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Fibroblasts from phenotypically normal palmar fascia exhibit molecular profiles highly similar to fibroblasts from active disease in Dupuytren's Contracture.

Satish L, LaFramboise WA, Johnson S, Vi L, Njarlangattil A, Raykha C, Krill-Burger JM, Gallo PH, O'Gorman DB, Gan BS, Baratz ME, Ehrlich GD, Kathju S - BMC Med Genomics (2012)

Bottom Line: Quantitative real time RT-PCR confirmed the differential expression of select genes validating the microarray data analyses.These data also demonstrate that a collagen-rich environment differentially alters gene expression in these cells.In addition, Ingenuity pathway analysis of the specific biological pathways that differentiate DC-derived cells from carpal tunnel-derived cells has identified the potential involvement of microRNAs in this fibroproliferative disorder.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Surgery, Division of Plastic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. latsat@hotmail.com.

ABSTRACT

Background: Dupuytren's contracture (DC) is a fibroproliferative disorder characterized by the progressive development of a scar-like collagen-rich cord that affects the palmar fascia of the hand and leads to digital flexion contractures. DC is most commonly treated by surgical resection of the diseased tissue, but has a high reported recurrence rate ranging from 27% to 80%. We sought to determine if the transcriptomic profiles of fibroblasts derived from DC-affected palmar fascia, adjacent phenotypically normal palmar fascia, and non-DC palmar fascial tissues might provide mechanistic clues to understanding the puzzle of disease predisposition and recurrence in DC.

Methods: To achieve this, total RNA was obtained from fibroblasts derived from primary DC-affected palmar fascia, patient-matched unaffected palmar fascia, and palmar fascia from non-DC patients undergoing carpal tunnel release (6 patients in each group). These cells were grown on a type-1 collagen substrate (to better mimic their in vivo environments). Microarray analyses were subsequently performed using Illumina BeadChip arrays to compare the transcriptomic profiles of these three cell populations. Data were analyzed using Significance Analysis of Microarrays (SAM v3.02), hierarchical clustering, concordance mapping and Venn diagram.

Results: We found that the transcriptomic profiles of DC-disease fibroblasts and fibroblasts from unaffected fascia of DC patients exhibited a much greater overlap than fibroblasts derived from the palmar fascia of patients undergoing carpal tunnel release. Quantitative real time RT-PCR confirmed the differential expression of select genes validating the microarray data analyses. These data are consistent with the hypothesis that predisposition and recurrence in DC may stem, at least in part, from intrinsic similarities in the basal gene expression of diseased and phenotypically unaffected palmar fascia fibroblasts. These data also demonstrate that a collagen-rich environment differentially alters gene expression in these cells. In addition, Ingenuity pathway analysis of the specific biological pathways that differentiate DC-derived cells from carpal tunnel-derived cells has identified the potential involvement of microRNAs in this fibroproliferative disorder.

Conclusions: These data show that the transcriptomic profiles of DC-disease fibroblasts and fibroblasts from unaffected palmar fascia in DC patients are highly similar, and differ significantly from the transcriptomic profiles of fibroblasts from the palmar fascia of patients undergoing carpal tunnel release.

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Unsupervised Hierarchical Clustering of Expression Values Based on Sample Origin. The sample distributions of significantly different transcripts (959 transcripts, SAM v. 3.02) are displayed based on unsupervised, hierarchical, agglomerative clustering (Partek: v. 6.4) of log base 2 intensity values. A primary branch of the dendrogram distinguishes the expression values obtained from transcripts of the palmar fascia- and Dupuytren's-derived fibroblasts from those of the carpal tunnel-derived fibroblasts, indicating a distinct difference based on these tissues of origin. Dupuytren's and palmar fascia-derived fibroblasts also formed distinct clusters separate from each other at the next branching level despite their matched patient origin
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Figure 3: Unsupervised Hierarchical Clustering of Expression Values Based on Sample Origin. The sample distributions of significantly different transcripts (959 transcripts, SAM v. 3.02) are displayed based on unsupervised, hierarchical, agglomerative clustering (Partek: v. 6.4) of log base 2 intensity values. A primary branch of the dendrogram distinguishes the expression values obtained from transcripts of the palmar fascia- and Dupuytren's-derived fibroblasts from those of the carpal tunnel-derived fibroblasts, indicating a distinct difference based on these tissues of origin. Dupuytren's and palmar fascia-derived fibroblasts also formed distinct clusters separate from each other at the next branching level despite their matched patient origin

Mentions: Unsupervised hierarchical clustering was performed using the Partek program on log base 2 intensity values of the differentially expressed transcripts identified by the SAM program. Agglomerative clustering was performed to detect dissimilarity based on Euclidean distance with clusters linked based on average values in order to determine if major variations existed in gene expression profiles among the 3 groups [26]. The program was set to delineate the maximum number of clusters based on individual sample comparisons. The primary branch of the resulting dendrogram separated the transcripts of the PF and DC-derived fibroblasts from those of the CT-derived fibroblasts, indicating that significant differences in expression were based on patient origin (Figure 3). However, the DC- and PF-derived fibroblasts also formed clearly distinct clusters separate from each other at the next level of branching. Thus, all three cell groups exhibited distinctly different expression signatures with the greatest difference between the unpaired and the paired (DC-derived) samples.


