Single-cell RNA sequencing of cells from fresh or frozen tissue reveals a signature of freezing marked by heightened stress and activation

Thawing of viably frozen human tissue T cells, ILCs, and NK cells and subsequent single-cell RNA sequencing reveals that recovery of cellular subclusters is variably impacted. While freeze-thawing does not alter the transcriptional profiles of cells, it upregulates genes and gene pathways associated with stress and activation.

EtOH-LN cryoembedding workflow to minimize freezing artifact in frozen tissues: A pilot study in preparing tissues compatible with mass spectrometry-based spatial proteomics application

Coolant-assisted liquid nitrogen (LN) flash freezing of frozen tissues has been widely adopted to preserve tissue morphology for histopathological annotations in mass spectrometry-based spatial proteomics techniques. However, existing coolants pose health risks upon inhalation and are expensive. To overcome this challenge, we present our pilot study by introducing the EtOH-LN workflow, which demonstrates the feasibility of using 95 % ethanol as a safer and easily accessible alternative to existing coolants for LN-based cryoembedding of frozen tissues. Our study reveals that both the EtOH-LN and LN-only cryoembedding workflows exhibit significantly reduced freezing artifacts compared to cryoembedding in cryostat (p < 0.005), while EtOH-LN (SD = 0.56) generates more consistent results compared to LN-only (SD = 1.29). We have modified a previously reported morphology restoration method to incorporate the EtOH-LN workflow, which successfully restored the tissue architecture from freezing artifacts (p < 0.05). Additional studies are required to validate the impact of the EtOH-LN workflow on the molecular profiles of tissues.

Staining Hypoxic Areas of Frozen and FFPE Tissue Sections with Hypoxyprobe™

Hypoxia occurs due to inadequate levels of oxygen in tissue and has been implicated in numerous diseases such as cancer, diabetes, cardiovascular, and neurodegenerative diseases. Hypoxia activates hypoxia-inducible factors (HIF) which mediate the expression of several downstream genes. Within the context of cancer biology, these genes affect cellular processes including metabolism, proliferation, migration, invasion, and metastasis. Pimonidazole hydrochloride (HCl) is an exogenous marker that is reduced and binds to thiols under hypoxic conditions resulting in adducts that can be visualized using antibodies such as Hypoxyprobe™. This chapter describes a method for using Hypoxyprobe™ to detect hypoxic areas in frozen and FFPE mouse samples by immunofluorescence (IF) and immunohistochemistry (IHC) staining.

Assessment of MYC and TERT copy number variations in lung cancer using digital PCR

OBJECTIVE

Lung cancer is the second most frequent cancer type and the most common cause of cancer-related deaths worldwide. Alteration of gene copy numbers are associated with lung cancer and the determination of copy number variations (CNV) is appropriate for the discrimination between tumor and non-tumor tissue in lung cancer. As telomerase reverse transcriptase (TERT) and v-myc avian myelocytomatosis viral oncogene homolog (MYC) play a role in lung cancer the aims of this study were the verification of our recent results analyzing MYC CNV in tumor and non-tumor tissue of lung cancer patients using an independent study group and the assessment of TERT CNV as an additional marker.

RESULTS

TERT and MYC status was analyzed using digital PCR (dPCR) in tumor and adjacent non-tumor tissue samples of 114 lung cancer patients. The difference between tumor and non-tumor samples were statistically significant (p < 0.0001) for TERT and MYC. Using a predefined specificity of 99% a sensitivity of 41% and 51% was observed for TERT and MYC, respectively. For the combination of TERT and MYC the overall sensitivity increased to 60% at 99% specificity. We demonstrated that a combination of markers increases the performance in comparison to individual markers. Additionally, the determination of CNV using dPCR might be an appropriate tool in precision medicine.

Isolation of Nuclei from Human Snap-frozen Liver Tissue for Single-nucleus RNA Sequencing

Single-nucleus RNA sequencing (snRNA-seq) provides a powerful tool for studying cell type composition in heterogenous tissues. The liver is a vital organ composed of a diverse set of cell types; thus, single-cell technologies could greatly facilitate the deconvolution of liver tissue composition and various downstream omics analyses at the cell-type level. Applying single-cell technologies to fresh liver biopsies can, however, be very challenging, and snRNA-seq of snap-frozen liver biopsies requires some optimization given the high nucleic acid content of the solid liver tissue. Therefore, an optimized protocol for snRNA-seq specifically targeted for the use of frozen liver samples is needed to improve our understanding of human liver gene expression at the cell-type resolution. We present a protocol for performing nuclei isolation from snap-frozen liver tissues, as well as guidance on the application of snRNA-seq. We also provide guidance on optimizing the protocol to different tissue and sample types.

