Effects Of Tissue Processing Research Articles

Abstract B031: The effects of tissue processing and microfluidic factors on single-cell RNA-sequencing data quality in colorectal tissues

Abstract Our HTAN (Human Tumor Atlas Network) study presented in Chen et al. documented single-cell RNA-sequencing (scRNA-seq) data on 128 human colonic specimens for mapping out distinct paths for polyp to cancer transformations. What we have not detailed is our optimizations on the droplet-based scRNA-seq approach that generate high quality data from challenging tissues such as the colonic epithelium. In this work, we provide a systematic dissection of tissue processing and microfluidic encapsulation factors that affect data quality generated on colonic epithelial cells using an open droplet-based scRNA-seq platform (inDrops). We optimized our process based on these factors to significantly decrease dying cell bodies and ambient RNA from being co-encapsulated with true cells, which led to the development of the current scRNA-seq protocol used for human specimens. We have also developed pre-filtering data metrics to score data quality stemming from degree of ambient contamination. We envision that these experimental optimizations reduce the amount of introduced artifacts, leading to more rigorous biological interpretations. Citation Format: Deronisha L. Arceneaux, Zhengyi Chen, Joey Simmons, Bob Chen, Cody Heiser, Yanwen Xu. The effects of tissue processing and microfluidic factors on single-cell RNA-sequencing data quality in colorectal tissues [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B031.

A mechanical non-enzymatic method for isolation of mouse embryonic fibroblasts.

Mouse embryonic fibroblasts (MEFs) accessibility coupled with their simple generation make them as a typical embryonic cell model and feeder layer for in vitro expansion of pluripotent stem cells (PSCs). In this study, a mechanical isolation technique was adopted to isolate MEFs and the efficiency of this technique was compared with enzymatic digestion method.The suspended MEFs were prepared either by mechanical method or 0.25% trypsin enzymatic digestion. The effect of tissue processing on cell apoptosis/necrosis, morphology, viable cell yield, population doubling time, surface marker expression, and the capacity to support PSCs were determined. The mechanical method yielded a significantly higher number of viable cells. However, it showed similar morphology and proliferation characteristics as compared to enzymatic digestion. The mechanical method induced slight apoptosis in MEFs; however, it did not exert the necrotic effect of trypsinization. Treatment of tissue slurry with trypsin solution caused cell lysis and subsequently cell clump formation. Mechanically isolated cells exhibited a higher expression of the MEF surface antigens Sca1, CD106, and CD105. The PSCs on mechanically isolated MEFs displayed a higher expression of pluripotency genes, and formed more compact colonies with a stronger tendency to crowding compared with those cultured on cells isolated by enzymatic digestion.The mechanical method based on tissue inter-syringe processing is relatively a rapid and simple method for MEF isolation. Compared to the enzymatic digestion, the cells obtained from this method show higher expression of embryonic fibroblasts markers and a more functional capacity in supporting PSCs culture.

Effects of tissue processing on bioactivity of cartilage matrix-based hydrogels encapsulating osteoconductive particles

In the treatment of severe traumatic brain injury (TBI), decompressive craniectomy is commonly used to remove a large portion of calvarial bone to allow unimpeded brain swelling. Hydrogels have the potential to revolutionize TBI treatment by permitting a single-surgical intervention, remaining pliable during brain swelling, and tuned to regenerate bone after swelling has subsided. With this motivation, our goal is to present a pliable material capable of regenerating calvarial bone across a critical size defect. We therefore proposed the use of a methacrylated solubilized decellularized cartilage (MeSDCC) hydrogel encapsulating synthetic osteogenic particles of hydroxyapatite nanofibers, bioglass microparticles, or added rat bone marrow-derived mesenchymal stem cells (rMSCs) for bone regeneration in critical-size rat calvarial defects. Fibrin hydrogels were employed as a control material for the study. MeSDCC hydrogels exhibited sufficient rheological performance for material placement before crosslinking ( > 500 Pa), and sufficient compressive moduli post-crosslinking (E > 150 kPa). In vitro experiments suggested increased calcium deposition for cells seeded on the MeSDCC material; however, in vivo bone regeneration was minimal in both MeSDCC and fibrin groups, even with colloidal materials or added rMSCs. Minimal bone regeneration in the MeSDCC test groups may potentially be attributed to cartilage solubilization after decellularization, in which material signals may have degraded from enzymatic treatment. Looking to the future, an improvement in the bioactivity of the material will be crucial to the success of bone regeneration strategies for TBI treatment.

