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Biomarkers of disease differentiation: HCV recurrence versus acute cellular rejection.

Gehrau R, Mas V, Archer K, Maluf D - Fibrogenesis Tissue Repair (2012)

Bottom Line: Liver Transplantation (LT) is the optimal surgical treatment for HCV-cirrhotic patients at end-stage liver disease.The accurate differential diagnosis between both conditions is critical for treatment choice, and similar histological features represent a challenge for pathologists.Whole-genome gene expression (WGE) analyses through well-defined oligonucleotide microarray platforms represent a powerful tool for the molecular characterization of biological process.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Virginia, Department of Surgery, Transplant Division, P.O. Box 800625, 904 Lane Rd, Charlottesville, VA, 22908-0625, USA.

ABSTRACT
The wound-healing process induced by chronic hepatitis C virus (HCV) infection triggers liver damage characterized by fibrosis development and finally cirrhosis. Liver Transplantation (LT) is the optimal surgical treatment for HCV-cirrhotic patients at end-stage liver disease. However, acute cellular rejection (ACR) and HCV recurrence disease represent two devastating complications post-LT. The accurate differential diagnosis between both conditions is critical for treatment choice, and similar histological features represent a challenge for pathologists. Moreover, the HCV recurrence disease severity is highly variable post-LT. HCV recurrence disease progression is characterized by an accelerated fibrogenesis process, and almost 30% of those patients develop cirrhosis at 5-years of follow-up. Whole-genome gene expression (WGE) analyses through well-defined oligonucleotide microarray platforms represent a powerful tool for the molecular characterization of biological process. In the present manuscript, the utility of microarray technology is applied for the ACR and HCV-recurrence biological characterization in post-LT liver biopsy samples. Moreover, WGE analysis was performed to identify predictive biomarkers of HCV recurrence severity in formalin-fixed paraffin-embedded liver biopsies prospectively collected.

No MeSH data available.


Related in: MedlinePlus

Molecular characterization of HCV recurrence samples at diagnosis time for disease severity progression prediction. A. Schematic illustration of a retrospective analysis using prospectively collected FFPE liver biopsy samples at HCV recurrence diagnosis (A) and 3-years of follow-up (B) as time-point for classification. B. METAVIR score criteria used for the classification of FFPE liver biopsy samples. Liver biopsy samples at HCV recurrence diagnosis time were classified in three groups (G1, G2, and G3) depending on the fibrosis severity of paired 3-years follow-up biopsy samples. C. Dendrogram illustrating a supervised agglomerative hierarchical clustering with 50 differentially expressed beads identified between G1 vs. G3 using DASL assay.
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Figure 4: Molecular characterization of HCV recurrence samples at diagnosis time for disease severity progression prediction. A. Schematic illustration of a retrospective analysis using prospectively collected FFPE liver biopsy samples at HCV recurrence diagnosis (A) and 3-years of follow-up (B) as time-point for classification. B. METAVIR score criteria used for the classification of FFPE liver biopsy samples. Liver biopsy samples at HCV recurrence diagnosis time were classified in three groups (G1, G2, and G3) depending on the fibrosis severity of paired 3-years follow-up biopsy samples. C. Dendrogram illustrating a supervised agglomerative hierarchical clustering with 50 differentially expressed beads identified between G1 vs. G3 using DASL assay.

