Evolutionary genetics of lactase persistence in Eurasian human populations

Although ability to digest lactose generally declines after weaning in all mammals, in some human populations it persists also in adult individuals, a condition named lactase persistence (LP). Studies on the prevalence of the LP phenotype in worldwide human populations have shown that the frequency of this trait is highly variable in different ethnic groups, appearing to be positively correlated with the importance of milk in the diet. In particular, several single-nucleotide polymorphisms (SNPs) in the proximity of the LCT gene have been proved to be associated with LP. Nevertheless, few studies have till now analyzed genetic variation underlying LP in a wide set of Eurasian populations and, especially, in the Italian one. In the present study, we thus typed 40 SNPs surrounding the LCT gene in more than 1,000 samples from Italian and Arabic peninsulas to investigate patterns of LP-related genetic diversity in two regions which have played a pivotal role in the recent human evolutionary history according to their geographical position and historical/archaeological records. Our results underline a high and complex variability of the explored genomic region in both studied populations. In particular, a clear diversification of Northern Italian groups from the rest of the peninsula, was observed, with the formers being genetically more similar to Northern European populations than to Southern Italians. These observation are consistent with known decreasing pattern of LP from Northern to Southern Italy and suggest the possibility of an independent evolution of LP-associated genotypes in Northern Italy. A similar scenario was observed in the Arabian peninsula, with Dhofari Arabs from Southern Oman and Yemeni clustering together with respect to Arabs from Northern Oman and the subgroup of Omanis of Asian origin which appeared instead to be genetically closer to Europeans than to the rest of Arabic groups.

Evolutionary epigenetics of modern human populations

Epigenetic variability is a new mechanism for the study of human microevolution, because it creates both phenotypic diversity within an individual and within population. This mechanism constitutes an important reservoir for adaptation in response to new stimuli and recent studies have demonstrated that selective pressures shape not only the genetic code but also DNA methylation profiles. The aim of this thesis is the study of the role of DNA methylation changes in human adaptive processes, considering the Italian peninsula and macro-geographical areas. A whole-genome analysis of DNA methylation profile across the Italian penisula identified some genes whose methylation levels differ between individuals of different Italian districts (South, Centre and North of Italy). These genes are involved in nitrogen compound metabolism and genes involved in pathogens response. Considering individuals with different macro-geographical origins (individuals of Asians, European and African ancestry) more significant DMRs (differentially methylated regions) were identified and are located in genes involved in glucoronidation, in immune response as well as in cell comunication processes. A "profile" of each ancestry (African, Asian and European) was described. Moreover a deepen analysis of three candidate genes (KRTCAP3, MAD1L and BRSK2) in a cohort of individuals of different countries (Morocco, Nigeria, China and Philippines) living in Bologna, was performed in order to explore genetic and epigenetic diversity. Moreover this thesis have paved the way for the application of DNA methylation for the study of hystorical remains and in particular for the age-estimation of individuals starting from biological samples (such as teeth or blood). Noteworthy, a mathematical model that considered methylation values of DNA extracted from cementum and pulp of living individuals can estimate chronological age with high accuracy (median absolute difference between age estimated from DNA methylation and chronological age was 1.2 years).

Evaluation of glycoconjugate antigens as vaccine candidates against group A Streptococcus and human immunodeficiency virus infections