Laser micro-ablation of fibrocartilage tissue: Effects of tissue processing on porosity modification and mechanics.

The temporomandibular joint disk (TMJd) is an extremely dense and avascular fibrocartilaginous extracellular matrix (ECM) resulting in a limited regenerative capacity. The use of decellularized TMJd as a biocompatible scaffold to guide tissue regeneration is restricted by innate subcellular porosity of the ECM that hinders cellular infiltration and regenerative events. Incorporation of an artificial microporosity through laser micro-ablation (LMA) can alleviate these cell and diffusion based limitations. In this study, LMA was performed either before or after decellularization to assess to effect of surfactant treatment on porosity modification as well as the resultant mechanical and physical scaffold properties. Under convective flow or agitation schemes, pristine and laser ablated disks were decellularized using either low (0.1% w/v) or high (1% w/v) concentrations of sodium dodecyl sulfate (SDS). Results show that lower concentrations of SDS minimized collagen degradation and tissue swelling while retaining its capacity to solubilize cellular content. Regardless of processing scheme, laser ablated channels incorporated after SDS treatment were relatively smaller and more uniform than those incorporated before SDS treatment, indicating an altered laser interaction with surfactant treated tissues. Smaller channels correlated with less disruption of native biomechanical properties indicating surfactant pre-treatment is an important consideration when using LMA to produce artificial porosity in ex vivo derived tissues. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1858-1868, 2018.

Techniques for Maximizing the Performance of Molecular Pathology Testing: Responsibilities of All Pathologists.

Molecular pathological analysis has an expanding role in patient diagnosis and management. The performance of these techniques relies on excellent laboratory procedures. However, the crucial step is obtaining the best samples for molecular analysis. Archiving and selection of these are the responsibilities of all pathologists even if they are not working at a center with molecular pathological facilities. This review focuses on the features of different types of materials for molecular pathological analysis. Many steps that might affect the results, including communication between the pathologist and the oncology team, features of different types of materials (cytological, tissue blocks, biopsy, circulating tumor cells (CTCs) and cell-free circulating nucleic acids), effects of tissue processing, methods for selecting the best material, and tissue saving and tumor enrichment methods are discussed. The procedures for referral to a center for molecular pathological analysis are also mentioned. Awareness of the importance of the cytopathological and histopathological material of the patients for future molecular pathological analysis by pathologists is of the utmost importance.

Effect of Tissue Processing on Clinical Outcomes of Primary Anterior Cruciate Ligament Reconstruction Using Allograft

Effect of Tissue Processing on Clinical Outcomes of Primary Anterior Cruciate Ligament Reconstruction Using Allograft

Effect of Tissue Processing on Clinical Outcomes of Primary ACL Reconstuction Using Allograft (SS-04)

Effect of Tissue Processing on Clinical Outcomes of Primary ACL Reconstuction Using Allograft (SS-04)

Analysis of differential shrinkage in frozen brain sections and its implications for the use of guard zones in stereology

Increasing numbers of neuroanatomists are using stereological methods, and unbiased stereological estimation rules recommend the use of guard zones with the optical disector method to count objects of interest within a volume. Although these methods are statistically unbiased, we believe there is a need to explore sources of systematic bias (e.g., effects of tissue processing and sectioning) that may be affecting estimates of object number. Toward this end, we evaluated neuron distribution through, and tissue shrinkage in, non-embedded tissue cut on a freezing microtome. Our data show that in the x- and y-planes there are minimal changes in tissue area during tissue processing, sectioning, and staining. In the z-axis (perpendicular to the cutting surface), however, sections shrink to ∼25% of the cut thickness. This z-axis shrinkage was quite variable between sections (coefficient of variation about 10%) but stable within the same section (coefficient of variation about 3%). Lastly, individual particle densities are non-uniform through the thickness of the section when the densities should have been uniform. We advise experimenters to use a new protocol, a modified optical disector, for estimation when objects to be counted are marked such that the x-, y-, and z-coordinates are recorded through the full thickness of a section and guard zones are applied post data collection based on the characteristics of the object distribution along the z-axis. It is likely that individual experiments with different embedding materials and histological processing steps could require guard zones of varying sizes, or none at all, depending on object distribution in the z-axis.

