Influence of Different Evolutive Forces on GDF5 Gene Variability.

The GDF5 gene is involved in the development of skeletal elements, synovial joint formation, tendons, ligaments, and cartilage. Several polymorphisms are present within the gene, and two of them, rs143384 and 143383, were reported to be correlated with osteoarticular disease or muscle flexibility. The aim of this research is to verify if the worldwide distribution of the rs143384 polymorphism among human populations was shaped by selective pressure, or if it was the result of random genetic drift events. Ninety-four individuals of both the male and female sexes, 18-28 years old, from Sardinia were analyzed. We observed the following genotype frequencies: 28.72% of AA homozygotes, 13.83% of GG homozygotes, and 57.45% of AG heterozygotes. The allele frequencies were 0.574 for allele A and 0.426 for allele G. The relationships between the populations were verified via Multidimensional Scaling (MDS). Our data show (i) a clear heterogeneity within the African populations; (ii) a strong differentiation between the African populations and the other populations; and that (iii) the Sardinian population is placed within the European cluster. To reveal possible traces of selective pressure, the Population Branch Statistic (PBS) was calculated; both the rs143384 and 143383 SNPs have low PBS values, suggesting that there are no signals of selective pressure in those areas of the gene.

From old markers to next generation: reconstructing the history of the peopling of Sardinia.

CONTEXT: For many years the Sardinian population has been the object of numerous studies because of its unique genetic structure. Despite the extreme abundance of papers, various aspects of the peopling and genetic structure of Sardinia still remain uncertain and sometimes controversial. OBJECTIVE: We reviewed what has emerged from different studies, focussing on some still open questions, such as the origin of Sardinians, their relationship with the Corsican population, and the intra-regional genetic heterogeneity. METHODS: The various issues have been addressed through the analysis of classical markers, molecular markers and, finally, genomic data through next generation sequencing. RESULTS AND CONCLUSIONS: Although the most ancient human remains date back to the end of the Palaeolithic, Mesolithic populations brought founding lineages that left evident traces in the modern population. Then, with the Neolithic, the island underwent an important demographic expansion. Subsequently, isolation and genetic drift contributed to maintain a significant genetic heterogeneity, but preserving the overall homogeneity on a regional scale. At the same time, isolation and genetic drift contributed to differentiate Sardinia from Corsica, which saw an important gene flow from the mainland. However, the isolation did not prevent gene flow from the neighbouring populations whose contribution are still recognisable in the genome of Sardinians.

Estimating population genetics and forensic efficiency of the GlobalFiler PCR amplification kit in the population of Sardinia (Italy).

GlobalFiler is a new PCR amplification kit that includes 21 autosomal short tandem repeats and three sex-determining loci. In the present research, for the first time, the GlobalFiler kit was tested to analyze a sample of 500 unrelated individuals from 18 villages encompassing the entire area of Sardinia (Italy). We tested if the kit, which is a powerful tool in forensic studies, may also find application in the field of population genetics. In agreement with data from the literature on forensic parameters values, marker SE33 showed the highest degree of polymorphism, whereas TPOX was the least informative locus. Seventeen out of twenty-one autosomal markers included in the kit resulted highly polymorphic, and therefore Globalfiler turned out to be highly useful for forensic analysis in the Sardinian population. Moreover, our data suggest developing different STR databases in different populations, like Sardinians, to increase the statistical power of autosomal STR profiling. On the other hand, due to the presence of some very highly polymorphic markers, the efficiency of Globalfiler in detecting geographical variability is affected. Indeed, the differentiation previously observed between the Sardinian and Italian populations appeared greatly reduced and even the presence of genetic isolates, previously recorded when uniparental markers was not revealed.

Worldwide variation of the COL14A1 gene is shaped by genetic drift rather than selective pressure.

