Gene expression changes reveal patterns of aging in the rat digestive tract

DNA Methylation Analysis Validates Organoids as a Viable Model for Studying Human Intestinal Aging

BACKGROUND & AIMS

The epithelia of the intestine and colon turn over rapidly and are maintained by adult stem cells at the base of crypts. Although the small intestine and colon have distinct, well-characterized physiological functions, it remains unclear if there are fundamental regional differences in stem cell behavior or region-dependent degenerative changes during aging. Mesenchyme-free organoids provide useful tools for investigating intestinal stem cell biology in vitro and have started to be used for investigating age-related changes in stem cell function. However, it is unknown whether organoids maintain hallmarks of age in the absence of an aging niche. We tested whether stem cell-enriched organoids preserved the DNA methylation-based aging profiles associated with the tissues and crypts from which they were derived.

METHODS

To address this, we used standard human methylation arrays and the human epigenetic clock as a biomarker of age to analyze in vitro-derived, 3-dimensional, stem cell-enriched intestinal organoids.

RESULTS

We found that human stem cell-enriched organoids maintained segmental differences in methylation patterns and that age, as measured by the epigenetic clock, also was maintained in vitro. Surprisingly, we found that stem cell-enriched organoids derived from the small intestine showed striking epigenetic age reduction relative to organoids derived from colon.

CONCLUSIONS

Our data validate the use of organoids as a model for studying human intestinal aging and introduce methods that can be used when modeling aging or age-onset diseases in vitro.

Structural, functional and molecular analysis of the effects of aging in the small intestine and colon of C57BL/6J mice

BACKGROUND

By regulating digestion and absorption of nutrients and providing a barrier against the external environment the intestine provides a crucial contribution to the maintenance of health. To what extent aging-related changes in the intestinal system contribute to the functional decline associated with aging is still under debate.

METHODS

Young (4 M) and old (21 M) male C57BL/6J mice were fed a control low-fat (10E%) or a high-fat diet (45E%) for 2 weeks. During the intervention gross energy intake and energy excretion in the feces were measured. After sacrifice the small and large intestine were isolated and the small intestine was divided in three equal parts. Swiss rolls were prepared of each of the isolated segments for histological analysis and the luminal content was isolated to examine alterations in the microflora with 16S rRNA Q-PCR. Furthermore, mucosal scrapings were isolated from each segment to determine differential gene expression by microarray analysis and global DNA methylation by pyrosequencing.

RESULTS

Digestible energy intake was similar between the two age groups on both the control and the high-fat diet. Microarray analysis on RNA from intestinal scrapings showed no marked changes in expression of genes involved in metabolic processes. Decreased expression of Cubilin was observed in the intestine of 21-month-old mice, which might contribute to aging-induced vitamin B12 deficiency. Furthermore, microarray data analysis revealed enhanced expression of a large number of genes involved in immune response and inflammation in the colon, but not in the small intestine of the 21-month-old mice. Aging-induced global hypomethylation was observed in the colon and the distal part of the small intestine, but not in the first two sections of the small intestine.

CONCLUSION

In 21-month old mice the most pronounced effects of aging were observed in the colon, whereas very few changes were observed in the small intestine.

Melatonin, and to a lesser extent growth hormone, restores colonic smooth muscle physiology in old rats