Effect of Tissue Processing on Assessment of Endoscopic Intestinal Biopsies in Dogs and Cats

Prior studies failed to detect significant association between hypoalbuminemia and small intestinal lesions. Use of pictorial templates will enhance consistency of interpathologist interpretation and identification of intestinal lesions associated with hypoalbuminemia. Tissues from 62 dogs and 25 cats examined as clinical cases at 7 referral veterinary practices in 4 countries. Retrospective, observational study. Histopathology slides from sequential cases undergoing endoscopic biopsy were examined by 4 pathologists by pictorial templates. Changes for 9 microscopic features were recorded as normal, mild, moderate or severe, and 2- and 4-point scales were tested for consistency of interpretation. Logistic regression models determined odds ratios (OR) of histologic lesions being associated with hypoalbuminemia while kappa statistics determined agreement between pathologists on histologic lesions. There was poor agreement (kappa = -0.013 to 0.3) between pathologists, and institution of origin of slides had effect (kappa = 1.0 for 3 of 4 lesions on slides from Institution 5) on agreement between pathologists on selected histologic features. Using 2 point as opposed to 4-point grading scale increased agreement between pathologists (maximum kappa = 0.69 using 4-point scale versus maximum kappa = 1.0 using 2-point scale). Significant association (P = .019- .04; 95% OR = 3.14-10.84) between lacteal dilation and hypoalbuminemia was found by 3 pathologists. Substantial inconsistency between pathologists remains despite use of pictorial template because of differences in slide processing. Distinguishing between mild and moderate lesions might be important source of the disagreement among pathologists.

Combined effects of formalin fixation and tissue processing on immunorecognition

It is accepted that aldehyde-based fixation of cells can affect immunodetection of antigens; however, the effects of tissue processing on immunodetection have not been analyzed systematically. We investigated the effects of aldehyde-based fixation and the various cumulative steps of tissue processing on immunohistochemical detection of specific antigens. DU145 (prostate) and SKOV3 (ovarian) cancer cell lines were cultured as monolayers on microscope slides. Immunohistochemical detection of Ki67/MIB-1 and proliferating cell nuclear antigen (PCNA) was evaluated after various fixation times in 10% neutral buffered formalin and after each of the several cumulative steps of tissue processing. The effect of antigen retrieval (AR) was evaluated concomitantly as an additional variable. Our results indicate that in addition to fixation, each of the tissue processing steps has effects on immunorecognition of the epitopes recognized by these antibodies. Extensive dehydration through ethanols to absolute ethanol had only modest effects, except for the detection of Ki67/MIB-1 in SKOV-3 cells where the effect was stronger. In general, however, establishment of a hydrophobic environment by xylene resulted in the greatest decrease in immunorecognition. AR compensated for most, but not all, of the losses in staining following fixation and exposure to xylene; however, AR gave consistent results for most steps of tissue processing, which suggests that AR also should be used for staining PCNA. The cellular variations that were observed indicate that the effects of fixation and other steps of tissue processing may depend on how antigens are packaged by specific cells.

