Increase in the ratio of 18S RNA to 28S RNA in the cytoplasm of mouse tissues during aging

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.

Effects of post-mortem and physical degradation on RNA integrity and quality

The precision and reliability of quantitative nucleic acid analysis depends on the quality of the sample analyzed and the integrity of the nucleic acids. The integrity of RNA is currently primarily assessed by the analysis of ribosomal RNA, which is the by far dominant species. The extrapolation of these results to mRNAs and microRNAs, which are structurally quite different, is questionable. Here we show that ribosomal and some nucleolar and mitochondrial RNAs, are highly resistant to naturally occurring post-mortem degradation, while mRNAs, although showing substantial internal variability, are generally much more prone to nucleolytic degradation. In contrast, all types of RNA show the same sensitivity to heat. Using qPCR assays targeting different regions of mRNA molecules, we find no support for 5' or 3' preferentiality upon post-mortem degradation.

Variation of Peripheral Blood Mononuclear Cell RNA Quality in Archived Samples

The Infectious Diseases BioBank (IDB) has consistently archived peripheral blood mononuclear cell (PBMNC) RNA for transcriptome analyses. RNA is particularly labile, and hence, these samples provide a sensitive indicator for assessing the IDB's quality-assurance measures. Independent analyses of 104 PBMNC RNA specimens from 26 volunteers revealed that the mean RNA integrity number (RIN) was high (9.02), although RIN ranged between scores of 7 and 10. This variation of RIN values was not associated with ischemic time, PBMNC quality, number of samples processed per day, self-medication after immunization, freezer location, donor characteristics, differential white blood cell counts, or daily variation in RNA extractions (all P>0.05). RIN values were related to the date of collection, with those processed during mid-summer having highest RIN scores (P=0.0001). Amongst specimens with the lowest RIN scores, no common feature could be identified. Thus, no technical explanation for the variation in RNA quality could be ascertained and these may represent normal physiological variations. These data provide strong evidence that current IDB protocols for the isolation and preservation PBMNC RNA are robust.

Identification of radiation-induced expression changes in nonimmortalized human T cells

In the event of a radiation accident or attack, it will be imperative to quickly assess the amount of radiation exposure to accurately triage victims for appropriate care. RNA-based radiation dosimetry assays offer the potential to rapidly screen thousands of individuals in an efficient and cost-effective manner. However, prior to the development of these assays, it will be critical to identify those genes that will be most useful to delineate different radiation doses. Using global expression profiling, we examined expression changes in nonimmortalized T cells across a wide range of doses (0.15-12 Gy). Because many radiation responses are highly dependent on time, expression changes were examined at three different times (3, 8, and 24 h). Analyses identified 61, 512 and 1310 genes with significant linear dose-dependent expression changes at 3, 8 and 24 h, respectively. Using a stepwise regression procedure, a model was developed to estimate in vitro radiation exposures using the expression of three genes (CDKN1A, PSRC1 and TNFSF4) and validated in an independent test set with 86% accuracy. These findings suggest that RNA-based expression assays for a small subset of genes can be employed to develop clinical biodosimetry assays to be used in assessments of radiation exposure and toxicity.

Collection and preparation of rodent tissue samples for histopathological and molecular studies in carcinogenesis

Histology, as a mean of tissue visualization on a cellular level, is a fundamental tool in the study of cancer. The need for simultaneous delivery of quality histological material for pathological evaluation and subsequent genomic and proteomic studies, however, requires modification of traditional practices to include rapid isolation and stabilization of target tissue to preserve molecular integrity. Informative molecular analysis depends on the integrity of target molecules (RNA, DNA, and proteins) in the tissue during and after its collection. A reliable systematic approach to routine and genomic/proteomic sample collection and preparation presented is supported by detailed protocols.

Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology

The quality of results from microarray studies depends on RNA quality, which can be significantly influenced by postmortem factors. The aim of this study was to determine which postmortem factors and/or RNA electropherogram characteristics best correspond to microarray output and can be used to prospectively screen RNA prior to microarray analysis. Total RNA was extracted (N=125) from gray and white matter of postmortem frontal and occipital lobe tissue, acquired from normal controls, and patients with schizophrenia, bipolar disorder or major depression. Electropherograms were generated by the Agilent BioAnalyzer 2100, allowing calculation of the 28S/18S ratio, the 18S/baseline peak ratio and the RNA Integrity Number (RIN). These values were compared to post-hybridization image analysis of Affymetrix microarrays. The postmortem variables correlated with some quality measures but could not be used as effective screening tools. Logistic regression demonstrated that all three electropherogram measures were predictive for microarray quality, and that the RIN threshold predictive of "good quality" (>35% present calls) was most consistent with that of prior studies. The optimal RIN must be determined by the investigator's specifications for false inclusion and false exclusion. In contrast to RIN, the quality threshold for the 28S/18S ratio has proven unacceptably variable, due to sensitivity to slight differences in protocol and/or tissue source. In conclusion, the measures we found useful as screening criteria do not replace the need to exclude samples after a microarray analysis is performed, as an acceptable percent call rate and other measures of microarray quality represent the desired endpoint.

Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces

While it is universally accepted that intact RNA constitutes the best representation of the steady-state of transcription, there is no gold standard to define RNA quality prior to gene expression analysis. In this report, we evaluated the reliability of conventional methods for RNA quality assessment including UV spectroscopy and 28S:18S area ratios, and demonstrated their inconsistency. We then used two new freely available classifiers, the Degradometer and RIN systems, to produce user-independent RNA quality metrics, based on analysis of microcapillary electrophoresis traces. Both provided highly informative and valuable data and the results were found highly correlated, while the RIN system gave more reliable data. The relevance of the RNA quality metrics for assessment of gene expression differences was tested by Q-PCR, revealing a significant decline of the relative expression of genes in RNA samples of disparate quality, while samples of similar, even poor integrity were found highly comparable. We discuss the consequences of these observations to minimize artifactual detection of false positive and negative differential expression due to RNA integrity differences, and propose a scheme for the development of a standard operational procedure, with optional registration of RNA integrity metrics in public repositories of gene expression data.

Evaluating RNA status for RT-PCR in extracts of postmortem human brain tissue

Total RNA was extracted from 105 individual postmortem human brain samples representing a range of postmortem conditions. To improve upon parameters currently used to screen for RNA quality, electropherogram patterns generated by the Agilent Bioanalyzer 2100 were compared to the average score in random hexamer-primed reverse transcription real-time PCR for four housekeeping genes in each RNA sample. The ribosomal ratio (28S to 18S) was found to be unrelated to the housekeeping gene score (r = -0.06; P = 0.50), and there was no threshold value in the ratio that could be applied to effectively categorize the RNA degradation. Although the housekeeping gene score correlated significantly with the percentage of area in the electropherogram corresponding to moderate to high molecular weight intact mRNA (r = 0.41; P = 0.0001), the best discriminator was determined to be the ratio of the 18S peak height to the highest peak in the tRNA to 18S rRNA baseline. Applying a lower boundary of 2.12 for the ratio allowed for the screening out of samples with the lowest housekeeping gene scores without excluding better-quality samples. This measure represents a marked improvement over the 28S to 18S ratio, which proved to be a misleading indicator of the state of the mRNA for use in random hexamer-primed reverse transcription PCR.

Change with donor age in the degradation rate of endogenous proteins of mouse hepatocytes in primary culture

The degradation rate of [(3)H]leucine labeled intracellular proteins was compared in hepatocytes derived from young (4-7-month-old) and aged (23-month-old) mice. Average half-lives of long-lived proteins were 40 h and 65 h in the cells from young and old animals, respectively. This observation confirms our earlier results that half-lives of foreign proteins introduced into the cells from old mice are 50-60% longer than those of younger counterparts (Ishigami and Goto, 1988, Mech. Ageing Dev., 46, 125-133; Ishigami and Goto, 1990, Arch. Biochem. Biophys., 277, 189-195).

Accumulation of heat-labile elongation factor 2 in the liver of mice and rats

Age-related changes of polypeptide chain elongation factor 2 (EF-2) in mouse and rat livers were investigated. The percentage of heat-labile components in EF-2 was 5 to 10% in young animals and 15 to 45% in old ones. These results and other findings (Takahashi et al., in press) support the idea that decrease in translational activity in old animals is due, in part, to alterations of protein components of the translational system.

