Data management and data analysis in the large European projects GEHA (GEnetics of Healthy Aging) and NU-AGE (NUtrition and AGEing): a bioinformatic approach

The aging process is characterized by the progressive fitness decline experienced at all the levels of physiological organization, from single molecules up to the whole organism. Studies confirmed inflammaging, a chronic low-level inflammation, as a deeply intertwined partner of the aging process, which may provide the “common soil” upon which age-related diseases develop and flourish. Thus, albeit inflammation per se represents a physiological process, it can rapidly become detrimental if it goes out of control causing an excess of local and systemic inflammatory response, a striking risk factor for the elderly population. Developing interventions to counteract the establishment of this state is thus a top priority. Diet, among other factors, represents a good candidate to regulate inflammation. Building on top of this consideration, the EU project NU-AGE is now trying to assess if a Mediterranean diet, fortified for the elderly population needs, may help in modulating inflammaging. To do so, NU-AGE enrolled a total of 1250 subjects, half of which followed a 1-year long diet, and characterized them by mean of the most advanced –omics and non –omics analyses. The aim of this thesis was the development of a solid data management pipeline able to efficiently cope with the results of these assays, which are now flowing inside a centralized database, ready to be used to test the most disparate scientific hypotheses. At the same time, the work hereby described encompasses the data analysis of the GEHA project, which was focused on identifying the genetic determinants of longevity, with a particular focus on developing and applying a method for detecting epistatic interactions in human mtDNA. Eventually, in an effort to propel the adoption of NGS technologies in everyday pipeline, we developed a NGS variant calling pipeline devoted to solve all the sequencing-related issues of the mtDNA.

Mitochondrial DNA rearrangements during human aging: a study on liver, muscle and adipose tissue

Aging is characterized by a chronic, low-grade inflammatory state called “inflammaging”. Mitochondria are the main source of reactive oxygen species (ROS), which trigger the production of pro-inflammatory molecules. We are interested in studying the age-related modifications of the mitochondrial DNA (mtDNA), which can be affected by the lifelong exposure to ROS and are responsible of mitochondrial dysfunction. Moreover, increasing evidences show that telomere shortening, naturally occurring with aging, is involved in mtDNA damage processes and thus in the pathogenesis of age-related disorders. Thus the primary aim of this thesis was the analysis of mtDNA copy number, deletion level and integrity in different-age human biopsies from liver, vastus lateralis skeletal muscle of healthy subjects and patients with limited mobility of lower limbs (LMLL), as well as adipose tissue. The telomere length and the expression of nuclear genes related to mitobiogenesis, fusion and fission, mitophagy, mitochondrial protein quality control system, hypoxia, production and protection from ROS were also evaluated. In liver the decrease in mtDNA integrity with age is accompanied with an increase in mtDNA copy number, suggesting the existence of a “compensatory mechanism” able to maintain the functionality of this organ. Different is the case of vastus lateralis muscle, where any “compensatory pathway” is activated and mtDNA integrity and copy number decrease with age, both in healthy subjects and in patients. Interestingly, mtDNA rearrangements do not incur in adipose tissue with advancing age. Finally, in all tissues a marked gender difference appears, suggesting that aging and also gender diversely affect mtDNA rearrangements and telomere length in the three human tissues considered, likely depending on their different metabolic needs and inflammatory status.