Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.

The inability to digest lactose, due to lactase nonpersistence, is a common trait in adult mammals, except in certain human populations that exhibit lactase persistence. It is not known how the lactase gene is dramatically downregulated with age in most individuals but remains active in some individuals. We performed a comprehensive epigenetic study of human and mouse small intestines, by using chromosome-wide DNA-modification profiling and targeted bisulfite sequencing. Epigenetically controlled regulatory elements accounted for the differences in lactase mRNA levels among individuals, intestinal cell types and species. We confirmed the importance of these regulatory elements in modulating lactase mRNA levels by using CRISPR-Cas9-induced deletions. Genetic factors contribute to epigenetic changes occurring with age at the regulatory elements, because lactase-persistence and lactase-nonpersistence DNA haplotypes demonstrated markedly different epigenetic aging. Thus, genetic factors enable a gradual accumulation of epigenetic changes with age, thereby influencing phenotypic outcome.

Replication study of ulcerative colitis risk loci in a Lithuanian-Latvian case-control sample.

BACKGROUND: Differences between populations might be reflected in their different genetic risk maps to complex diseases, for example, inflammatory bowel disease. We here investigated the role of known inflammatory bowel disease-associated single nucleotide polymorphisms (SNPs) in a subset of patients with ulcerative colitis (UC) from the Northeastern European countries Lithuania and Latvia and evaluated possible epistatic interactions between these genetic variants. METHODS: We investigated 77 SNPs derived from 5 previously published genome-wide association studies for Crohn's disease and UC. Our study panel comprised 444 Lithuanian and Latvian patients with UC and 1154 healthy controls. Single marker case-control association and SNP-SNP epistasis analyses were performed. RESULTS: We found 14 SNPs tagging 9 loci, including 21q21.1, NKX2-3, MST1, the HLA region, 1p36.13, IL10, JAK2, ORMDL3, and IL23R, to be associated with UC. Interestingly, the association of UC with previously identified variants in the HLA region was not the strongest association in our study (P = 4.34 × 10, odds ratio [OR] = 1.25), which is in contrast to all previously published studies. No association with any disease subphenotype was found. SNP-SNP interaction analysis showed significant epistasis between SNPs in the PTPN22 (rs2476601) and C13orf31 (rs3764147) genes and increased risk for UC (P = 1.64 × 10, OR = 2.44). The association has been confirmed in the Danish study group (P = 0.04, OR = 3.25). CONCLUSIONS: We confirmed the association of the 9 loci (21q21.1, 1p36.13, NKX2-3, MST1, the HLA region, IL10, JAK2, ORMDL3, and IL23R) with UC in the Lithuanian-Latvian population. SNP-SNP interaction analyses showed that the combination of SNPs in the PTPN22 (rs2476601) and C13orf31 (rs3764147) genes increase the risk for UC.

Incidence of inflammatory bowel disease in Kaunas region, Lithuania.

OBJECTIVE: The aim of this study was to evaluate the incidence of inflammatory bowel disease in Kaunas and its region during a 3-year period. MATERIAL AND METHODS: The study was conducted during the 3-year period (2007-2009) and enrolled the patients from Kaunas with its region, which has a population of 381,300 inhabitants. The data were collected from all practices in the area where the diagnosis of inflammatory bowel disease was made by practicing gastroenterologists and consulting pediatricians along with endoscopists. Only new cases of inflammatory bowel disease were included into analysis. The diagnosis of ulcerative colitis and Crohn's disease was strictly made according to the Copenhagen criteria. Age- and sex-standardized incidence was calculated for each year of the study period. RESULTS: A total of 108 new inflammatory bowel disease cases were diagnosed during the study period: 87 had ulcerative colitis, 16 Crohn's disease, and 5 indeterminate colitis. The incidence of ulcerative colitis, Crohn's disease, and indeterminate colitis for each study year was 6.85, 5.33, and 7.38 per 100,000; 0.95, 1.11, and 1.57 per 100,000; and 0.47, 0.21, and 0.42 per 100,000, respectively. The average 3-year standardized incidence of ulcerative colitis, Crohn's disease, and indeterminate colitis was 6.52, 1.21, and 0.37 per 100,000, respectively. The mean patients' age at onset of ulcerative colitis, indeterminate colitis, and Crohn's disease was 49.95 (SD, 17.03), 49.80 (SD, 17.71), and 34.94 years (SD, 0.37), respectively. CONCLUSIONS: The average 3-year incidence of ulcerative colitis in Kaunas region was found to be lower as compared with that in many parts of Central and Western Europe. The incidence of Crohn's disease was low and very similar to other countries of Eastern Europe. Age at onset of the diseases appeared to be older than that reported in the Western industrialized countries.

Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis.

BACKGROUND & AIMS: Interactions between genetic and environmental factors are believed to be involved in onset and initiation of inflammatory bowel disease. We analyzed the interaction between gastrointestinal mucosal microbiota and host genes in twin pairs discordant for ulcerative colitis (UC) to study the functional interaction between microbiota and mucosal epithelium. METHODS: Biopsy were collected from sigmoid colon of UC patients and their healthy twins (discordant twin pairs) and from twins without UC. Microbiota profiles were determined from analysis of 16S ribosomal DNA libraries; messenger RNA profiles were determined by microarray analysis. RESULTS: Patients with UC had dysbiotic microbiota, characterized by less bacterial diversity and more Actinobacteria and Proteobacteria than that of their healthy siblings; healthy siblings from discordant twins had more bacteria from the Lachnospiraceae and Ruminococcaceae families than twins who were both healthy. In twins who were both healthy, 34 mucosal transcripts correlated with bacterial genera, whereas only 25 and 11 correlated with bacteria genera in healthy individuals and their twins with UC, respectively. Transcripts related to oxidative and immune responses were differentially expressed between patients with UC and their healthy twins. CONCLUSIONS: The transcriptional profile of the mucosa appears to interact with the colonic microbiota; this interaction appears to be lost in colon of patients with UC. Bacterial functions, such as butyrate production, might affect mucosal gene expression. Patients with UC had different gene expression profiles and lower levels of biodiversity than their healthy twins, as well as unusual aerobic bacteria. Patients with UC had lower percentages of potentially protective bacterial species than their healthy twins.

NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease.

AIM: To investigate the frequency of NOD2, IL23R and ATG16L1 genetic variants in a case-control panel for inflammatory bowel disease (IBD) from Lithuania. METHODS: One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (UC)] and 186 healthy controls were genotyped for the following known genetic susceptibility variants: NOD2 - Arg702Trp (rs2066844), Gly908Arg (rs2066845) and Leu1007insC (rs2066847), as well as IL23R - Arg381Gln (rs11209026) and ATG16L1 - Thr300Ala (rs2241880). RESULTS: The effect that carriership of at least one NOD2 risk allele predisposes to CD was replicated in the Lithuanian population (41.1% CD vs 16.9% controls, P = 2 x 10(-4), OR = 3.48, 95% CI: 1.81-6.72). In the allelic single marker analysis, Leu1007insC was strongly associated with CD (21.4% CD vs 4.7% controls, P = 3.687 x 10(-8), OR = 5.54, 95% CI: 2.85-10.75). Neither the other two NOD2 variants, nor the known variants in IL23R and ATG16L1 were found to be risk factors for CD, UC or IBD. However, our relatively small study population was underpowered to demonstrate such weak to moderate disease associations. CONCLUSION: The results support a strong association between CD susceptibility and the Leu1007insC variant in NOD2 in the Lithuanian study population.

Genetic control of global gene expression levels in the intestinal mucosa: a human twin study.

Phenotypic variation between individuals, such as different mRNA expression levels, is influenced by genetic and nongenetic factors. Although several studies have addressed the interplay between genotypes and expression profiles in various model organisms in the recent years, the detailed and relative contributions of genetic and nongenetic factors in regulating plasticity of gene expression in barrier organs (e.g., skin, gut), which are exposed to continuous environmental challenge, are still poorly understood. Here we systematically monitored the level of genetic control over genomewide mRNA expression profiles in the healthy intestinal mucosa of 10 monozygotic and 10 dizygotic human twin pairs with microarray analyses. Our results, which are supported by real-time PCR and analysis of molecular phylogenetic conservation, indicate that genes associated with energy metabolism and cell and tissue regeneration pathways are under strong genetic control. Conversely, genes associated with immune response seem to be mainly controlled by exogenous factors. Further insights into the relative extent of genetic and nongenetic determinants of transcriptomal profiles and their influence on physiological and pathophysiological mechanisms are crucial to understanding the key role played by gene-environment interactions in health and disease.

Immune system alterations in patients with inflammatory bowel disease during remission.

