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Cruz, M. A., Ulfenborg, B., Blomstrand, P., Faresjö, M., Ståhl, F. & Karlsson, S. (2022). Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden. Scientific Reports, 12(1), Article ID 12670.
Open this publication in new window or tab >>Characterization of methylation patterns associated with lifestyle factors and vitamin D supplementation in a healthy elderly cohort from Southwest Sweden
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2022 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 12670Article in journal (Refereed) Published
Abstract [en]

Numerous studies have shown that lifestyle factors, such as regular physical activity and vitamin D intake, may remarkably improve overall health and mental wellbeing. This is especially important in older adults whose vitamin D deficiency occurs with a high prevalence. This study aimed to examine the influence of lifestyle and vitamin D on global DNA methylation patterns in an elderly cohort in Southwest of Sweden. We also sought to examine the methylation levels of specific genes involved in vitamin D's molecular and metabolic activated pathways. We performed a genome wide methylation analysis, using Illumina Infinium DNA Methylation EPIC 850kBeadChip array, on 277 healthy individuals from Southwest Sweden at the age of 70–95. The study participants also answered queries on lifestyle, vitamin intake, heart medication, and estimated health. Vitamin D intake did not in general affect methylation patterns, which is in concert with other studies. However, when comparing the group of individuals taking vitamin supplements, including vitamin D, with those not taking supplements, a difference in methylation in the solute carrier family 25 (SCL25A24) gene was found. This confirms a previous finding, where changes in expression of SLC25A24 were associated with vitamin D treatment in human monocytes. The combination of vitamin D intake and high physical activity increased methylation of genes linked to regulation of vitamin D receptor pathway, the Wnt pathway and general cancer processes. To our knowledge, this is the first study detecting epigenetic markers associated with the combined effects of vitamin D supplementation and high physical activity. These results deserve to be further investigated in an extended, interventional study cohort, where also the levels of 25(OH)D3 can be monitored.

Place, publisher, year, edition, pages
Nature Publishing Group, 2022
National Category
Nursing Public Health, Global Health, Social Medicine and Epidemiology
Identifiers
urn:nbn:se:hb:diva-28381 (URN)10.1038/s41598-022-15924-x (DOI)000830116000026 ()2-s2.0-85134761700 (Scopus ID)
Available from: 2022-08-15 Created: 2022-08-15 Last updated: 2022-09-15Bibliographically approved
Gillsjö, C., Sandra, K., Ståhl, F. & Eriksson, I. (2021). Lifestyle's influence on community-dwelling older adults' health: A mixed-methods study design. Contemporary Clinical Trials Communication, 21, 1-4, Article ID 100687.
Open this publication in new window or tab >>Lifestyle's influence on community-dwelling older adults' health: A mixed-methods study design
2021 (English)In: Contemporary Clinical Trials Communication, ISSN 2451-8654, Vol. 21, p. 1-4, article id 100687Article in journal (Refereed) Published
Abstract [en]

Background: Aging often involves health problems and difficulties, such as physical and psychological impairments, isolation, and loneliness, causing social and existential consequences. Studies have explored aging from different perspectives. However, few studies have examined healthy older adults’ genetic backgrounds, lifestyles, and meaning in life separately or in combination. This study aims to describe how healthy older adults experience aging, health, lifestyles, and meaning in life and explore potential genetic correlations.

Methods and Design:The project will comprise three main parts: a quantitative section featuring the development and testing of a lifestyle questionnaire, a quantitative genetic analysis, and a qualitative interview study. Participants will be community-dwelling, healthy, older adults between 70 and 95 years of age. A sample size of 800 older adults will be invited to participate in seminars in collaboration with the national Swedish association Active Seniors. Data will be collected through lifestyle questionnaire, DNA extracted from saliva samples, and interviews. Based on questionnaire responses, profile groups will be created and compared statistically with variations in genetic backgrounds, providing the basis for recruiting participants to the qualitative interviews.

Discussion: This study’s expected outcome will be to gain knowledge about variations in genetic backgrounds correlated with individual experiences regarding aging, health, and meaning in life. This knowledge can improve the understanding of motivations for healthy lifestyle changes. The results can reveal potential implications for individual prerequisites to healthy aging and how health-promoting aging and lifestyle counseling can be adjusted to meet individual needs.