BACKGROUND: The aim of this study is to analyze the worldwide distribution of SNP rs4870723 in COL14A1 gene to check if there are significant genetic differences among different populations and to test if the gene is a trait under selection. METHODS: Genomic DNA was extracted from 69 unrelated individuals from Sardinia and genotyped for SNP rs4870723. Data were compared with 26 different populations, clustered in 5 super-populations, from the public 1000 genomes database. Allele frequency and heterozygosity were calculated with Genepop. The Hardy-Weinberg equilibrium and pairwise population differentiation through analysis of molecular variance (AMOVA FST) were determined with Arlequin. RESULTS: Allele frequencies of COL14A1 rs4870723 were compared in 27 populations clustered in 5 super-populations. All populations were in the Hardy-Weinberg equilibrium. In almost all populations, allele C was the most frequent allele, reaching the highest values in East Asia. The 27 populations showed an appreciable structure, with significant differences observed between European, African, and Asian populations. CONCLUSION: Significant differences were observed in the rs4870723 SNP distribution among the populations studied. However, we found no evidence for a selective pressure. Rather, the differentiation among the populations is likely the result of founder effect, genetic drift, and cultural factors, all events known to establish and maintain genetic diversity between populations.

Telomere attrition and inflammatory load in severe psychiatric disorders and in response to psychotropic medications.

Individuals with severe psychiatric disorders have a reduced life expectancy compared to the general population. At the biological level, patients with these disorders present features that suggest the involvement of accelerated aging, such as increased circulating inflammatory markers and shorter telomere length (TL). To date, the role of the interplay between inflammation and telomere dynamics in the pathophysiology of severe psychiatric disorders has been scarcely investigated. In this study we measured T-lymphocytes TL with quantitative fluorescent in situ hybridization (Q-FISH) and plasma levels of inflammatory markers in a cohort comprised of 40 patients with bipolar disorder (BD), 41 with schizophrenia (SZ), 37 with major depressive disorder (MDD), and 36 non-psychiatric controls (NPC). TL was shorter in SZ and in MDD compared to NPC, while it was longer in BD (model F6, 137 = 20.128, p = 8.73 × 10-17, effect of diagnosis, F3 = 31.870; p = 1.08 × 10-15). There was no effect of the different classes of psychotropic medications, while duration of treatment with mood stabilizers was associated with longer TL (Partial correlation controlled for age and BMI: correlation coefficient = 0.451; p = 0.001). Levels of high-sensitivity C-Reactive Protein (hsCRP) were higher in SZ compared to NPC (adjusted p = 0.027), and inversely correlated with TL in the whole sample (r = -0.180; p = 0.042). Compared to NPC, patients with treatment resistant (TR) SZ had shorter TL (p = 0.001), while patients with TR MDD had higher levels of tumor necrosis factor-α (TNFα) compared to NPC (p = 0.028) and to non-TR (p = 0.039). Comorbidity with cardio-metabolic disorders did not influence the observed differences in TL, hsCRP, and TNFα among the diagnostic groups. Our study suggests that patients with severe psychiatric disorders present reduced TL and increased inflammation.

Differences in telomere length between patients with bipolar disorder and controls are influenced by lithium treatment.

Aim: To assess the role of lithium treatment in the relationship between bipolar disorder (BD) and leukocyte telomere length (LTL). Materials & methods: We compared LTL between 131 patients with BD, with or without a history of lithium treatment, and 336 controls. We tested the association between genetically determined LTL and BD in two large genome-wide association datasets. Results: Patients with BD with a history lithium treatment showed longer LTL compared with never-treated patients (p = 0.015), and similar LTL compared with controls. Patients never treated with lithium showed shorter LTL compared with controls (p = 0.029). Mendelian randomization analysis showed no association between BD and genetically determined LTL. Conclusion: Our data support previous findings showing that long-term lithium treatment might protect against telomere shortening.

A multidisciplinary approach to mental illness: do inflammation, telomere length and microbiota form a loop? A protocol for a cross-sectional study on the complex relationship between inflammation, telomere length, gut microbiota and psychiatric disorders.