Profiling Single-Cell Genome and Transcriptome by scONE-Seq

Single-cell multi-omics technologies can provide a unique perspective on tumor cellular heterogeneity. We have developed a versatile method for simultaneous transcriptome and genome profiling of single cells or single nuclei in one tube reaction, named scONE-seq. It is conveniently compatible with frozen tissue from biobanks, which are a major source of patient samples for research. Here, we describe the detailed procedures to profile single-cell/nucleus transcriptome and genome. The sequencing library is compatible with both Illumina and MGI sequencers; it is also compatible with frozen tissue from biobanks, which are a major source of patient samples for research and drug discovery.

Lysine Acetylation Stoichiometry Analysis at the Proteome Level

Lysine acetylation is a widespread posttranslational modification (PTM) in all kingdoms of live. A large number of proteins involved in most of biological pathways are targets of this PTM. The lysine acetylation is a reversible modification controlled by two main groups of enzymes, lysine acetyltransferases responsible for transferring the acetyl group of acetylCoA to the side chain of lysine residues and lysine deacetylases which effectively remove the acetyl tag. Dysregulation of enzymes that control acetylation and/or target proteins have been associated with a growing number of human pathologies. Lysine acetylation is largely a modification that occurs at low stoichiometry at its target sites. Here we describe a method to identify lysine acetylation sites and estimate their site occupancy at the proteome scale. The method relies on a high-resolution mass spectrometry-based proteomics approach, which includes a specific chemical acetylation reaction on unmodified lysine residues that carry heavy isotopes. The procedures described here have been applied to cell line cultures and to clinically relevant samples stored as both snap-frozen and formalin-fixed paraffin-embedded (FFPE) tissues.

Dog cloning from post-mortem tissue frozen without cryoprotectant

Successful reproductive cloning depends on obtaining intact donor nuclei from viable cells, ideally isolated by tissue biopsy of a living donor. However, owners and veterinarians often freeze deceased animals, which eventually causes damage to cellular micro-organelles due to the formation of intracellular water crystals. In the present study, we have reported the production of viable cloned puppies using donor nuclei of cells obtained from frozen carcasses. Five cases of deceased and frozen canine specimens were presented to be cloned. Skin fibroblast cell lines were successfully established for four specimens. Significant longer time was needed for the cell growth from frozen tissues (4 days) to reach 80% confluency compared to fresh tissue and frozen tissues frozen for 1- or 2-days. Similarly, SA-βgal positive cells (death cells) were significantly higher in frozen cells for 2- or 4- days compared to samples from fresh or frozen (1 day) sources. The cloning efficiency (CE) and the pregnancy rates (PR) of frozen cells were lower than those obtained from fresh or living donors (CE 2.4 ± 1.8% vs. 0.6 ± 0.3%, PR 21.7 ± 16.1% vs. 7.7 ± 5.3% for fresh vs. frozen, respectively). Here we demonstrate is the possibility to produce healthy offspring from cell lines obtained from frozen tissue collected post-mortem.

Principles and methods of integrative chromatin analysis in primary tissues and tumors

Recent methodological advances have enabled the genome-wide interrogation of chromatin from primary tumor tissues. Integrative analysis of histone post-translational modifications, transcription factor (TF) binding and open chromatin sites in tumors across cancer stages can elucidate the aberrant epigenetic states accompanying tumor progression. Cancer-associated chromatin alterations can activate or inactivate enhancers at genes involved in cancer while still respecting cell-of-origin constrictions. Accordingly, enhancer analysis in cancer could have uses for biomarker discovery to further refine patient diagnosis and potentially sub-classify patients for tailored therapy. Methodologies used for chromatin analyses of primary tissues need to address issues distinct from cell line studies including the specific sources of variability coming from the heterogeneous cellular composition of tissues and from inter-individual (epi)genetic differences. This leads to requirements for careful histological analysis to select the specific samples and cells of interest. In analyzing tumors somatic changes should be taken into account to distinguish the genuine epigenetic changes across tumor specimens from any genetic alterations such as copy number variations (CNV). In this contribution we review a selection of current results from chromatin profiling, examine experimental methodologies and discuss specific analysis approaches. We also review specific considerations regarding tissue preparation for epigenetic analysis and conclude with our perspectives on emerging approaches that will impact studies of chromatin landscapes of clinical samples in the future.