Special symposium: fixation and tissue processing models

Fixation and processing of tissue to paraffin blocks permit thin (4-5 µm) sections of tissues to be cut. Tissues and their subcellular components and surrounding stroma are visualized by cutting thin sections and staining them histochemically or immunohistochemically and viewing the sections using a bright field microscope. During the last century, anatomists and pathologists have used fixation with 10% neutral buffered formalin (10% NBF) as the fixative of choice. Also, both human and veterinary pathologists have trained to use fixation with 10% NBF, so these professionals are reluctant to change the familiar microscopic appearance of diagnostic tissues by using different fixatives. In addition, the effects of tissue processing on the microscopic appearance of tissue essentially has been ignored in most studies. Archives of paraffin blocks of pathological tissue contain essentially paraffin blocks fixed in 10% NBF. Therefore, if retrospective studies use archival paraffin blocks to correlate the molecular features of diseases with their outcomes, the studies must be based on tissue fixed in 10% NBF. Studies of how fixation in 10% NBF interacts with histochemical and immunohistochemical staining are limited in number and most are based on relatively long fixation times (≥36 h). Currently, fixation times in 10% NBF have been reduced to <24 h. Little is known about fixation in 10% NBF and its interaction with tissue processing for any period of fixation, especially short times. Less is known about how fixation of tissues with 10% NBF interacts with more modern assays using immunohistochemistry, real time quantitative polymerise chain reaction (PCR), and techniques that depend on analysis of proteins extracted from paraffin blocks including multiplex immunoassays or mass spectrometry. In general, multiple antibody–antigen combinations are reported not to work in tissues fixed in 10% NBF, i.e., loss of immunorecognition is nearly complete for such antibody–antigen combinations as Ki67/MIB, estrogen receptor alpha (ERα) and Progesterone receptor (PR), and partial for Bcl-2. Several models have been developed to study the interactions of tissue fixation and immunorecognition, but most have viewed the problem with immunorecognition as completely caused by fixation. Also, some of the models discussed in this special symposium do not predict the effects of fixation on frozen tissues fixed in 10% NBF and not processed to paraffin blocks. This article is a brief review of issues attending the use of 10% NBF combined with tissue processing as an interrelated process to study biomarkers identified by immunohistochemistry.

Tubular and Interstitial Nephrocalcinosis

We determined whether nephrocalcinosis is common and whether its detection is influenced by renal tissue processing. Renal cortical and papillary tissue was obtained from the unaffected parts of 15 kidneys removed due to an oncological indication. The effect of tissue processing on the loss of crystals was studied in a kidney with nephrocalcinosis due to chronic pyelonephritis. Immediately frozen and formaldehyde fixed sections were analyzed by polarized light and Raman spectroscopy, and stained for calcium (Yasue) and hyaluronan. Although 13 of 15 snap-frozen sections from tumor kidneys contained birefringent particles (mean +/- SD 3.2 +/- 2.9 particles per cm(2)) in the renal tubules, this was not considered nephrocalcinosis because the crystals were not attached to the epithelial lining. Interstitial nephrocalcinosis was found on Yasue stain in 3 of 15 kidneys with tumor (20%). Calcium deposits were found in the papillary interstitium only, always together with hyaluronan. Formaldehyde fixed sections from the pyelonephritis kidney contained fewer renal tubular cell associated birefringent particles than immediately frozen sections (9.4 +/- 1.9 vs 41.6 +/- 1.2 per cm(2)). Particles were composed of calcium oxalate monohydrate (Yasue and Raman). There are 2 distinct forms of nephrocalcinosis, including tubular nephrocalcinosis, which seems to be reserved for specific conditions such as chronic pyelonephritis, and interstitial nephrocalcinosis. The incidence of tubular calcium oxalate nephrocalcinosis could be underestimated due to the loss of crystals during tissue processing for routine histology. The crystal binding molecule hyaluronan may have a role in the 2 forms of nephrocalcinosis.

Effect of Tissue Processing on the Ability to Recover Nucleic Acid from Specific Renal Tissue Compartments by Laser Capture Microdissection

The anatomic heterogeneity of the nephron poses obstacles to microdissection of individual renal compartments for analysis of gene expression. We have systematically analyzed the effects of fixation time and nuclear staining on the ability to recover nucleic acid from individual renal compartments by laser capture microdissection (LCM). Formalin-fixed kidney sections from Wistar rats and archival human renal biopsies were used for DNA analysis. From 1 to 10 individual glomeruli and from 1 to 10 individual proximal tubules were captured sequentially onto polymer films. DNA for β-globin could be amplified by PCR from even a single glomerulus or tubule. Optimal conditions for DNA amplification were brief (1- or 2-day) formalin fixation. Use of nuclear counterstains, including Weigert’s hematoxylin, Harris’s hematoxylin, Mayer’s hematoxylin, or methyl green, did not adversely affect the ability to extract and amplify DNA. For RNA extraction, glomeruli and tubules were microdissected from renal cryostat sections stored for up to 6 months. By RT-PCR, mRNA expression of the glomerulus-specific gene, Wilms’ tumor-1, was identified in as few as 5 microdissected glomeruli and of the tubule-specific gene, aminopeptidase N, in as few as 5 microdissected tubules, with no cross-contamination between renal compartments. Our findings indicate that the LCM method can successfully microdissect pure glomerular and tubular tissue compartments and that the optimal fixation and staining conditions are those employed routinely for renal biopsies, namely overnight formalin fixation and hematoxylin counterstain for DNA extraction, and cryostat sectioning with hematoxylin counterstain for RNA extraction. The specificity of LCM coupled with the sensitivity of RT-PCR should prove a powerful tool for the analysis of gene expression in specific renal compartments from archival human renal biopsies.