INTRODUCTION: Severe psychiatric disorders are typically associated with a significant reduction in life expectancy compared with the general population. Among the different hypotheses formulated to explain this observation, accelerated ageing has been increasingly recognised as the main culprit. At the same time, telomere shortening is becoming widely accepted as a proxy molecular marker of ageing. The present study aims to fill a gap in the literature by better defining the complex interaction/s between inflammation, age-related comorbidities, telomere shortening and gut microbiota in psychiatric disorders. METHODS AND ANALYSIS: A cross-sectional study is proposed, recruiting 40 patients for each of three different diagnostic categories (bipolar disorder, schizophrenia and major depressive disorder) treated at the Section of Psychiatry and at the Unit of Clinical Pharmacology of the University Hospital Agency of Cagliari (Italy), compared with 40 age-matched and sex-matched non-psychiatric controls. Each group includes individuals suffering, or not, from age-related comorbidities, to account for the impact of these medical conditions on the biological make-up of recruited patients. The inflammatory state, microbiota composition and telomere length (TL) are assessed. ETHICS AND DISSEMINATION: The study protocol was approved by the Ethics Committee of the University Hospital Agency of Cagliari (PG/2018/11693, 5 September 2018). The study is conducted in accordance with the principles of good clinical practice and the Declaration of Helsinki, and in compliance with the relevant Italian national legislation. Written, informed consent is obtained from all participants. Participation in the study is on a voluntary basis only. Patients will be part of the dissemination phase of the study results, during which a local conference will be organised and families of patients will also be involved. Moreover, findings will be published in one or more research papers and presented at national and international conferences, in posters or oral communications.

Analysis of uniparental markers reveals a complex pattern of migration within Sardinia.

BACKGROUND: From the genetic viewpoint, Sardinia is well differentiated from other surrounding populations. In spite of a common ancestral origin, substantial genetic heterogeneity is observed within the island. Matrimonial pattern, as well as past migration movements, may account for the complex genetic structure of Sardinia. AIM: To compare data from uniparental markers in order to highlight the migration pattern of male and female lineages and check their congruence with the demographic data. SUBJECTS AND METHODS: Genomic DNA was obtained from 279 unrelated males selected from three isolated villages and from three open populations representative of North, Central and South Sardinia. The hypervariable region 1 of mtDNA was sequenced and 17 Y-chromosome loci were genotyped. Parameters of within and among populations diversity were calculated and analysis of migration was performed. RESULTS: When analysed as a whole population, demographic data show a balanced movement of males and females in Sardinia, unlike other Italian and European populations. Remarkably, when the island is divided into geographic areas, different migration patterns are clearly recognisable. Whereas North and Central Sardinia populations show a stronger male migration rate, the South Sardinia population shows a stronger female migration rate. CONCLUSION: Distinct migration patterns of male and female lineages affect the areas investigated differently. These past migration movements are major contributors to the complex genetic structure currently observed in the Sardinian population.

GLO1 gene polymorphisms and their association with retinitis pigmentosa: a case-control study in a Sicilian population.

Glyoxalase 1 (GLO1) is a ubiquitous cellular enzyme involved in detoxification of methylglyoxal (MGO), a cytotoxic byproduct of glycolysis, whose excess can cause oxidative stress. In retinitis pigmentosa (RP), the prevalent cause of blindness just during working life in the industrialized countries, oxidative stress represents one of the possible mechanisms leading to death of cones following that of rods in the retina. To date, the causes of secondary death of cones remain unclear and among proposed mechanisms are: the deprivation of trophic factors normally produced by healthy rods, a compromised uptake of nutrients to cones due to irreversible destruction of RPE-cone outer segment, microglial activation and following release of pro-inflammatory cytokines and rod-derived toxins. In present paper, role of oxidative stress due to an excess of MGO was evaluated. In particular, we wanted to determine whether single nucleotide polymorphisms (SNPs) in GLO1 influence enzyme activity, contributing to cone death in advanced RP. 120 healthy controls and 80 RP patients from Sicilian population were genotyped for three GLO1 common SNPs, rs1130534 (c.372A>T, p.G124G), rs2736654 (c.A332C, p.E111A) and rs1049346 (c.-7C>T, 5'-UTR). While c.A332C polymorphism was not associated with RP, c.372A>T showed an allelic association (T372 allele frequency = 70% vs 60% in controls, p = 0.0071). Conversely, c.-7C>T showed both genotypic (χ2 = 68.0952; p = 1.634e-15) and allelic associations (χ2 = 51.7094; p = 6.435e-13): mutated allele frequency was higher in controls than in patients, suggesting its possible protective role. RP susceptibility may be associated with two of the analyzed GLO1 polymorphisms (rs1130534 and rs1049346).

Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale.

Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalis musimon, were used as probes for hybridization on genomic DNA and on metaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 are sequences respectively belonging to the 1.715 and 1.714 DNA satellite I families. Southern blots and fluorescence in situ hybridization experiments showed completely coherent results: the Bovini probe Bt1 hybridized only to members of the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1 hybridized only to members of the Caprini tribe and not to members of Bovini. Hybridization signals were detected in the heterochromatic regions of every acrocentric autosome, except for two pairs of autosomes from Capra hircus that did not show hybridization to probe Om1. No signal was detected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1 showed almost 100% homology with a bacterial sequence reported in Helicobacter pylori.

Linguistic, geographic and genetic isolation: a collaborative study of Italian populations.

The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliari, Pisa and Roma Sapienza) started a collaborative study in 2007, which was funded by the Italian Ministry of Education, University and Research and received partial support by the Istituto Italiano di Antropologia. In this paper, we present an account of the results obtained in the course of this initiative. Four case-studies relative to linguistic minorities from the Eastern Alps, Sardinia, Apennines and Southern Italy are first described and discussed, focusing on their micro-evolutionary and anthropological implications. Thereafter, we present the results of a systematic analysis of the relations between linguistic, geographic and genetic isolation. Integrating the data obtained in the course of the long-term study with literature and unpublished results on Italian populations, we show that a combination of linguistic and geographic factors is probably responsible for the presence of the most robust signatures of genetic isolation. Finally, we evaluate the magnitude of the diversity of Italian populations in the European context. The human genetic diversity of our country was found to be greater than observed throughout the continent at short (0-200 km) and intermediate (700-800km) distances, and accounted for most of the highest values of genetic distances observed at all geographic ranges. Interestingly, an important contribution to this pattern comes from the "linguistic islands"( e.g. German speaking groups of Sappada and Luserna from the Eastern Italian Alps), further proof of the importance of considering social and cultural factors when studying human genetic variation.

Genetic analysis of putative familial relationships in a captive chimpanzee (Pan troglodytes) population.

Twelve autosomal dinucleotide repeat loci were analyzed in chimpanzees genomes by DNA amplification using primers designed for analysis of human loci. The markers span the entire length of human chromosomes 21 and 22. Nine markers were polymorphic in chimpanzee as well, with a somewhat comparable level of polymorphism and allele size range. Even in the presence of very limited information and in spite of missing samples, it was possible to reconstruct a complex pedigree and to provide molecular data that corroborate family relationships that were deduced from cage history and behavioral data. The conclusions were further supported by mitochondrial DNA analysis. The data presented in this report show that the extremely abundant source of human markers may be exploited to validate, with molecular evidence, hypotheses on individual relationship or alleged pedigrees, based upon behavioral observations.

FMO3 allelic variants in Sicilian and Sardinian populations: trimethylaminuria and absence of fish-like body odor.

