Use of DNA Microarrays to Monitor Host Response to Virus and Virus-Derived Gene Therapy Vectors

Piersanti, Stefania; Martina, Yuri; Cherubini, Gioia; Avitabile, Daniele; Saggio, Isabella

doi:10.2165/00129785-200404060-00002

Cited by 21 publications

(19 citation statements)

References 49 publications

(13 reference statements)

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“…Compared with a similar study that focused on the complex, double-stranded-DNA bacterial virus PRD1, it was evident that there were no universal responses to viral infection. However, in both cases, translation was affected in infected cells.Over the past few years, microarray technology has been employed to probe the global effects of viral infection on host gene expression (26,27). The earliest microarray-based studies of host gene expression provided a very general, genome-wide picture of changes induced by viral infection.…”

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Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Ravantti

Ruokoranta

Alapuranen

et al. 2008

J Virol

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The infectious cycles of viruses are known to cause dramatic changes to host cell function. The development of microarray technology has provided means to monitor host cell responses to viral infection at the level of global changes in mRNA levels. We have applied this methodology to investigate gene expression changes caused by a small, icosahedral, single-stranded-RNA phage, PRR1 (a member of the Leviviridae family), on its host, Pseudomonas aeruginosa, at different times during its growth cycle. Viral infection in this system resulted in changes in expression levels of <4% of P. aeruginosa genes. Interestingly, the number of genes affected by viral infection was significantly lower than the number of genes affected by changes in growth conditions during the experiment. Compared with a similar study that focused on the complex, double-stranded-DNA bacterial virus PRD1, it was evident that there were no universal responses to viral infection. However, in both cases, translation was affected in infected cells.Over the past few years, microarray technology has been employed to probe the global effects of viral infection on host gene expression (26,27). The earliest microarray-based studies of host gene expression provided a very general, genome-wide picture of changes induced by viral infection. These studies, however, provided little information about the specific changes in individual genes across the entire host genome. Furthermore, investigations using this technology have largely focused on viral infections in animals and, to a lesser extent, in plants (21,30,35) or fungi (2, 3). Microarrays have been employed to detect phage-specific transcripts in infected cells (11,19), changes in the host genome (14,20), and changes in the transcriptional profiles of bacteria parasitized by lysogenic phages (7). However, to our knowledge, only two studies of virusinduced changes in host gene expression span the entire host genome. One of these studies involved a plant virus (21), and the other focused on an icosahedral, membrane-containing, double-stranded-DNA (dsDNA) phage, PRD1 (27).PRR1 is an icosahedral, single-stranded-RNA (ssRNA) phage (24) that is related to well-studied members (MS2, Qbeta, etc.) of the Leviviridae family (13). PRR1 is unique among members of the Leviviridae family in that it infects a wide range of gram-negative bacteria (8, 24), but only if they harbor an IncP-type conjugative plasmid. The PRR1 genome contains 3,573 nucleotides with only four protein-encoding genes, namely, those for the polymerase, the maturation and coat proteins, and the lytic factor (28). The PRR1 replication cycle and its effects on host cell physiology are described elsewhere (G. Daujotaitë, R. Daugelavièius, and D. H. Bamford, submitted for publication). The optimal bacterial host for PRR1 is Pseudomonas aeruginosa (24), a gram-negative, opportunistic human pathogen (15,16,18). At 6.3 million base pairs (containing 5,570 open reading frames [ORFs]), the P. aeruginosa genome is one of the largest bacterial genomes that ha...

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confidence: 99%

“…Over the past few years, microarray technology has been employed to probe the global effects of viral infection on host gene expression (26,27). The earliest microarray-based studies of host gene expression provided a very general, genome-wide picture of changes induced by viral infection.…”

mentioning

confidence: 99%

Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Ravantti

Ruokoranta

Alapuranen

et al. 2008

J Virol

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“…DNA microarrays/chips stand out for their simplicity, comprehensiveness, robustness, data consistency and high-throughput. They can be devided for form 's sake into viral chips and host chips ( Piersanti et al, 2004 ;, but the majority of applications can inherently be categorized as genotyping, resequencing, or gene expression. Viral microarrays/chips provide a particularly powerful tool to reap these benefi ts.…”

Section: Discussionmentioning

confidence: 99%

Viral Chip Technology in Genomic Medicine

Földes-Papp¹

2009

Genomic and Personalized Medicine

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“…Such a human-response chip can be used to determine a patient's response to potentially toxic antimicrobial treatments in advance of delivery. If the patient lacks enzymes to break down toxins or cannot metabolize a drug effectively, alternative therapies can be used to avoid dangerous adverse effects [46]. In another prospective microarray-based test, human leukocyte response to various infectious agents may be used to pinpoint the etiology before the agent itself can be detected [47].…”

Section: Microarray Technologymentioning

confidence: 99%

Implications of New Technology for Infectious Diseases Practice

Reller¹,

Weinstein²,

Baron

2006

Clinical Infectious Diseases

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New assays for the diagnosis of infectious diseases--particularly those that use molecular technologies--will revolutionize infectious diseases practices, but the fulfillment of the promise is several years away. Problems with currently available molecular assays include a lack of knowledge about the extent of microbial nucleic acid in "normal" hosts, concentration of agent material in small volume samples, lack of microbiologist expertise, lack of adequate reimbursement, and difficulty with validation based on conventional methods. Clinicians must appreciate the shortcomings of new technology to use it effectively and appropriately. However, we are realizing tangible progress in our ability to detect new etiological agents; the availability of rapid, accurate diagnostic tests for previously difficult infections; and advances into new, human response-based paradigms for diagnostic testing.

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Use of DNA Microarrays to Monitor Host Response to Virus and Virus-Derived Gene Therapy Vectors

Cited by 21 publications

References 49 publications

Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Global Transcriptional Responses of Pseudomonas aeruginosa to Phage PRR1 Infection

Viral Chip Technology in Genomic Medicine

Implications of New Technology for Infectious Diseases Practice

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