Mentions: Molecular profiling at early stages of the disease might provide important information regarding mechanisms involved in accelerated fibrogenesis progression as HCV recurrence severity indicator. Even more, analysis of historical liver biopsy samples represents a feasible research scenario. In this regard, genome-wide gene expression analysis has been performed in Formalin-Fixed Paraffin-Embedded (FFPE) liver biopsies at the time of HCV recurrence diagnosis [13,28]. HCV recurrence was defined as post-transplant increased serum level of Alanine Aminotransferase (ALT) and positive PCR for HCV as previously shown [28]. Progression of the disease was determined by the fibrosis severity in FFPE biopsy samples at 36 months post-LT (Figure 4A). Fibrosis stages were determined using METAVIR score system [29]. A total of 42 unique samples from 21 adult patients who underwent LT between 1995 and 2006 were included. Samples at HCV recurrence diagnosis time were grouped as Mild (G1; n = 8), Intermediate (G2; n = 5), and Severe (G3; n = 8) referred to the follow-up biopsy at 3-years post-LT (Figure 4B). The study population were composed by 25 (58%) and 18 (42%) white male and female HCV recipients. All patients did not receive HCV treatment, and the mean time from LT to HCV recurrence was 5.5 ± months. The predominant HCV genotype were 1 (84%), and 7 patients were infected with genotypes 2 or 3. Total RNA was isolated using Recover All™ Total Nucleic Acid Isolation Kit (Ambion, Austin, TX, USA). Quality control parameters for required RNA purity for WGE analysis have been established and tested [28]. Differential gene expression analysis among study groups were performed using WGE-DASL® Assay following manual instructions (Illumina Inc., USA). HumanRef-8 Expression BeadChips (Illumina, Inc., USA) hybridization and followed analyses were described in Mas et al 2011 [28]. From the analysis, a total of 57 bead types were found to be significant (p ≤ 0.001) and differentially expressed after a moderate F test statistical assay. By linear contrast examination, fourteen beads were found between G1 vs. G2, five beads between G2 vs. G3, and fifty beads between G1 vs. G3. Agglomerative hierarchical clustering analysis was performed by incorporating only the 50 beads differentially expressed between G1 vs. G3. The analysis displayed two independent groups composed by G1 or G3 samples. Interestingly, G2 samples were found to be randomly associated within both clusters may be reflecting a pathology miss-classification component (Figure 4C). Gene ontology and gene pathway analysis, using only those 50 beads, identified 9 gene-associated networks, whereas the top-scored was involved in cellular development, infection mechanism, and antigen presentation. The molecular and cellular function analysis associated those beads with cell-to-cell signaling and interaction, cell death, cell morphology, and carbohydrates metabolism. Interestingly, genes associated with T cells biology such as IL-28RA, IL-28, suppressor of T cell receptor signaling 1 (STS1), and CAP-GLY domain containing linker protein 4 (CLIP4) were found to be significantly increased in samples with predicted severe fibrosis [28].


Biomarkers of disease differentiation: HCV recurrence versus acute cellular rejection.

Gehrau R, Mas V, Archer K, Maluf D - Fibrogenesis Tissue Repair (2012)

Molecular characterization of HCV recurrence samples at diagnosis time for disease severity progression prediction. A. Schematic illustration of a retrospective analysis using prospectively collected FFPE liver biopsy samples at HCV recurrence diagnosis (A) and 3-years of follow-up (B) as time-point for classification. B. METAVIR score criteria used for the classification of FFPE liver biopsy samples. Liver biopsy samples at HCV recurrence diagnosis time were classified in three groups (G1, G2, and G3) depending on the fibrosis severity of paired 3-years follow-up biopsy samples. C. Dendrogram illustrating a supervised agglomerative hierarchical clustering with 50 differentially expressed beads identified between G1 vs. G3 using DASL assay.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368799&req=5