Improved detectability of sex steroids from frozen sections of breast cancer tissue using GC-triple quadrupole-MS

Sex steroids in clinical endocrinology have been mainly investigated with peripheral blood and urine samples, while there is limited information regarding the local levels within tissues. To improve analytical properties of sex steroids from trace amounts of tissue samples, two-phase extractive ethoxycarbonlyation and subsequent pentafluoropropionyl derivatization coupled to gas chromatography-tandem mass spectrometry (GC-MS/MS) was developed. The optimized analytical conditions led to excellent chromatographic separation of 15 estrogens, 6 androgens, and 2 progestins. The quantitative results were calculated based on in-house control samples as the steroid-free tissues, and the precision and accuracy were 4.2%-26.8% and 90.8%-116.4%, respectively. The on-column limit of quantification was from 180 fg to 0.5 pg for androgens and estrogens, and 1.25 pg for progestins, which were found to be linear (r²> 0.990). The validated method was then applied to quantify 7 sex steroids from three 100-μm-thick frozen breast tissue slices from postmenopausal patients with breast cancer. This is the first report on the improved GC-MS/MS method for the detection of androgens and pregnenolone from breast cancer tissues, and it can be a useful technique to measure the local levels of sex steroids, thus, enhancing our understanding of the pathophysiological significances of steroidogenesis.

Laser Capture Microdissection and Isolation of High-Quality RNA from Frozen Endometrial Tissue

Laser capture microdissection (LCM) allows expression profiling of specific cell populations within tissues. However, isolation of high-quality RNA from laser capture microdissected frozen tissue is beset by problems arising from intrinsic tissue RNase activity. Herein, we describe an optimized staining/LCM/RNA extraction protocol developed for the isolation of epithelial RNA from frozen tissue sections using human endometrial cancer as a model tissue. This method combines excellent, reproducible visualization of tissue morphology with the isolation of high-integrity RNA suitable for downstream applications such as expression microarray analysis. We present quantitative and qualitative RNA data obtained from >200 endometrial epithelial samples (normal, hyperplastic, and cancerous), where 92% of samples had RIN values of 7 and above and highlight common pitfalls faced by investigators. This method should also be broadly applicable to a range of other tissue types.

Laser Microdissection Workflow for Isolating Nucleic Acids from Fixed and Frozen Tissue Samples

Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.

Probing Glioblastoma Tissue Heterogeneity with Laser Capture Microdissection

Among various methods now available to isolate distinct cell populations or even single cells for DNA/RNA and proteomic analysis, laser capture microdissection (LCM) offers a unique opportunity to study cells in their topological contexts. This chapter focuses on the preparation of LCM membrane slides, tissue staining and laser microdissection of cells of interest from frozen or formalin-fixed, paraffin-embedded glioblastoma tissue.

Retrieval of kidney tissue for light microscopy from frozen tissue processed for immunofluorescence: A simple procedure to avoid repeat kidney biopsies

We highlight a method that is helpful in situations where the tissue sent for LM is inadequate whereas the tissue sent for IF showed glomeruli useful for interpretation. We utilized the leftover frozen tissue after the sections for IF were taken. This tissue was post-fixed in formalin for the purpose of light microscopic diagnosis. The glomerular pathology could be commented upon with a fair degree of accuracy and a repeat biopsy was avoided in 74.7% of the cases. However, the tubules showed marked fixation artefact and tubular pathology was distorted. This procedure can help to reach a correct diagnosis in large percentage of cases otherwise labeled as inadequate biopsy and hence, save the patient from the trauma of a repeat biopsy.

Detection of immunoglobulins and complement components in formalin fixed and paraffin embedded renal biopsy material by immunoflourescence technique

BACKGROUND

The technique of direct immunoflourescence (IF) is essential in the accurate diagnosis of renal glomerular diseases. The optimal results are obtained when the procedure is done on fresh frozen tissue (IF-F). However, techniques are available for IF study on formalin fixed and paraffin embedded (FFPE) renal biopsy specimens with variable reported success rates.

OBJECTIVES

We evaluated three such techniques on FFPE tissue and compared the results with those obtained by IF-F from the same patients.

MATERIALS AND METHODS

Heat treatment with Tris buffer and citrate buffer, and pronase treatment of the FFPE material was carried out. Direct IF was done for renal panel immunoglobulins and complement components on all biopsies and the results were compared with the historical IF-F study.

RESULTS

When compared to the IF-F, the immunoflourescence staining on the paraffin sections was less sensitive and less intense in all immune complex-mediated renal diseases, but the diagnostic findings were detected in majority of the cases.

CONCLUSIONS

In conclusion, it is possible to establish the diagnosis in most cases of immune complex-mediated glomerular diseases with IF on paraffin embedded tissue specimens.