Parameters Affecting Tissue Quality of Biopsy/Surgical and Postmortem Tissues

Tissue pHNucleic acids: Gene expressionBrain• pH is a good marker of perimortem tissue quality,178,233 but pH is insensitive to freeze/thaw degradation178,233,235
• pH is constant across all brain regions, and it is well represented by the cerebellum pH233,235
• pH and RIN are highly correlated when pH <7233
• pH is not correlated with either postmortem delays or time in storage178
• pH is not correlated with freezing method or tissue packing178
• Gender has a significant influence on pH (male subjects more than female subjects), even across different ages178
• pH of postmortem brain tissue is most dependent on agonal factors and ischemia before death178,236
• Lower tissue pH is associated with a decrease in gene expression involved in energy metabolism and proteolytic activities, and a consistent increase of genes encoding stress response proteins and transcription factors236
Agonal factorsNucleic acids: RNA integrity; Gene expression profilesBrain• Predeath medical conditions correlate with tissue pH236
• Agonal factors decrease brain tissue pH and facilitate RNA degradation232,235
• Prolonged agonal states are associated with lower tissue pH and changes in gene expression patterns involved in mitochondria respiratory function and stress response236
• Brief PMIs are associated with normal tissue pH and stable gene expression236
• ASR-based matching provides better results of agonal effect than using tissue pH237
• Agonal factors affect RNA integrity and divergent global gene expression profiles in microarrays232
• The brain has the lowest RNA integrity, which may be due to antemortem brain acidosis by prolonged agony232,238,239
• The ACI is a reliable indicator of agonal factor influence on brain acidosis and RNA integrity232
• mRNA degradation and altered gene expression profiles occur in cell types more vulnerable to agonal stressors232
HistologyNucleic acids: RNA integrity, protein degradationBrain• DNA/RNA stability in histologic samples depends on the fixative solution used and on the time of tissue storage in the fixative before paraffin embedding229
• DNA preservation in paraffin blocks is variable. Tissue quality increases with a short buffered formalin fixation time229
• Generally, DNA degrades in fixation solutions and embedding processing225,229
• Increased PMIs (from 4 to 18 h) did not decrease protein signals by immunohistochemistry240
• Protein immunoreactivity is generally stable when tissue is stored as paraffin-embedded blocks for extended periods241
Intestine• Use a new formalin-free fixative called FineFIX (Milestone, Bergamo, Italy) that allows for stable DNA amplicons of 2400 bp, RNA fragments of 600 bp, and proteins comparable in quality with those obtained from fresh frozen tissues242
BMIRNA integritySkeletal muscle• BMI influences RNA integrity230
Autolysis (self-digestion)Heart• RNA integrity is reduced up to 24 h autolysis78
• >24 h at RT autolysis maintains gene expression profile78
• Multiple probe-based exon arrays reliably determine gene expression profiles in tissue with extended autolysis78
• Protein expression, as detected by IHC, remains intact up to 24 h after autolysis, but degradation is noticeable at 48 h78
PMIsNucleic acids: Gene expression; Protein degradationCardiac muscle• RNA degradation is increased with longer PMI230
Blood vessel• IHC staining intensity is not influenced by a PMI of 24 h243
• PMIs increase the levels of triglycerides and very-low-density lipoprotein cholesterol but not levels of total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol244
Posttranslational modificationsFetal tissues• DNA yield and purity are not influenced by PMIs between 2 and 10 d67
LipidsCornea• Many structural changes including increased cell loss occur in the corneal epithelium with a PMI up to 7 d245
• Epithelial regeneration and survival of epithelial cells in the cultured cornea organ can occur even with PMI up to 6 to 7 d246
• The RIN values from corneal and trabecular meshwork tissue were significantly higher than those from the ciliary body at an early PMI (<6 h) but were similar after 8 h247
• Rapid preservation and processing of postmortem human donor eye tissue (especially for vascularized ocular tissues) is imperative247
Olfactory bulb/tract• PMI delay increases olfactory bulb fragility on dissection from postmortem brain, being more accessible in female subjects than male subjects248,249
Brain• RNA quality does not correlate with PMIs ranging from 6 to 40 h233 or from 28 to 114 h56
• PMI and pH do not correlate in brain233
• PMI delays cause RNA degradation with a decreased gene expression (>3.5 h)177
• IHC is used to detect protein signals in tissue with a PMI of 24 h250
• PMIs >40 h result in protein degradation233,241,251
• PMIs from 4 to 18 h increased protein oxidation/nitrate events and expression of glial fibrillary acidic protein, synaptophysin, and neurofilament240
• Proteins that were frozen at 5, 8, 23, and 50 h after death showed more severe patterns of protein degradation compared with those stored at 2 h234
• Delayed PMI results in alterations in expression levels of τ, MAP2, MAP1B, and MAP5252
• PMI delays increase tryptophan levels55
• PMI delays cause nucleoside degradation253
• PMI duration is not associated with an increased risk of postmortem translocation of micro-organisms from mucosal surfaces into the body104
• With the exception of Gαq and Gαo, which decrease with PMIs from 5 to 21 h, all other G proteins are stable during extended PMIs in brain251
• PMI >50 h results in τ dephosphorylation234,254
• Nucleosomal DNA remains attached to histones during the first 30 h after death, suggesting preservation of methylation histone residues with longer PMIs,210 and is maintained within a range of autolysis and tissue pH255
Gender and ageNucleic acids: RNA integrity; Protein degradationBrain• Gender and age at death influence measurement of mRNA levels256
• Female subjects have lower mRNA levels256
• Variable correlations between mRNA and age at death256,257
• Gender and age affect gene expression in psychiatric disorders232,258
• Decreased levels of the GTP-binding proteins Gαq and Gαo were significantly correlated with increased age (2%–4% loss per decade)251
• Tryptophan levels are variable with age or gender55,259,260
• Glutamate decarboxylase activity is higher in male subjects55
Relative humidityNucleic acids: RNA qualityBrain• RNA quality is reduced by the relative humidity at ≥31%231
• RNA is stable with a low relative humidity (6%–23%) when extracted with LCM, stained, and fixed231
• Relative humidity must be maintained at ≤23% to facilitate LCM high-efficiency capture231
  • ACI, the average correlation index; ASR, agonal stress rating; GTP, guanosine triphosphate; IHC, immunohistochemistry; LCM, laser microdissection; MAP, microtubule-associated proteins; mRNA, messenger RNA; RT, room temperature.