There is increasing evidence that aging is associated with oxidative damage, inflammation, and apoptosis in different cell types. However, there is limited information regarding aging mechanisms in colon smooth muscle. Old male Wistar rats (22 months) were treated for 10 wks with melatonin or growth hormone (GH). Animals were sacrificed at 24 months of age by decapitation. The colon was dissected and the smooth muscle homogenized. H(2)O(2) and malonyl dialdehyde (MDA) content and catalase and glutathione peroxidase (GPX) activities were determined using colorimetric kits. Expression of nuclear factor kappa B (NF-κB), cyclooxygenase 2 (COX-2), caspase-3, and caspase-9 were determined by Western blot. Aging of colon smooth muscle correlated with an increase in H(2)O(2) and MDA levels when compared with young animals in both proximal and distal segments; these changes were associated with a decrease in the catalase activity in the distal colon. Oxidative stress correlated with an increase in COX-2 and NF-κB expression, which were accompanied by an enhanced expression of the pro-apoptotic enzyme caspase-3 and its upstream enzyme, caspase-9. Melatonin treatment normalized the oxidative, inflammatory, and apoptotic patterns, whereas GH replacement, although effective in reducing oxidative stress in distal colon, did not reverse the age-related inflammation or apoptosis. These results suggest that melatonin should be the treatment of choice to most effectively recover physiological functions in aged colonic smooth muscle.

Measurements of the binding of a large protein using a substrate density-controlled DNA chip

The DNA chip that immobilizes DNA oligonucleotides on a solid plate surface is used for many diagnostic applications. For maximizing the detection sensitivity and accuracy, it is important to control the DNA density on a chip surface and establish a convenient method for optimizing the density. Here, the binding of DNA mismatch-binding protein MutS to the DNA substrate on the chip was investigated, which can be applied for high-throughput single-nucleotide polymorphism analysis in a genome. We prepared the DNA chips where the DNA substrate density was changed simply by using a mixed DNA solution. The binding of MutS was significantly influenced by the amount of DNA substrate on the chip as a consequence of steric crowding, and the moderate density that gave the distance between the DNA substrates greater than the size of the protein was appropriate to obtain accurate kinetic parameters. The substrate density-controlled DNA chip prepared using the mixed DNA solution has distinctive advantages for maximizing the detection capability and kinetic analysis of the binding of MutS and probably also other large proteins.

[Age-related microscopic and molecular changes of the human colon, and their role in the development of colorectal cancer in elderly people]

The gastrointestinal effect of aging, the recognition of its molecular background and the mapping its connections with several diseases like sporadic colorectal cancer of elder people are a new and promising area of molecular gastroenterology. Nowadays, it is a well-known fact that some age-related molecular changes (e.g.: DNA methylation, telomere shortening) can be detected in several types of colorectal cancers. The known epidemiologic and molecular biologic features of sporadic colorectal cancer are not enough to explain the genetic, gene expression or epigenetic changes that may be involved in the increase of the disease over 45-50 age years. The connections of these alterations to the process of aging are also unclear. The understanding and custom-tailored modification of these mechanisms are of great clinical importance regarding of prevention and modern therapeutic strategies. In this review, we aimed to summarize the age-related microscopic and molecular changes of the human colon, as well as their role in the development of colorectal cancer of the elder people.

The association among gene expression responses to nine abiotic stress treatments in Arabidopsis thaliana

The identification and analysis of genes exhibiting large expression responses to several different types of stress may provide insights into the functional basis of multiple stress tolerance in plant species. This study considered whole-genome transcriptional profiles from Arabidopsis thaliana root and shoot organs under nine abiotic stress conditions (cold, osmotic stress, salt, drought, genotoxic stress, ultraviolet light, oxidative stress, wounding, and high temperature) and at six different time points of stress exposure (0.5, 1, 3, 6, 12, and 24 hr). In roots, genomewide correlations between transcriptional responses to different stress treatments peaked following 1 hr of stress exposure, while in shoots, correlations tended to increase following 6 hr of stress exposure. The generality of stress responses at the transcriptional level was therefore time and organ dependent. A total of 67 genes were identified as exhibiting a statistically significant pattern of gene expression characterized by large transcriptional responses to all nine stress treatments. Most genes were identified from early to middle (1-6 hr) time points of stress exposure. Analysis of this gene set indicated that cell rescue/defense/virulence, energy, and metabolism functional classes were overrepresented, providing novel insight into the functional basis of multiple stress tolerance in Arabidopsis.