Place, publisher, year, edition, pages
Amsterdam: Elsevier, 2021
Keywords
Aging, Lifestyle, Genetics
National Category
Medical and Health Sciences
Research subject
The Human Perspective in Care
Identifiers
urn:nbn:se:hb:diva-24660 (URN)10.1016/j.conctc.2020.100687 (DOI)000636276300011 ()33385096 (PubMedID)2-s2.0-85098090972 (Scopus ID)
Available from: 2021-01-14 Created: 2021-01-14 Last updated: 2021-07-07Bibliographically approved
Karlsson, S., Ståhl, F. & Larsson, D. (2013). Molecular diagnostic markers in endometrial carcinoma: an overview. Journal of Oncopathology, 1(2), 145-150
Open this publication in new window or tab >>Molecular diagnostic markers in endometrial carcinoma: an overview
2013 (English)In: Journal of Oncopathology, ISSN 2052-5931, Vol. 1, no 2, p. 145-150Article in journal (Refereed) Published
Abstract [en]

Endometrial, ovarian, and cervical cancers are three of the most common malignancies of the female reproductive organs and the most common cause of gynecological cancer deaths in the Western world. Approximately 80% or more of endometrial cancers are low-grade, estrogen-dependent, endometrioid adenocarcinoma (type I), whereas 20% are high-grade endometrial carcinomas (type II) associated with poor prognosis. Although endometrial cancer is usually diagnosed at an early stage, still almost 20% of the patients present with advanced disease. Thus, there is a need for highly sensitive markers that can distinguish between high- and low-risk endometrial carcinoma. To date, however, there are no validated molecular markers for endometrial cancer. Recent genomic and proteomic-based anaes show great promise for the discovery of new and more useful biomarkers. In this review, we will discuss the currently reported biomarkers that hold potential as diagnostic tools for endometrial cancer.

Place, publisher, year, edition, pages
Optimal Clinical Ltd., 2013
Keywords
endometrial carcinoma, Medicin
National Category
Cancer and Oncology
Research subject
Integrated Caring Science
Identifiers
urn:nbn:se:hb:diva-1619 (URN)2320/12696 (Local ID)2320/12696 (Archive number)2320/12696 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2018-02-20Bibliographically approved
Larsson, D., Adele, J., Bergsten, N., Ståhl, F. & Karlsson, S. (2012). Membrane Initiated Effects of 1?,25-Dihydroxyvitamin D3 in Prostate Cancer Cells: Effects on AP1 and CREB Mediated Transcription. In: Stevo Najman (Ed.), Current Frontiers and Perspectives in Cell Biology: (pp. 153-162). InTech
Open this publication in new window or tab >>Membrane Initiated Effects of 1?,25-Dihydroxyvitamin D3 in Prostate Cancer Cells: Effects on AP1 and CREB Mediated Transcription
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2012 (English)In: Current Frontiers and Perspectives in Cell Biology / [ed] Stevo Najman, InTech , 2012, p. 153-162Chapter in book (Other academic)
Abstract [sv]

Vitamin D effekter på progression av cancer i prostata

Place, publisher, year, edition, pages
InTech, 2012
Keywords
prostatacancer, vitamin D, Medicinsk genetik
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:hb:diva-5122 (URN)2320/11900 (Local ID)978-953-51-0544-2 (ISBN)2320/11900 (Archive number)2320/11900 (OAI)
Available from: 2015-12-17 Created: 2015-12-17 Last updated: 2018-01-10
Andersson, L. & Ståhl, F. (2010). Distribution of candidate genes for experimentally induced arthritis in rats. BMC Genomics, 11(146)
Open this publication in new window or tab >>Distribution of candidate genes for experimentally induced arthritis in rats
2010 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 11, no 146Article in journal (Refereed) Published
Abstract [en]

Background: Rat models are frequently used to link genomic regions to experimentally induced arthritis in quantitative trait locus (QTL) analyses. To facilitate the search for candidate genes within such regions, we have previously developed an application (CGC) that uses weighted keywords to rank genes based on their descriptive text. In this study, CGC is used for analyzing the localization of candidate genes from two viewpoints: distribution over the rat genome and functional connections between arthritis QTLs. Methods: To investigate if candidate genes identified by CGC are more likely to be found inside QTLs, we ranked 2403 genes genome wide in rat. The number of genes within different ranges of CGC scores localized inside and outside QTLs was then calculated. Furthermore, we investigated if candidate genes within certain QTLs share similar functions, and if these functions could be connected to genes within other QTLs. Based on references between genes in OMIM, we created connections between genes in QTLs identified in two distinct rat crosses. In this way, QTL pairs with one QTL from each cross that share an unexpectedly high number of gene connections were identified. The genes that were found to connect a pair of QTLs were then functionally analysed using a publicly available classification tool. Results: Out of the 2403 genes ranked by the CGC application, 1160 were localized within QTL regions. No difference was observed between highly and lowly rated genes. Hence, highly rated candidate genes for arthritis seem to be distributed randomly inside and outside QTLs. Furthermore, we found five pairs of QTLs that shared a significantly high number of interconnected genes. When functionally analyzed, most genes connecting two QTLs could be included in a single functional cluster. Thus, the functional connections between these genes could very well be involved in the development of an arthritis phenotype. Conclusions: From the genome wide CGC search, we conclude that candidate genes for arthritis in rat are randomly distributed between QTL and non-QTL regions. We do however find certain pairs of QTLs that share a large number of functionally connected candidate genes, suggesting that these QTLs contain a number of genes involved in similar functions contributing to the arthritis phenotype.