This PhD thesis discusses the rationale for design and use of synthetic oligosaccharides for the development of glycoconjugate vaccines and the role of physicochemical methods in the characterization of these vaccines. The study concerns two infectious diseases that represent a serious problem for the national healthcare programs: human immunodeficiency virus (HIV) and Group A Streptococcus (GAS) infections. Both pathogens possess distinctive carbohydrate structures that have been described as suitable targets for the vaccine design. The Group A Streptococcus cell membrane polysaccharide (GAS-PS) is an attractive vaccine antigen candidate based on its conserved, constant expression pattern and the ability to confer immunoprotection in a relevant mouse model. Analysis of the immunogenic response within at-risk populations suggests an inverse correlation between high anti-GAS-PS antibody titres and GAS infection cases. Recent studies show that a chemically synthesized core polysaccharide-based antigen may represent an antigenic structural determinant of the large polysaccharide. Based on GAS-PS structural analysis, the study evaluates the potential to exploit a synthetic design approach to GAS vaccine development and compares the efficiency of synthetic antigens with the long isolated GAS polysaccharide. Synthetic GAS-PS structural analogues were specifically designed and generated to explore the impact of antigen length and terminal residue composition. For the HIV-1 glycoantigens, the dense glycan shield on the surface of the envelope protein gp120 was chosen as a target. This shield masks conserved protein epitopes and facilitates virus spread via binding to glycan receptors on susceptible host cells. The broadly neutralizing monoclonal antibody 2G12 binds a cluster of high-mannose oligosaccharides on the gp120 subunit of HIV-1 Env protein. This oligomannose epitope has been a subject to the synthetic vaccine development. The cluster nature of the 2G12 epitope suggested that multivalent antigen presentation was important to develop a carbohydrate based vaccine candidate. I describe the development of neoglycoconjugates displaying clustered HIV-1 related oligomannose carbohydrates and their immunogenic properties.

Human papillomavirus (HPV) and associated diseases: between applied diagnostic and basic research

Human Papillomavirus (HPV) is the cause of cervical cancers (among these, adenocarcinoma, AdCa) and is associated to a subgroup of oropharyngeal carcinomas (OPSCCs). Even if the risk for cancer development is linked to the infection by some viral genotypes, mainly HPV16 and 18, viral DNA alone seems not to be sufficient for diagnosis. Moreover, the role of the virus in OPSCCs has not been totally clarified yet. In the first part of the thesis, the performances concerning viral genotyping in clinical cervical samples of a new pyrosequencing-based test and a well-known hybridization-based assay have been compared. Similar results between the methods have been obtained. However, the former showed advantages in detecting intratype variants, higher specificity and a broader spectrum of detectable HPV types. The second part deals with the evaluation of virological markers (genotyping, viral oncoproteins expression, viral load, physical state and CpG methylation of HPV16 genome) in the diagnosis/prognosis of cervical AdCa and HPV-associated OPSCCs. HPV16 has been confirmed the most prevalent genotype in both the populations. Interestingly, the mean methylation frequency of viral DNA at the early promoter showed the tendency to be associated to invasion for cervical AdCa and to a worse prognosis for OPSCCs, suggesting a promising role as diagnostic/prognostic biomarker. The experiments of the third part were performed at the DKFZ in Heidelberg (Germany) and dealt with the analysis of the response to IFN-k transfection in HPV16-positive cervical cancer and head&neck carcinoma cell lines to evaluate its potential role as new treatment. After 24h, we observed increased IFN-b expression which lead to the up-regulation of genes involved in the antigens presentation pathway (MHC class I and immunoproteasome) and antiviral response as well, in particular in cervical cancer cell lines. This fact suggested also the presence of different HPV-mediated carcinogenic pathways between the two anatomical districts.

Comparing genetic and linguistic diversity in African populations with a focus on the Khoisan of southern Africa

The interaction between disciplines in the study of human population history is of primary importance, profiting from the biological and cultural characteristics of humankind. In fact, data from genetics, linguistics, archaeology and cultural anthropology can be combined to allow for a broader research perspective. This multidisciplinary approach is here applied to the study of the prehistory of sub-Saharan African populations: in this continent, where Homo sapiens originally started his evolution and diversification, the understanding of the patterns of human variation has a crucial relevance. For this dissertation, molecular data is interpreted and complemented with a major contribution from linguistics: linguistic data are compared to the genetic data and the research questions are contextualized within a linguistic perspective. In the four articles proposed, we analyze Y chromosome SNPs and STRs profiles and full mtDNA genomes on a representative number of samples to investigate key questions of African human variability. Some of these questions address i) the amount of genetic variation on a continental scale and the effects of the widespread migration of Bantu speakers, ii) the extent of ancient population structure, which has been lost in present day populations, iii) the colonization of the southern edge of the continent together with the degree of population contact/replacement, and iv) the prehistory of the diverse Khoisan ethnolinguistic groups, who were traditionally understudied despite representing one of the most ancient divergences of modern human phylogeny. Our results uncover a deep level of genetic structure within the continent and a multilayered pattern of contact between populations. These case studies represent a valuable contribution to the debate on our prehistory and open up further research threads.