflammatory effect. Interferometry of a 72-hour old biofilm highlighted the contribution of PA5oct in biofilm matrix degradation. Interestingly, two virion-associated proteins, gp162 and gp205, have been found as putative enzymes that can degrade matrix exopolysaccharides. Two third of biofilm clones developed PA5oct phage-resistance and the cross-resistance to both LPS- and pili-dependent phages. Simultaneously, all clones resistant to phage PA5oct maintain the phage DNA within the population, strongly reducing bacterial virulence in vivo. These properties can be considered as key parameters for the application of this bacterial virus in phage therapy settings.\n\nOriginality-Significance StatementThe emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. However, this fundamental property also has implications for bacterial eradication in phage therapy settings. Here, we analyze the impact of PA5oct jumbo phage treatment of planktonic/cell line associated and sessile P. aeruginosa population in a preclinical evaluation of this phage for therapeutic applications. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population is correlated to reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This, phenomenon combined with the loss or modification of the phage receptor makes most of the phage-resistant clones significantly less pathogenic in in vivo model. During phage therapy treatment, phage-resistance is considered as an adverse effect, but our results indicate that it leads to diminished bacterial virulence and increased clearance of the infected host. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.

microbiology

Parental allele-specific genome architecture and transcription during the cell cycle

A normal human somatic cell inherits two haploid genomes. Individual chromosomes of each pair have distinct parental origins and parental alleles are known to unequally contribute to cellular function. We integrated chromosome conformation (form) and gene transcription (function) analyses to dissect the dynamics of the maternal and paternal genomes in lymphoblastoid cells during the cell cycle. We found a distinct set of homologous alleles with very different activity often located close to boundaries of euchromatin and heterochromatin domains. We also identified a set of allele-biased topologically associating domains (TADs) that were small sized and had higher gene density. Thousands of genes show allelically biased expression (ABE) with false discovery rate < 0.05, and 98% of them have no allelic switching during G1, S, and G2/M phases. A subset of ABE genes are preferentially localized near TAD boundaries, enriched with chromatin organization transcription factor binding sites, and contained higher number of sequence variants in CCCTC-binding factor sites. Our results extend previous findings of sequence variation as a basis for unequal functional parental genomes. Investigation of haplotype-resolved form-function dynamics may further our understanding of phenotypic traits, genetic diseases, vulnerability to complex disorders, and the development of cancers.

genomics

Genome Architecture Leads a Bifurcation in Cell Identity

Genome architecture is important in transcriptional regulation and study of its features is a critical part of fully understanding cell identity. Altering cell identity is possible through overexpression of transcription factors (TFs); for example, fibroblasts can be reprogrammed into muscle cells by introducing MYOD1. How TFs dynamically orchestrate genome architecture and transcription as a cell adopts a new identity during reprogramming is not well understood. Here we show that MYOD1-mediated reprogramming of human fibroblasts into the myogenic lineage undergoes a critical transition, which we refer to as a bifurcation point, where cell identity definitively changes. By integrating knowledge of genome-wide dynamical architecture and transcription, we found significant chromatin reorganization prior to transcriptional changes that marked activation of the myogenic program. We also found that the local architectural and transcriptional dynamics of endogenous MYOD1 and MYOG reflected the global genomic bifurcation event. These TFs additionally participate in entrainment of biological rhythms. Understanding the system-level genome dynamics underlying a cell fate decision is a step toward devising more sophisticated reprogramming strategies that could be used in cell therapies.

cell biology