Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease processes. A technical challenge remains for high-throughput miRNA expression analysis as the number of miRNAs continues to increase with <it>in silico </it>prediction and experimental verification. Our study critically evaluated the performance of a novel miRNA expression profiling approach, quantitative RT-PCR array (qPCR-array), compared to miRNA detection with oligonucleotide microchip (microarray).</p> <p>Results</p> <p>High reproducibility with qPCR-array was demonstrated by comparing replicate results from the same RNA sample. Pre-amplification of the miRNA cDNA improved sensitivity of the qPCR-array and increased the number of detectable miRNAs. Furthermore, the relative expression levels of miRNAs were maintained after pre-amplification. When the performance of qPCR-array and microarrays were compared using different aliquots of the same RNA, a low correlation between the two methods (r = -0.443) indicated considerable variability between the two assay platforms. Higher variation between replicates was observed in miRNAs with low expression in both assays. Finally, a higher false positive rate of differential miRNA expression was observed using the microarray compared to the qPCR-array.</p> <p>Conclusion</p> <p>Our studies demonstrated high reproducibility of TaqMan qPCR-array. Comparison between different reverse transcription reactions and qPCR-arrays performed on different days indicated that reverse transcription reactions did not introduce significant variation in the results. The use of cDNA pre-amplification increased the sensitivity of miRNA detection. Although there was variability associated with pre-amplification in low abundance miRNAs, the latter did not involve any systemic bias in the estimation of miRNA expression. Comparison between microarray and qPCR-array indicated superior sensitivity and specificity of qPCR-array.</p

Altered Macrophage Phenotype Transition Impairs Skeletal Muscle Regeneration

Monocyte/macrophage polarization in skeletal muscle regeneration is ill defined. We used CD11b-diphtheria toxin receptor transgenic mice to transiently deplete monocytes/macrophages at multiple stages before and after muscle injury induced by cardiotoxin. Fat accumulation within regenerated muscle was maximal when ablation occurred at the same time as cardiotoxin-induced injury. Early ablation (day 1 after cardiotoxin) resulted in the smallest regenerated myofiber size together with increased residual necrotic myofibers and fat accumulation. However, muscle regeneration after late (day 4) ablation was similar to controls. Levels of inflammatory cells in injured muscle following early ablation and associated with impaired muscle regeneration were determined by flow cytometry. Delayed, but exaggerated, monocyte [CD11b+(CD90/B220/CD49b/NK1.1/Ly6G)−(F4/80/I-Ab/CD11c)−Ly6C+/−] accumulation occurred; interestingly, Ly6C+ and Ly6C− monocytes were present concurrently in ablated animals and control mice. In addition to monocytes, proinflammatory, Ly6C+ macrophage accumulation following early ablation was delayed compared to controls. In both groups, CD11b+F4/80+ cells exhibited minimal expression of the M2 markers CD206 and CD301. Nevertheless, early ablation delayed and decreased the transient accumulation of CD11b+F4/80+Ly6C−CD301− macrophages; in control animals, the later tissue accumulation of these cells appeared to correspond to that of anti-inflammatory macrophages, determined by cytokine production and arginase activity. In summary, impairments in muscle regeneration were associated with exaggerated monocyte recruitment and reduced Ly6C− macrophages; the switch of macrophage/monocyte subsets is critical to muscle regeneration

Plasminogen activator levels are influenced by location and varicosity in greater saphenous vein

AbstractPurpose: The plasminogen system, which includes tissue type plasminogen activator (tPA), urokinase type plasminogen activator (uPA), and their main inhibitor, plasminogen activator inhibitor type 1 (PAI-1), plays a major role in both fibrinolysis and tissue remodeling. This study compares the levels of tPA, uPA, and PAI-1 at the groin and ankle in normal and varicose greater saphenous vein (GSV).Methods: GSV was collected from patients undergoing varicose vein (VV) removal and from normal vein (NV) from arterial bypass procedures. Portions of the GSV at the groin and the ankle were minced and placed in serum-free media for 48 hours. Assays of the supernatants were obtained for tPA, uPA, and PAI-1 protein by enzyme-linked immunosorbent assay. Cyclohexamide and actinomycin D were also added to the media of the VV tissue explant supernatants to inhibit protein and RNA synthesis, respectively.Results: Levels of tPA were significantly higher at the groin (11 ± 2) than the ankle (5 ± 1) in the VV ( p < 0.005), and this trend was also seen in the NV (groin 10 ± 2 and ankle 7 ± 3). Levels of uPA were significantly higher in the groin VV (14 ± 4.3) than in NV (3.0 ± 0.8, p < 0.05). This difference, although not statistically significant, applied to the ankle as well (VV 14.5 ± 6.3 and NV 5.3 ± 2.7). No significant difference was seen between NV and VV for PAI-1 (NV, groin 155 ± 73 and ankle 113 ± 53, VV, groin 161 ± 20 and ankle 142 ± 38) or tPA. Inhibitor studies revealed no significant difference among control, cyclohexamide, and actinomycin D supernatants for tPA, suggesting release of protein rather than active synthesis. In contrast, inhibitor supernatants were significantly lower for uPA and PAI-1 than control supernatants ( p < 0.05), suggesting that uPA and PAI-1 were actively synthesized.Conclusions: In the tissue explant supernatant model uPA and PAI-1 are actively synthesized, but tPA is not. Levels of PAI-1 were comparable in all four groups. Levels of uPA in the varicose GSV were higher than in NV, suggesting a role for uPA in the pathologic makeup of VV. Levels of tPA were higher at the groin versus the ankle position, potentially explaining the previously described increased fibrinolytic activity seen at the groin. (J Vasc Surg 1996;24:719-24.