Fibroblasts from phenotypically normal palmar fascia exhibit molecular profiles highly similar to fibroblasts from active disease in Dupuytren's Contracture.

Satish L, LaFramboise WA, Johnson S, Vi L, Njarlangattil A, Raykha C, Krill-Burger JM, Gallo PH, O'Gorman DB, Gan BS, Baratz ME, Ehrlich GD, Kathju S - BMC Med Genomics (2012)

Unsupervised Hierarchical Clustering of Expression Values Based on Sample Origin. The sample distributions of significantly different transcripts (959 transcripts, SAM v. 3.02) are displayed based on unsupervised, hierarchical, agglomerative clustering (Partek: v. 6.4) of log base 2 intensity values. A primary branch of the dendrogram distinguishes the expression values obtained from transcripts of the palmar fascia- and Dupuytren's-derived fibroblasts from those of the carpal tunnel-derived fibroblasts, indicating a distinct difference based on these tissues of origin. Dupuytren's and palmar fascia-derived fibroblasts also formed distinct clusters separate from each other at the next branching level despite their matched patient origin
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3375203&req=5

Figure 3: Unsupervised Hierarchical Clustering of Expression Values Based on Sample Origin. The sample distributions of significantly different transcripts (959 transcripts, SAM v. 3.02) are displayed based on unsupervised, hierarchical, agglomerative clustering (Partek: v. 6.4) of log base 2 intensity values. A primary branch of the dendrogram distinguishes the expression values obtained from transcripts of the palmar fascia- and Dupuytren's-derived fibroblasts from those of the carpal tunnel-derived fibroblasts, indicating a distinct difference based on these tissues of origin. Dupuytren's and palmar fascia-derived fibroblasts also formed distinct clusters separate from each other at the next branching level despite their matched patient origin
Mentions: Unsupervised hierarchical clustering was performed using the Partek program on log base 2 intensity values of the differentially expressed transcripts identified by the SAM program. Agglomerative clustering was performed to detect dissimilarity based on Euclidean distance with clusters linked based on average values in order to determine if major variations existed in gene expression profiles among the 3 groups [26]. The program was set to delineate the maximum number of clusters based on individual sample comparisons. The primary branch of the resulting dendrogram separated the transcripts of the PF and DC-derived fibroblasts from those of the CT-derived fibroblasts, indicating that significant differences in expression were based on patient origin (Figure 3). However, the DC- and PF-derived fibroblasts also formed clearly distinct clusters separate from each other at the next level of branching. Thus, all three cell groups exhibited distinctly different expression signatures with the greatest difference between the unpaired and the paired (DC-derived) samples.

Bottom Line: Quantitative real time RT-PCR confirmed the differential expression of select genes validating the microarray data analyses.These data also demonstrate that a collagen-rich environment differentially alters gene expression in these cells.In addition, Ingenuity pathway analysis of the specific biological pathways that differentiate DC-derived cells from carpal tunnel-derived cells has identified the potential involvement of microRNAs in this fibroproliferative disorder.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Surgery, Division of Plastic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. latsat@hotmail.com.

ABSTRACT

Background: Dupuytren's contracture (DC) is a fibroproliferative disorder characterized by the progressive development of a scar-like collagen-rich cord that affects the palmar fascia of the hand and leads to digital flexion contractures. DC is most commonly treated by surgical resection of the diseased tissue, but has a high reported recurrence rate ranging from 27% to 80%. We sought to determine if the transcriptomic profiles of fibroblasts derived from DC-affected palmar fascia, adjacent phenotypically normal palmar fascia, and non-DC palmar fascial tissues might provide mechanistic clues to understanding the puzzle of disease predisposition and recurrence in DC.

Methods: To achieve this, total RNA was obtained from fibroblasts derived from primary DC-affected palmar fascia, patient-matched unaffected palmar fascia, and palmar fascia from non-DC patients undergoing carpal tunnel release (6 patients in each group). These cells were grown on a type-1 collagen substrate (to better mimic their in vivo environments). Microarray analyses were subsequently performed using Illumina BeadChip arrays to compare the transcriptomic profiles of these three cell populations. Data were analyzed using Significance Analysis of Microarrays (SAM v3.02), hierarchical clustering, concordance mapping and Venn diagram.

Results: We found that the transcriptomic profiles of DC-disease fibroblasts and fibroblasts from unaffected fascia of DC patients exhibited a much greater overlap than fibroblasts derived from the palmar fascia of patients undergoing carpal tunnel release. Quantitative real time RT-PCR confirmed the differential expression of select genes validating the microarray data analyses. These data are consistent with the hypothesis that predisposition and recurrence in DC may stem, at least in part, from intrinsic similarities in the basal gene expression of diseased and phenotypically unaffected palmar fascia fibroblasts. These data also demonstrate that a collagen-rich environment differentially alters gene expression in these cells. In addition, Ingenuity pathway analysis of the specific biological pathways that differentiate DC-derived cells from carpal tunnel-derived cells has identified the potential involvement of microRNAs in this fibroproliferative disorder.

Conclusions: These data show that the transcriptomic profiles of DC-disease fibroblasts and fibroblasts from unaffected palmar fascia in DC patients are highly similar, and differ significantly from the transcriptomic profiles of fibroblasts from the palmar fascia of patients undergoing carpal tunnel release.

Show MeSH
Related in: MedlinePlus