Microassay for the assessment of low levels of hydroxyproline.

Microassay for the assessment of low levels of hydroxyproline.

Effect of tissue processing on colloidal gold cytochemistry.

The aim of cytochemical techniques is to localize specific biochemical components in particular tissue and cell compartments. However, since preparation of tissues for structural observation results in major alterations of the properties of their components, a major problem is to retain an adequate degree of their biochemical properties as well as adequate structural preservation. In the present study, we describe results obtained using various colloidal gold cytochemical techniques on tissues processed through different approaches. We found that any manipulation of the tissue during its processing can result in modifications of tissue components, leading to problems in cytochemistry. Indeed, washing of the tissue before fixation, the nature of the fixative solution, the chemical basis of the resins, and the physical conditions of embedding can all introduce changes in tissue components which can be cytochemically demonstrated. This has been illustrated with application of the protein A-gold, lectin-gold, and enzyme-gold cytochemical techniques on tissues submitted to different processings: fixation by perfusion or by immersion; glutaraldehyde vs paraformaldehyde fixative solutions; cryo-ultramicrotomy; embedding in epoxy, GMA, Lowicryl, or LR resins. The results obtained have demonstrated that conditions for optimal labeling must be worked out for each class of binding sites, and that no single procedure can be recommended as THE best approach in cytochemistry.

Immunocytochemical methods: a technical overview

The most commonly used immunocytochemical techniques and their applications are described. Problems relating to retention of tissue immunoreactivity and specificity of antibodies are discussed with special reference to the effects of tissue processing, presence of cross-reacting antibodies and lineage non-specificity of monoclonal antibodies.

Effect of tissue processing on the immunostaining of inflammatory cell surface epitopes identified by monoclonal antibodies

Optimal tissue processing conditions were defined for the immunohistochemical detection of inflammatory cell surface epitopes identified by OKT3, OKT4, OKT6, OKT8, OKIa1, OKM1, Leu7 and pan B cell antibodies. Snap-freezing in isopentan was superior to liquid nitrogen in preservation of morphology. Embedding of the tissues in Tissue-Tek II O.C.T. Compound diminished the intensity of immunostaining with all antibodies studied; however, the embedded tissues tolerated longer storage without drying. Optimal fixation with satisfactory preservation of morphology and immunogenicity was achieved with fixation of the frozen sections in acetone at 4 degrees C for 5 min. Blocking of the endogenous peroxidase with methanol-H2O2 treatment destroyed all epitopes studied except those identified with OKIa1, OKT6 and Leu7.

The Effects of Tissue Processing on Markers for T and B Cells from Solid Tissues

Suspensions of lymphoid cells from tissues have been used for the determination of the quantitative relationship between the T and B cell populations. The distribution of the lymphocytes within a given tissue, however, cannot be demonstrated once such a suspension has been prepared. Various methods of characterizing lymphocytes within tissues were evaluated. The method of tissue preparation can alter the capability of detecting the lymphocyte markers. Fluorescein-labeled anti-immunoglobulin sera reacted equally well with lymphocytes in tissue regardless of the method of tissue preparation. Complement-coated sheep erythrocytes were less effective in detecting lymphocyte markers in tissue sections than in cell suspensions. Quantitative assays of lymphocytes could be done in suspensions only. Unaltered sheep erythrocytes did not bind to T lymphocytes in tissue. T lymphocytes could be identified in tissue sections, however, by the use of anti-human T cell serum.