Patency of arterial repairs from wartime extremity vascular injuries

Background: Extremity vascular injury (EVI) causes significant disability in Veterans of the Afghanistan/Iraq conflicts. Advancements in acute trauma care improved survival and decreased amputations. The study of wartime EVI has relied on successful limb salvage as a surrogate for vascular repair. We used imaging studies as a specific measure of arterial repair durability. Methods: Service members with EVI were identified using the Department of Defense Trauma Registry and validated by chart abstraction. Inclusion criteria for the arterial patency subgroup included an initial repair attempt with subsequent imaging reports (duplex ultrasound, CT angiography, and angiogram) documenting initial patency. Results: The cohort of 527 included 140 Veterans with available imaging studies for 143 arterial repairs; median follow-up from injury time to last available imaging study was 19 months (Q1-Q3: 3-58; range: 1-175). Injury mechanism was predominantly explosions (52%) and gunshot wounds (42%). Of the 143 arterial repairs, 81% were vein grafts. Eight repairs were occluded, replaced or included in extremity amputations. One upper extremity and three transtibial late amputations were performed for chronic pain and poor function averaging 27 months (SD: 4; range: 24-32). Kaplan-Meier analysis estimated patency rates of 99%, 97%, 95%, 91% and 91% at 3, 6, 12, 24, and 36 months, respectively, with similar results for upper and lower extremity repairs. Explosive and gunshot wound injury mechanisms had similar patency rates and upper extremity injuries repaired with vein grafts had increased patency. Conclusions: Arterial repair mid-term patency in combat-related extremity injuries is excellent based on imaging studies for 143 repairs. Assertive attempts at acute limb salvage and vascular repair are justified with decisions for amputation versus limb salvage based on the overall condition of the patient and degree of concomitant nerve, orthopedic and soft tissue injuries rather than the presence of arterial injuries. Level of evidence: Therapeutic/care management, level IV

Temporal microRNA expression during in vitro myogenic progenitor cell proliferation and differentiation: regulation of proliferation by miR-682

MicroRNAs (miRNAs) regulate gene expression by repressing target genes at the posttranscriptional level. Since miRNAs have unique expression profiles in different tissues, they provide pivotal regulation of many biological processes. The present study defined miRNA expression during murine myogenic progenitor cell (MPC) proliferation and differentiation to identify miRNAs involved in muscle regeneration. Muscle-related gene expression analyses revealed that the time course and expression of myosin heavy chain (MHC) and transcription factors (Myf5, MyoD, myogenin, and Pax7) were similar during in vitro MPC proliferation/differentiation and in vivo muscle regeneration. Comprehensive profiling revealed that 139 or 16 miRNAs were significantly changed more than twofold [false discovery rate (FDR) < 0.05] during MPC differentiation or proliferation, respectively; cluster analyses revealed five distinct patterns of miRNA expression during the time course of MPC differentiation. Not unexpectedly, the largest miRNA changes occurred in muscle-specific miRNAs (miR-1, -133a, and -499), which were upregulated >10-fold during MPC differentiation (FDR < 0.01). However, several previously unreported miRNAs were differentially expressed, including miR-10b, -335-3p, and -682. Interestingly, the temporal patterns of miR-1, -499, and -682 expression during in vitro MPC proliferation/differentiation were remarkably similar to those observed during in vivo muscle regeneration. Moreover, in vitro inhibition of miR-682, the only miRNA upregulated in proliferating compared with quiescent MPC, led to decreased MPC proliferation, further validating our in vitro assay system for the identification of miRNAs involved in muscle regeneration. Thus the differentially expressed miRNAs identified in the present study could represent new regulatory elements in MPC proliferation and differentiation