Optimal molecular profiling of tissue and tissue components

Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This article reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies, and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing, and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high quality, appropriately anatomically tagged scientific results. In optimized protocols is a source of inefficiency in current life science research. Improvement in this area will significantly increase life science quality and productivity. The article is divided into introduction, materials, protocols, and notes sections. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this article, readers are advised to read through the entire article first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.     

Metaplasia of aortic tissue into tracheal tissue. Surgical perspectives

Tracheal reconstruction after extensive resection remains an unsolved surgical problem. Numerous attempts have been made using tracheal grafts or prosthetic conduits with disappointing results. In this study, we propose a new alternative using an aortic autograft as tracheal substitute. In a first series of experiments, a half circumference of two rings was replaced with an autologous carotid artery patch. In a second series, a complete segment of trachea was replaced with an autologous aortic graft supported by an endoluminal tracheal stent. No dehiscence or stenosis was observed. Microscopic examinations at 3 and 6 months showed the replacement of the aortic tissue by tracheal tissue comprising neoformation of cartilage and mucociliary or non-keratinizing metaplastic polystratified squamous epithelium. Although these results need to be confirmed by a larger series of experiments, they showed that a vascular tissue placed in a different environment with a different function can be submitted to a metaplastic transformation which tends to restore a normal structure adapted to its new function. These remarkable findings offer new perspectives in tracheal reconstruction in human.     

Soft tissue vibrations within one soft tissue compartment

The concept of muscle tuning suggests that vibrations of the soft tissue compartments of the leg initiated by impacts are minimized by muscular activity prior to heel-strike of heel-toe running. For the quantification of muscle tuning it has been assumed (1) that the soft tissue compartment acts as one lumped mass and (2) that vibration energy dissipation does occur within one muscle. The purpose of this study was to test these two assumptions. It was hypothesized that (H1) the movement of the soft tissue compartment is not homogeneous, (H2) the vibration frequencies for different muscles within one soft tissue compartment are different and (3) attenuation of vibration movement within one muscle does occur. Soft tissue vibrations were measured using accelerometers on four locations on the quadriceps soft tissue compartment during heel-toe running. There were differences in the peak soft tissue acceleration and time of peak acceleration between accelerometer locations. The dominant frequency was similar throughout the soft tissue compartment, however; there was an attenuation of high-frequency vibration energy between distal and proximal points overlying one muscle. This evidence suggests that accelerometer placement is important when quantifying the acceleration magnitude and timing of peak soft tissue compartment but not when estimating the resonant vibration characteristics of a soft tissue compartment. It also provides initial evidence to support the idea that vibration control through muscle tuning may be achieved through changes in energy dissipating properties within the soft tissue compartment.     

Proteolytic activation of tissue plasminogen activator by plasma and tissue enzymes

Tissue kallikrein and factor Xa were found to activate tissue plasminogen activator (t-PA) at a rate comparable with that of plasmin. During the activation reaction, the single-chain molecule was converted into a two-chain form. A slight t-PA activating activity was also found in plasma kallikrein. Other activated coagulation factors, factor XIIa, factor XIa, factor IXa, factor VIIa, thrombin and activated protein C had no effect on t-PA activation. t-PA was also activated by a tissue kallikrein-like enzyme that was isolated from the culture medium of melanoma cells. These results indicate that tissue kallikrein and factor Xa may participate in the extrinsic pathway of human fibrinolysis.     

Sensitivity of tissue differentiation and bone healing predictions to tissue properties

Computational models are employed as tools to investigate possible mechano-regulation pathways for tissue differentiation and bone healing. However, current models do not account for the uncertainty in input parameters, and often include assumptions about parameter values that are not yet established. The aim was to clarify the importance of the assumed tissue material properties in a computational model of tissue differentiation during bone healing. An established mechano-biological model was employed together with a statistical approach. The model included an adaptive 2D finite element model of a fractured long bone. Four outcome criteria were quantified: (1) ability to predict sequential healing events, (2) amount of bone formation at specific time points, (3) total time until healing, and (4) mechanical stability at specific time points. Statistical analysis based on fractional factorial designs first involved a screening experiment to identify the most significant tissue material properties. These seven properties were studied further with response surface methodology in a three-level Box–Behnken design. Generally, the sequential events were not significantly influenced by any properties, whereas rate-dependent outcome criteria and mechanical stability were significantly influenced by Young's modulus and permeability. Poisson's ratio and porosity had minor effects. The amount of bone formation at early, mid and late phases of healing, the time until complete healing and the mechanical stability were all mostly dependent on three material properties; permeability of granulation tissue, Young's modulus of cartilage and permeability of immature bone. The consistency between effects of the most influential parameters was high. To increase accuracy and predictive capacity of computational models of bone healing, the most influential tissue mechanical properties should be accurately quantified.     

Regeneration of corneal tissue

Penetrating wounds in rabbit corneas heal to form an opaque tissue that eventually becomes transparent. DNA content, dry weight, water content, and collagen content of the tissue gradually become more like that of normal cornea. The healing tissues also synthesize low-sulfated keratan sulfate, hyaluronic acid, and heparan sulfate. These glycosaminoglycans are not found in normal adult corneas but have been reported in fetal corneas. Previous studies have shown that collagen from healing corneal wounds and collagen from fetal corneas have very similar cross-linking patterns, but these patterns are different from those in normal adult collagen. The similarities between collagen and glycosaminoglycans in healing corneal wounds and in fetuses suggest some recapitulation of ontogenetic processes. The biochemical sequence and eventual return of transparency to the rabbit cornea indicate a capability for true regeneration of stromal tissue in the rabbit.     

Cryopreservation of adipose tissue

The main obstacle to achieving favorable outcome of soft-tissue augmentation after autologous fat transplantation is unpredictable long-term results due to the high rate of absorption in the grafted site. At the present time, adipose aspirates can only be used for immediate autologous fat grafting during the same procedure in which liposuction is performed; therefore adipose aspirates obtained from the procedure are usually discarded. it has been a strong desire of both surgeons and patients to be able to preserve the adipose aspirates, if an optimal technique were available, for potential future applications. For the last several years, cryopreservation of adipose tissue has been studied extensively in the author''s laboratory. Several findings from this exciting translational research will lead to develop a reliable method for long-term preservation of adipose tissue in the future. in addition, successful long-term preservation of adipose tissue may open a new era in adipose tissue related tissue regeneration.