Functional deterioration of mouse liver ribosomes during aging: translational activity and activity for formation of the 47 S initiation complex

The translational activities of ribosomes from young and old mouse livers were examined in an assay system dependent on rabbit globin mRNA. Old ribosomes showed 30-40% lower activity than young ribosomes. This observation, together with our previous findings (N. Mori, D. Mizuno and S. Goto, Mech. Ageing Dev., 10 (1979) 379-398), suggests functional deterioration of ribosomes of old animals. To examine the mechanism of the deterioration, the activities for formation of the initiation complex of 40 S ribosomal subunits in the livers of young and old mice were examined in vitro. The activity was found to be 15-20% lower in old mice (21 months old or more) than in young ones. This fact partly explains the decreased activity for ribosomal protein synthesis in old mice.

mRNA population in the liver, kidney and brain of young and senescent mice: analysis of in vitro translation products

Possible alterations in the population of poly(A)(+)mRNA during ageing were investigated by translation in vitro of poly(A)(+)mRNA from the liver, kidney and brain of male ddY mice of different ages. [35S]Methionine-labeled translation products were analysed by two-dimensional polyacrylamide gel electrophoresis followed by fluorography. A protein product with a molecular weight of 30 000 and isoelectric point of 6.5 was reproducibly observed only in the fluorograms of translation products of poly(A)(+)mRNA derived from the livers of senescent mice (24.5 months old). However, no age-related change was detected in the translation products of the kidney and brain. These results suggest that gene expression in liver cells changes at the level of the population of cytoplasmic poly(A)(+)mRNA during ageing.

Estimation of the single stranded region in the nuclear DNA of mouse tissues during aging with special reference to the brain

The proportion of single stranded DNA in various tissues of mouse during aging was examined by measuring sensitivity to a single-strand specific nuclease. Brain DNA from mice of more than 15 mth old contained 3% of the single stranded regions while that from younger animals contained 2%. The DNAs from liver, kidney, heart and spleen did not show significant age-associated changes.

Evidence that free polysomes are not the precursors of membrane-bound polysomes in rat liver

We tested, in rat liver, the postulate that free polysomes were precursors of membrane-bound polysomes. Three methods were used to isolate free and membrane-bound ribosomes from either post-nuclear or post-mitochondrial supernatants of rat liver. Isolation and quantitation of 28 S and 18 S rRNA allowed determination of the 40 S and 60 S subunit composition of free and membrane-bound ribosomal populations, while pulse labeling of 28 S and 18 S rRNA with [6-14C) orotic acid and inorganic (32P] phosphate allowed assessment of relative rates of subunit renewal. Throughout the extra-nuclear compartment, 40 S and 60 S subunits were present in essentially equal numbers, but, free ribosomes contained a stoichiometric excess of 40 S subunits, while membrane-bound ribosomes contained a complementary excess of 60 S subunits. Experiments with labeled precursors showed that throughout the extra-nuclear compartment, 40 S and 60 S subunits accumulated isotopes at essentially equal rates, however, free ribosomes accumulated isotopes faster than membrane-bound ribosomes. Among free ribosomes or polysomes, 40 S subunits accumulated isotopes faster than 60 S subunits, but, this relationship was not seen among membrane-bound ribosomes. Here, 40 S subunits accumulated isotope more slowly than 60 S subunits. This distribution of labeled precursors does not support the postulate that free polysomes are precursors of membrane-bound polysomes, but, these data suggest that membrane-bound polysomes could be precursors of free polysomes.

Age changes in the H1 group of histones from rat liver

Histones were obtained from young and old rat livers by extracting them in 0.25 N HCl. They were fractionated on 15% acid urea polyacrylamide gels containing 6.25 M urea and the changes in the ratio of the major histone fractions as a function of age were calculated. Data presented show a significant increase in the amount of H1 degree fraction in the liver of old rats as compared to young rats. This data is discussed and the possible involvement of H1 degree fraction in an increased resistance of old rat liver chromatin to micrococcal nuclease digestion of linker DNA is suggested. Finally, in connection with this increased resistance, some possible consequences in chromatin structure are discussed.

Conservation of ribosomal fidelity during ageing

The function of ribosomes prepared from the liver of young (2--5 months old) and senescent (15--26 months old) mice were compared in vitro. The conclusions that can be drawn from the liver of senescent mice is 10 to 40% lower than that of young mice; (2) the fidelity of translation does not change grossly with age; (3) the thermosensitivity of translational activity of ribosomes and the activity of ribosome-associated ribonuclease do not change with age; (4) there is an age-dependent accumulation of free 40S ribosomal subunits in the cytoplasm of mouse liver. The relation of age-dependent changes in the structure and function of ribosomes is discussed.