OBJECTIVE: Perturbed immune homeostasis elicited by misbalanced production of proinflammatory and anti-inflammatory cytokines is characteristic of inflammatory bowel disease. The aim of this study was to evaluate cytokine profile in patients with different forms of inflammatory bowel disease - ulcerative colitis and Crohn's disease - during clinical remission phase. MATERIAL AND METHODS: Production of proinflammatory Th1 cytokines (tumor necrosis factor-alpha (TNF-alpha), interferon-gamma (IFN-gamma)) and anti-inflammatory Th2 cytokines (interleukin-10 (IL-10) and interleukin-13 (IL-13)) was analyzed in peripheral blood mononuclear cells of patients with inflammatory bowel disease (9 with ulcerative colitis and 9 with Crohn's disease) and control subjects (n=11) by enzyme-linked immunosorbent assay (two-site ELISA). RESULTS: The results of the study revealed that the level of TNF-alpha after stimulation with phytohemagglutinin in patients with Crohn's disease was significantly higher in comparison to both patients with ulcerative colitis and controls (P<0.001 and P<0.01, respectively). The secretion of IFN-gamma both in patients with Crohn's disease and ulcerative colitis was lower than that in controls (P=0.05 and P<0.01, respectively), but it normalized after stimulation with phytohemagglutinin. The levels of IL-10 and IL-13 were significantly (P<0.01) higher in patients with Crohn's disease than in patients with ulcerative colitis and control group before and after stimulation with phytohemagglutinin. CONCLUSIONS: The results of our study provide evidence that in patients with inflammatory bowel disease, the imbalance between production of proinflammatory Th1 and anti-inflammatory Th2 cytokines persists even during remission of the disease, and disturbances of immune homeostasis are significantly more expressed in patients with Crohn's disease than in patients with ulcerative colitis.

[Dietary characteristics of patients with inflammatory bowel diseases]. / Pacientu, serganciu uzdegiminemis zarnu ligomis, mitybos ypatybes.

OBJECTIVE: To evaluate nutritional status and dietary habits of Lithuanian patients with ulcerative colitis and Crohn's disease and to compare with those of healthy controls. MATERIALS AND METHODS: A case-control study was conducted in the Department of Gastroenterology, Kaunas University of Medicine Hospital. A total of 101 patients with ulcerative colitis, 44 with Crohn's disease, and 178 healthy controls were examined with the help of standard self-report questionnaire about daily dietary habits. Healthy controls were evaluated in primary care centers during preventive examinations. Body mass index was calculated for all patients in a standard way. RESULTS: There was no statistically significant difference between patients and controls concerning consumption of coffee, tea, chewing gum, type of fat for meal preparation, white bread, cooked potatoes and sausages, non-carbonated water. Patients with inflammatory bowel diseases statistically significantly less frequently consumed fresh milk, cheese, fish, fried potatoes, and soda drinks. Patients with Crohn's disease statistically significantly less frequently consumed fresh fruits and patients with ulcerative colitis--fresh vegetables as compared to controls. Body mass index of patients with inflammatory bowel diseases was significantly lower compared to controls, and patients with Crohn's disease had significantly lower body mass index than ulcerative colitis patients. CONCLUSIONS: Patients with inflammatory bowel diseases have lower body mass index than healthy controls. Patients consume fresh milk, cheese, canned and fresh vegetables and fruits less frequently; therefore, primary care physicians and patients should be provided with teaching and more information about nutrition issues.

[Retrospective analysis of case histories of patients with ulcerative colitis and Crohn's disease]. / Ligoniu, sirgusiu opiniu kolitu ir Krono liga, ligos istoriju retrospektyvioji analize.

Consistent patterns of inflammatory bowel diseases (IBD), difficulties of diagnosis Crohn's disease and ulcerative colitis and peculiarities of their treatment have been studied on the basis of retrospective analysis of IBD patient case histories during 1995-2001 in the Department of Gastroenterology of Kaunas University of Medicine Hospital. Ulcerative colitis and Crohn's disease are chronic diseases that influence the quality of life, mortality and number of hospitalizations with their course varying in different countries. The number of cases hospitalized during the five years period was 273; 80% of which was ulcerative colitis, whereas the percentage of Crohn's disease was 20. The number of cases of ulcerative colitis increased every year while that of Crohn's disease started to grow in 2001. IBD is more common among males than females. It was at the expanse of young females that patients with Crohn's disease were statistically significantly younger than those with ulcerative colitis. Proctosigmoiditis (45.9%) and left colitis (27.1%) are common predominants in ulcerative colitis, while ileocolitis (63.6%) predominates in Crohn's disease. Ulcerative colitis correlates with stool frequency and extent of disease. Course of IBD is rather grave and relapses are quite frequent.