Gene expression clustering using self-organizing maps: analysis of the macrophage response to particulate biomaterials

Garrigues, Grant E.; Cho, David R.; Rubash, Harry E.; Goldring, Steven R.; Herndon, James H.; Shanbhag, Arun S.

doi:10.1016/j.biomaterials.2004.06.034

Cited by 55 publications

(37 citation statements)

References 52 publications

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“…In vitro culture of these cells with fibrinogen showed a switch over time from inflammatory to wound healing macrophages, evidenced by over-expression of genes such as IL-13Rα IL4Rα and arginase 1, and up-regulation of TGF-β signalling. These results are in line with an earlier study by Garrigues et al (2005) who identified a small number of genes which are highly regulated in macrophages exposed to wear debris from components of joint replacement prostheses. These included early changes (30 mins to 8 hours) in genes associated with ECM remodelling and angiogenesis, and also chemokines (IL-6), cytokines (RANTES, MIP-1α) and their receptors (TNFR1, 2 and IL2αR); other inflammatory cytokines (IL-1β, TNF-α, TGFβ3, oncostatin M) and IL6R-α subunit were upregulated slightly later (at 24 hours).…”

Section: What Regulates Tissue Capsule Development and Myofibroblast supporting

confidence: 93%

The Fibrotic Response to Implanted Biomaterials: Implications for Tissue Engineering

Rolfe¹,

Mooney²,

Zhang³

et al. 2011

Regenerative Medicine and Tissue Engineering - Cells and Biomaterials

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Section: What Regulates Tissue Capsule Development and Myofibroblast supporting

confidence: 93%

The Fibrotic Response to Implanted Biomaterials: Implications for Tissue Engineering

Rolfe¹,

Mooney²,

Zhang³

et al. 2011

Regenerative Medicine and Tissue Engineering - Cells and Biomaterials

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“…SOM analysis (Garrigues et al, 2005;Wang et al, 2002;Xiao et al, 2003) was performed on the complete dataset of 3182 transcriptionally active genes to construct a transcriptional map. SOM analysis organized the 3182 genes into 62 groups (0-61), with the number of genes in each group ranging from 23 to 337.…”

Section: Construction Of a Transcriptional Mapmentioning

confidence: 99%

Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis

2006

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In Mycobacterium tuberculosis the mechanism of septum formation and regulation of cell division remains undefined. In other bacterial species FtsZ polymerization and septum formation are influenced through protein interactions in addition to transcriptional regulation, and the combination of these provides tight regulation of this process. However, homologues of proteins known to affect FtsZ assembly have not been identified and substantiated in M. tuberculosis. This suggests that M. tuberculosis may possess unique processes for regulation of septum formation. To begin to address this poorly understood aspect of M. tuberculosis physiology, FtsZ inhibitors were used to block cell division and the effects on bacterial morphology and the transcriptional response were examined. Inhibition of septum formation prevented cell division and led to bacterial filamentation. Microarray-based transcriptional profiling allowed the evaluation of multiple metabolic processes in response to inhibition of septum formation and when coupled with bioinformatics provided a means to identify regulatory elements and other gene products that probably influence septum formation. INTRODUCTIONCell division at the molecular level has been well studied in a number of bacteria and it is recognized that septum formation is the first committed step of this event (Harry et al., 1999). In general, inhibition of bacterial division at the point of septum formation is characterized by normal chromosome replication and segregation that is not followed by cellular division leading to a filamentous phenotype . Septum formation is dependent on the assembly of FtsZ into the contractile Z-ring at the site of division (Den Blaauwen et al., 1999;Romberg & Levin, 2003) and additional proteins recruited to the septum site in a sequential fashion, resulting in constriction and cell division. In spite of this biochemical information, the current understanding of regulatory elements and the precise nature of the signals driving the coordination of cell division with other cell cycle processes is largely unknown, especially in Mycobacterium tuberculosis.Many of the proteins involved in cell division, such as FtsZ, are conserved across taxa, while others appear limited to one or a few bacterial groups Margolin, 2000). These include proteins known to interact with FtsZ and that modulate Z-ring assembly Romberg & Levin, 2003). The Z-ring is highly dynamic, and proper assembly of this structure and cell division are strongly influenced by direct interactions of FtsZ with ZipA, ZapA, FtsA, MinD, EzrA and SulA (Harry et al., 1999;Harry, 2001;Migocki et al., 2004;Romberg & Levin, 2003). These factors together with transcriptional regulators form a regulatory network that orchestrates the spatial and temporal control of cell division with other cell cycle processes. However, the underlying molecular mechanisms are only partially understood in model organisms and remain largely unknown for many unrelated organisms.Analysis of the M. tuberculosis genome sequence revealed t...

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“…Several studies have cited the relationship between the presence of wear debris, particle phagocytosis, and cytokine expression [3,[6][7][8], but only a few studies have characterized cytokine expression from monocytes/macrophages on textured surfaces [9,10]. These studies examined the effect of Ti topography on the activation and cytokine mRNA change of mouse RAW 264.7 monocytes and mouse J774A.1 macrophages using real-time PCR.…”

Section: Introductionmentioning

confidence: 99%

Response of monocytes exposed to phagocytosable particles and discs of comparable surface roughness

et al. 2007

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This in vitro study characterized the temporal cytokine expression profile from human monocytes exposed to phagocytosable Ti particles (0.78 ± 0.12 μm) and to Ti discs of comparable surface roughness. Human THP-1 monocytes were cultured in six well tissue culture polystyrene (TCPS) plates. Each well was either bare, contained Ti particles (the particles were clearly engulfed by the monocytes), or contained a Ti disc. Half of the wells were treated with 1 μg/mL lipopolysacchride (LPS), while the other half were left unstimulated. Unstimulated and LPS-stimulated cells in bare wells were the negative and positive controls, respectively. Supernatant was sampled from each well at 1, 6, 24, 48 and 72 h and assayed for the expression of nine different cytokines using a Luminex system. Three cytokines (IL-1β, GM-CSF and IL-13) gave little to no response under all conditions, while six cytokines (TNF-α, IL-6, MIP-1α, MCP-1, VEGF, and IL-1ra) were clearly detectable. Expression levels generally increased with culture time, particle concentration, and LPS stimulation. Most significantly, it was found that cells treated by Ti discs produced in many instances a higher cytokine expression than did particles.

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Gene expression clustering using self-organizing maps: analysis of the macrophage response to particulate biomaterials

Cited by 55 publications

References 52 publications

The Fibrotic Response to Implanted Biomaterials: Implications for Tissue Engineering

The Fibrotic Response to Implanted Biomaterials: Implications for Tissue Engineering

Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis

Response of monocytes exposed to phagocytosable particles and discs of comparable surface roughness

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