Place, publisher, year, edition, pages
BioMed Central Ltd., 2010
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:hb:diva-3069 (URN)10.1186/1471-2164-11-146 (DOI)2320/7611 (Local ID)2320/7611 (Archive number)2320/7611 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2024-01-17Bibliographically approved
Andersson, L., Petersen, G. & Ståhl, F. (2009). Ranking candidate genes in rat models of type 2 diabetes. Theoretical Biology Medical Modelling, 6(12)
Open this publication in new window or tab >>Ranking candidate genes in rat models of type 2 diabetes
2009 (English)In: Theoretical Biology Medical Modelling, ISSN 1742-4682, E-ISSN 1742-4682, Vol. 6, no 12Article in journal (Refereed) Published
Abstract [en]

Background Rat models are frequently used to find genomic regions that contribute to complex diseases, so called quantitative trait loci (QTLs). In general, the genomic regions found to be associated with a quantitative trait are rather large, covering hundreds of genes. To help selecting appropriate candidate genes from QTLs associated with type 2 diabetes models in rat, we have developed a web tool called Candidate Gene Capture (CGC), specifically adopted for this disorder. Methods CGC combines diabetes-related genomic regions in rat with rat/human homology data, textual descriptions of gene effects and an array of 789 keywords. Each keyword is assigned values that reflect its co-occurrence with 24 different reference terms describing sub-phenotypes of type 2 diabetes (for example "insulin resistance"). The genes are then ranked based on the occurrences of keywords in the describing texts. Results CGC includes QTLs from type 2 diabetes models in rat. When comparing gene rankings from CGC based on one sub-phenotype, with manual gene ratings for four QTLs, very similar results were obtained. In total, 24 different sub-phenotypes are available as reference terms in the application and based on differences in gene ranking, they fall into separate clusters. Conclusion The very good agreement between the CGC gene ranking and the manual rating confirms that CGC is as a reliable tool for interpreting textual information. This, together with the possibility to select many different sub-phenotypes, makes CGC a versatile tool for finding candidate genes. CGC is publicly available at http://ratmap.org/CGC.

Place, publisher, year, edition, pages
BioMed Central Ltd., 2009
Keywords
rats, genomics, Genetics medicine
National Category
Medical Genetics
Identifiers
urn:nbn:se:hb:diva-2771 (URN)10.1186/1742-4682-6-12 (DOI)2320/6039 (Local ID)2320/6039 (Archive number)2320/6039 (OAI)
Note

Sponsorship:

Swedish Medical Research Council, the Nilsson-Ehle Foundation, the Sven and Lilly Lawski Foundation, the Erik Philip-Sorensen Foundation, the Wilhelm and Martina Lundgren Research Foundation, and the SWEGENE Foundation.

Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2018-01-10Bibliographically approved
Petersen, G. & Ståhl, F. (2008). RGST: Rat Gene Symbol Tracker, a database for defining official rat gene symbols. BMC Genomics, 9(29)
Open this publication in new window or tab >>RGST: Rat Gene Symbol Tracker, a database for defining official rat gene symbols
2008 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 9, no 29Article in journal (Refereed) Published
Abstract [en]

Background The names of genes are central in describing their function and relationship. However, gene symbols are often a subject of controversy. In addition, the discovery of mammalian genes is now so rapid that a proper use of gene symbol nomenclature rules tends to be overlooked. This is currently the situation in the rat and there is a need for a cohesive and unifying overview of all rat gene symbols in use. Based on the experiences in rat gene symbol curation that we have gained from running the "Ratmap" rat genome database, we have now developed a database that unifies different rat gene naming attempts with the accepted rat gene symbol nomenclature rules. Description This paper presents a newly developed database known as RGST (Rat Gene Symbol Tracker). The database contains rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Conclusion This database fulfils the important need of unifying rat gene symbols into an automatic and cohesive nomenclature system. The RGST database is available directly from the RatMap home page: http://ratmap.org.

Place, publisher, year, edition, pages
BioMed Central Ltd., 2008
Keywords
rats, genomics, Genetics
National Category
Medical Genetics Natural Sciences
Identifiers
urn:nbn:se:hb:diva-2772 (URN)10.1186/1471-2164-9-29 (DOI)2320/6040 (Local ID)2320/6040 (Archive number)2320/6040 (OAI)
Note

Sponsorship:

the Swedish Medical Research Council, the Nilsson-Ehle Foundation, the Sven and Lilly Lawski Foundation, the Erik Philip-Sorensen Foundation, the Wilhelm and Martina Lundgren Research Foundation, and the SWEGENE Foundation.

Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2024-01-17Bibliographically approved
Andersson, L. & Ståhl, F. (2007). Candidate Gene Capture (CGC): a Tool for Selecting Potentially. In: : . Paper presented at The 9th Functional Genomics Conference: Synthetic Biology, Göteborg,.
Open this publication in new window or tab >>Candidate Gene Capture (CGC): a Tool for Selecting Potentially
2007 (English)Conference paper, Poster (with or without abstract) (Other academic)
Keywords
Genetics
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:hb:diva-5827 (URN)2320/3112 (Local ID)2320/3112 (Archive number)2320/3112 (OAI)
Conference
The 9th Functional Genomics Conference: Synthetic Biology, Göteborg,
Available from: 2015-12-22 Created: 2015-12-22 Last updated: 2016-11-18Bibliographically approved
Andersson, L., Petersen, G., Johnson, P. & Ståhl, F. (2005). A web tool for finding gene candidates associated with experimentally induced arthritis in rat. Arthritis Research & Therapy, 7(3), R485-R492
Open this publication in new window or tab >>A web tool for finding gene candidates associated with experimentally induced arthritis in rat
2005 (English)In: Arthritis Research & Therapy, ISSN 1478-6354, E-ISSN 1478-6362, Vol. 7, no 3, p. R485-R492Article in journal (Refereed) Published
Abstract [en]

Rat models are frequently used for finding genes contributing to the arthritis phenotype. In most studies, however, limitations in the number of animals result in a low resolution. As a result, the linkage between the autoimmune experimental arthritis phenotype and the genomic region, that is, the quantitative trait locus, can cover several hundred genes. The purpose of this work was to facilitate the search for candidate genes in such regions by introducing a web tool called Candidate Gene Capture (CGC) that takes advantage of free text data on gene function. The CGC tool was developed by combining genomic regions in the rat, associated with the autoimmune experimental arthritis phenotype, with rat/human gene homology data, and with descriptions of phenotypic gene effects and selected keywords. Each keyword was assigned a value, which was used for ranking genes based on their description of phenotypic gene effects. The application was implemented as a web-based tool and made public at http://ratmap.org/cgc. The CGC application ranks gene candidates for 37 rat genomic regions associated with autoimmune experimental arthritis phenotypes. To evaluate the CGC tool, the gene ranking in four regions was compared with an independent manual evaluation. In these sample tests, there was a full agreement between the manual ranking and the CGC ranking for the four highest-ranked genes in each test, except for one single gene. This indicates that the CGC tool creates a ranking very similar to that made by human inspection. The exceptional gene, which was ranked as a gene candidate by the CGC tool but not in the manual evaluation, was found to be closely associated with rheumatoid arthritis in additional literature studies. Genes ranked by the CGC tools as less likely gene candidates, as well as genes ranked low, were generally rated in a similar manner to those done manually. Thus, to find genes contributing to experimentally induced arthritis, we consider the CGC application to be a helpful tool in facilitating the evaluation of large amounts of textual information.

Place, publisher, year, edition, pages
BioMed Central Ltd., 2005
National Category
Mathematics
Identifiers
urn:nbn:se:hb:diva-3068 (URN)10.1186/ar1700 (DOI)2320/7610 (Local ID)2320/7610 (Archive number)2320/7610 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2017-12-01Bibliographically approved
Petersen, G., Johnson, P., Andersson, L., Klinga-Levan, K., Gomez-Fabre, P. & Ståhl, F. (2005). RatMap: rat genome tools and data. Nucleic Acids Research - Database Issue, 33(1 (suppl)), 492-494
Open this publication in new window or tab >>RatMap: rat genome tools and data
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2005 (English)In: Nucleic Acids Research - Database Issue, ISSN 0305-1048, Vol. 33, no 1 (suppl), p. 492-494Article in journal (Refereed) Published
Abstract [en]

The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB–Genetics at Göteborg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap. The database is under the supervision of the Rat Gene and Nomenclature Committee (RGNC); thus much attention is paid to rat gene nomenclature. RatMap presents information on rat idiograms, karyotypes and provides a unified presentation of the rat genome sequence and integrated rat linkage maps. A set of tools is also available to facilitate the identification and characterization of rat QTLs, as well as the estimation of exon/intron number and sizes in individual rat genes. Furthermore, comparative gene maps of rat in regard to mouse and human are provided.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:hb:diva-3062 (URN)10.1093/nar/gki125 (DOI)2320/7594 (Local ID)2320/7594 (Archive number)2320/7594 (OAI)
Available from: 2015-11-13 Created: 2015-11-13 Last updated: 2018-02-13Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-3043-622x

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