Figure 4: Molecular characterization of HCV recurrence samples at diagnosis time for disease severity progression prediction. A. Schematic illustration of a retrospective analysis using prospectively collected FFPE liver biopsy samples at HCV recurrence diagnosis (A) and 3-years of follow-up (B) as time-point for classification. B. METAVIR score criteria used for the classification of FFPE liver biopsy samples. Liver biopsy samples at HCV recurrence diagnosis time were classified in three groups (G1, G2, and G3) depending on the fibrosis severity of paired 3-years follow-up biopsy samples. C. Dendrogram illustrating a supervised agglomerative hierarchical clustering with 50 differentially expressed beads identified between G1 vs. G3 using DASL assay.
Mentions: Molecular profiling at early stages of the disease might provide important information regarding mechanisms involved in accelerated fibrogenesis progression as HCV recurrence severity indicator. Even more, analysis of historical liver biopsy samples represents a feasible research scenario. In this regard, genome-wide gene expression analysis has been performed in Formalin-Fixed Paraffin-Embedded (FFPE) liver biopsies at the time of HCV recurrence diagnosis [13,28]. HCV recurrence was defined as post-transplant increased serum level of Alanine Aminotransferase (ALT) and positive PCR for HCV as previously shown [28]. Progression of the disease was determined by the fibrosis severity in FFPE biopsy samples at 36 months post-LT (Figure 4A). Fibrosis stages were determined using METAVIR score system [29]. A total of 42 unique samples from 21 adult patients who underwent LT between 1995 and 2006 were included. Samples at HCV recurrence diagnosis time were grouped as Mild (G1; n = 8), Intermediate (G2; n = 5), and Severe (G3; n = 8) referred to the follow-up biopsy at 3-years post-LT (Figure 4B). The study population were composed by 25 (58%) and 18 (42%) white male and female HCV recipients. All patients did not receive HCV treatment, and the mean time from LT to HCV recurrence was 5.5 ± months. The predominant HCV genotype were 1 (84%), and 7 patients were infected with genotypes 2 or 3. Total RNA was isolated using Recover All™ Total Nucleic Acid Isolation Kit (Ambion, Austin, TX, USA). Quality control parameters for required RNA purity for WGE analysis have been established and tested [28]. Differential gene expression analysis among study groups were performed using WGE-DASL® Assay following manual instructions (Illumina Inc., USA). HumanRef-8 Expression BeadChips (Illumina, Inc., USA) hybridization and followed analyses were described in Mas et al 2011 [28]. From the analysis, a total of 57 bead types were found to be significant (p ≤ 0.001) and differentially expressed after a moderate F test statistical assay. By linear contrast examination, fourteen beads were found between G1 vs. G2, five beads between G2 vs. G3, and fifty beads between G1 vs. G3. Agglomerative hierarchical clustering analysis was performed by incorporating only the 50 beads differentially expressed between G1 vs. G3. The analysis displayed two independent groups composed by G1 or G3 samples. Interestingly, G2 samples were found to be randomly associated within both clusters may be reflecting a pathology miss-classification component (Figure 4C). Gene ontology and gene pathway analysis, using only those 50 beads, identified 9 gene-associated networks, whereas the top-scored was involved in cellular development, infection mechanism, and antigen presentation. The molecular and cellular function analysis associated those beads with cell-to-cell signaling and interaction, cell death, cell morphology, and carbohydrates metabolism. Interestingly, genes associated with T cells biology such as IL-28RA, IL-28, suppressor of T cell receptor signaling 1 (STS1), and CAP-GLY domain containing linker protein 4 (CLIP4) were found to be significantly increased in samples with predicted severe fibrosis [28].

Bottom Line: Liver Transplantation (LT) is the optimal surgical treatment for HCV-cirrhotic patients at end-stage liver disease.The accurate differential diagnosis between both conditions is critical for treatment choice, and similar histological features represent a challenge for pathologists.Whole-genome gene expression (WGE) analyses through well-defined oligonucleotide microarray platforms represent a powerful tool for the molecular characterization of biological process.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Virginia, Department of Surgery, Transplant Division, P.O. Box 800625, 904 Lane Rd, Charlottesville, VA, 22908-0625, USA.

ABSTRACT
The wound-healing process induced by chronic hepatitis C virus (HCV) infection triggers liver damage characterized by fibrosis development and finally cirrhosis. Liver Transplantation (LT) is the optimal surgical treatment for HCV-cirrhotic patients at end-stage liver disease. However, acute cellular rejection (ACR) and HCV recurrence disease represent two devastating complications post-LT. The accurate differential diagnosis between both conditions is critical for treatment choice, and similar histological features represent a challenge for pathologists. Moreover, the HCV recurrence disease severity is highly variable post-LT. HCV recurrence disease progression is characterized by an accelerated fibrogenesis process, and almost 30% of those patients develop cirrhosis at 5-years of follow-up. Whole-genome gene expression (WGE) analyses through well-defined oligonucleotide microarray platforms represent a powerful tool for the molecular characterization of biological process. In the present manuscript, the utility of microarray technology is applied for the ACR and HCV-recurrence biological characterization in post-LT liver biopsy samples. Moreover, WGE analysis was performed to identify predictive biomarkers of HCV recurrence severity in formalin-fixed paraffin-embedded liver biopsies prospectively collected.

No MeSH data available.


Related in: MedlinePlus