Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays

Grifantini, Renata; Bartolini, Erika; Muzzi, Alessandro; Draghi, Monia; Frigimelica, Elisabetta; Berger, Joel P.; Ratti, Giulio; Petracca, Roberto; Galli, G.; Agnusdei, Mauro; Giuliani, Marzia M.; Santini, Laura; Brunelli, Brunella; Tettelin, Hervé; Rappuoli, Rino; Randazzo, Filippo; Grandi, Guido

doi:10.1038/nbt728

Cited by 193 publications

(178 citation statements)

References 44 publications

Supporting

Mentioning

165

Contrasting

Unclassified

Order By: Relevance

“…DNA microarray analysis was performed as described (19). The hybridization probe was constituted by a mixture of the differently labeled cDNA derived from bacterial cultures grown under iron-replete or -depleted conditions.…”

Section: Methodsmentioning

confidence: 99%

“…These initial reports led us to postulate that pathogenic neisseriae possess a broad array of genes whose expression is under the control of the transcriptional regulatory protein Fur. To further define the gene repertoire that is regulated by iron and Fur in neisseriae, in the present study we used DNA microarray technology to monitor the kinetics of expression of the entire gene repertoire of Neisseria meningitidis MC58 (19,20) in response to iron.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis ofNeisseria meningitidisgroup B

Grifantini

Sebastian

Frigimelica

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

180

203

View full text Add to dashboard Cite

Iron is limiting in the human host, and bacterial pathogens respond to this environment by activating genes required for bacterial virulence. Transcriptional regulation in response to iron in Gramnegative bacteria is largely mediated by the ferric uptake regulator protein Fur, which in the presence of iron binds to a specific sequence in the promoter regions of genes under its control and acts as a repressor. Here we describe DNA microarray, computational and in vitro studies to define the Fur regulon in the human pathogen Neisseria meningitidis group B (strain MC58). After iron addition to an iron-depleted bacterial culture, 153 genes were up-regulated and 80 were down-regulated. Only 50% of the iron-regulated genes were found to contain Fur-binding consensus sequences in their promoter regions. Forty-two promoter regions were amplified and 32 of these were shown to bind Fur by gel-shift analysis. Among these genes, many of which had never been described before to be Fur-regulated, 10 were up-regulated on iron addition, demonstrating that Fur can also act as a transcriptional activator. Sequence alignment of the Fur-binding regions revealed that the N. meningitidis Fur-box encompasses the highly conserved (NATWAT)3 motif. Cluster analysis was effective in predicting Fur-regulated genes even if computer prediction failed to identify Fur-box-like sequences in their promoter regions. Microarray-generated gene expression profiling appears to be a very effective approach to define new regulons and regulatory pathways in pathogenic bacteria.

show abstract

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis ofNeisseria meningitidisgroup B

Grifantini

Sebastian

Frigimelica

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

180

203

View full text Add to dashboard Cite

show abstract

“…Reverse vaccinology, microarray -see text for details [9,26] Streptococcus pneumoniae Most common cause of fatal community-acquired pneumonia in the elderly and is also one of the most common causes of middle ear infections and meningitis in children.…”

Section: Neisseria Meningitidis B Major Cause Of Bacterial Septicemiamentioning

confidence: 99%

Post‐genomic vaccine development

2006

Self Cite

View full text Add to dashboard Cite

For over a century, vaccines were developed according to Pasteur's principles of isolating, inactivating and injecting the causative agent of an infectious disease. The availability of a complete microbial genome sequence in 1995 marked the beginning of a genomic era that has allowed scientists to change the paradigm and approach vaccine development starting from genomic information, a process named reverse vaccinology. This can be considered as one of the most powerful examples of how genomic information can be used to develop therapeutic interventions, which were difficult or impossible to tackle with conventional approaches. As the genomic era progressed, it became apparent that multi-strain genome analysis is fundamental to the design of universal vaccines. In the post-genomic era, the next challenge of the vaccine biologist will be the merging of the vaccinology with structural biology.

show abstract

“…Microarrays have demonstrated their applicability for a broad variety of applications such as cell differentiation [170], whole-genome expression analysis [67,152], cancer research [5,71,131], comparative genome hybridization (CGH) [146], drug discovery [39], vaccine development [72] or single nucleotide polymorphism (SNP) analysis [56].…”

Section: Introduction To Microarray Technologymentioning

confidence: 99%

Introduction to Microarray‐Based Detection Methods

Schrenzel

Kostić²,

Bodrossy

et al. 2009

Detection of Highly Dangerous Pathogens

View full text Add to dashboard Cite

Microarrays consist of an orderly arrangement of probes (oligonucleotides, DNA fragments, proteins, sugars or lectins) attached to a solid surface. The main advantages of microarray technology are high throughput, parallelism, miniaturization, speed and automation. Despite the fact that microarray analysis is a relatively novel technology, with the publication of the first microarray studies in 1995 [101,152], it is now broadly applied and the milestone of nearly 5000 published microarray papers was recorded in 2004 [80]. The scientific and technological background discussed here will be limited to DNA microarrays, excluding the new evolving fields of protein microarrays and glycomics [140].Analogous to antigen-antibody interactions on immunoarrays, DNA microarrays rely on sequence complementarity of the two strands. They put in practice the fundamentals of complementary base-pairing (hybridization) that were first described by Ed Southern [162]. In general, the strategy of microarray hybridization is reversed to that of a standard dot-blot, leading to recurring confusion in the nomenclature. Therefore, it has been suggested to describe tethered nucleic acid as the probe and free nucleic acid as the target [134].Earlier studies on duplex melting and reformation, carried out on DNA solutions, have provided the basic knowledge about the reaction kinetics. Furthermore, a method for computational determination of the melting point as a function of nucleic acid composition and salt concentration was established [6,148,149]. Much of the pioneering work can be linked to the use of nitrocellulose membranes [69], dot-blots [84] and Southern blots [162]. Development of cDNA or oligonucleotide arrays was possible by combined innovations in micro-engineering, molecular biology [33,120,123,156,163,164] and bioinformatics [59]. The real breakthrough in microarray technology was initiated by two key innovations: the use of non-porous solid supports (such as glass and silicon) and the development of methods for highdensity synthesis of oligonucleotides directly onto the microarray surface [59].

show abstract

Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays

Cited by 193 publications

References 44 publications

Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis ofNeisseria meningitidisgroup B

Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis ofNeisseria meningitidisgroup B

Post‐genomic vaccine development

Introduction to Microarray‐Based Detection Methods

Contact Info

Product

Resources

About