The N-oxygenation of amines by the human flavin-containing monooxygenase (form 3) (FMO3) represents an important means for the conversion of lipophilic nucleophilic heteroatom-containing compounds into more polar and readily excreted products. In healthy individuals, virtually all Trimethylamine (TMA) are metabolized to Trimethylamine N-oxide (TMAO). Several single nucleotide polymorphisms (SNPs) of the FMO3 gene have been described and result in an enzyme with decreased or abolished functional activity for TMA N-oxygenation thus leading to TMAU, or fish-like odor syndrome. Three coding region variants, c. G472A (p.E158K) in exon 4, c. G769A (p.V257M) in exon 6, and c.A923G (p.E308G) in exon 7, are common polymorphisms identified in all population examined so far and are associated with normal or slightly reduced TMA N-oxygenation activity. However, simultaneous occurrence of 158K and 308G variants results in a more pronounced decrease in FMO3 activity. A fourth polymorphism, c. G1424A (p.G475D) in exon 9, less common in the general population, was observed in individuals suffering severe or moderate trimethylaminuria. The aim of this study was to determine the allelic and genotypic distributions of these four FMO3 variants in 528 healthy individuals collected from the Sicilian and Sardinian populations together with haplotype and linkage analyses. Finally, we present data on the genotype-phenotype correlation by ESI-MS/MS TMA/TMAO urinary determination in 158KK/308EG individuals. Variant 158K shows the same frequency in Sicilian and Sardinian populations while variant 257M was not observed in the Sardinian sampling. No significant differences were found for 308G and 475D variants among two populations. Cis-linkage between 158K and 308G was confirmed with the compound variant (158K-308G) being found in a proportion of 0.9% and 0.3% of Sicilian subjects, and 0.01% and 0.5% in Sardinian population. Urinary determination of TMA/TMAO ratio in 158KK/308EG individuals showed a considerable reduction in FMO3 activity although they do not show the classical features of trimethylaminuria as a strong body odor and breath. Our data support the conclusion that trimethylaminuria is not always accompanied by a fish-like odor, despite the coexistence in the same individual of the two variants 158K and 308G, and other factors account for the expression of that phenotype.

Sampling strategies in a linguistic isolate: results from mtDNA analysis.

OBJECTIVES: Sampling strategies are crucial issues in population genetics and anthropological studies. The sampling choice is related to the research question and the type of markers used. In this research, we compared two different sampling strategies in the Sardinian linguistic isolate of Carloforte (Italy). METHODS: A first sampling (N = 49) was carried out through grandparents criterion: individuals selected for the study were born and resident in Carloforte, and unrelated for at least three generations. A second sampling (N = 50) was based on founders surnames (FS): selected participants were proved to be descendants of the village founders, and to have no ancestors in common, at least up to the grandparental generation. RESULTS: The group selected through FS showed a greater gene diversity, which was confirmed by both network and haplogroup analysis. Among the shared haplogroups, we find clear differences in their frequencies. Sampling through grandparents criterion showed essentially the same haplogroups found in Sardinia, and with similar frequencies. Interesting results came from genetic tree. The FS sampling clustered with Northern African populations and it is located very far from Italian and Sardinian populations, whereas the grandparents criterion sampling clustered with Italian populations and it is located close to the other Sardinian populations. CONCLUSIONS: Results showed that different sampling strategies can lead to contrasting results. As sampling through grandparents criterion is influenced by recent gene flow, we hypothesize that the difference observed with the two sampling strategies is due to the merging of Carloforte with Sardinian populations.

Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia.

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.

Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia

We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.

Pilot study on schizophrenia in Sardinia.

OBJECTIVE: Based on a small sample of cases with schizophrenia and control individuals from an isolated population, a genome-wide association study was undertaken to find variants conferring susceptibility to this disease. METHODS: Standard association tests were employed, followed by newer multilocus association methods (genotype patterns). RESULTS: Individually, no variant produced a significant result. However, the best two variants (rs1360382 on chromosome 9 and rs1303 on chromosome 14) showed significantly different genotype pattern distributions between patients and control individuals. The risk genotype pattern AA-TT is highly predictive of schizophrenia, with estimated sensitivity and specificity of 1 and 0.96, respectively. CONCLUSIONS: These findings support the hypothesis that schizophrenia is partly due to multiple genetic variants, each with a relatively small effect.

Analysis of 31 STR loci in the genetic isolate of Carloforte (Sardinia, Italy).

The genotypes of 31 autosomal short tandem repeat loci in the population of Carloforte were analyzed, these representing a linguistic and genetic isolate located on the island of Sardinia (Italy). The markers span the entire length of chromosomes 19, 20, 21 and 22. Allele frequencies and statistical parameters were presented for all loci. Observed heterozygosity ranged from 0.279 to 0.884, and polymorphism information content from 0.552 to 0.886. All but two loci showed Hardy-Weinberg equilibrium after Bonferroni correction. The 31 short tandem repeat loci examined in the present work provide additional data on the genetic structure of the Carloforte population.

Analysis of 31 STR loci in the genetic isolate of Carloforte (Sardinia, Italy)

The genotypes of 31 autosomal short tandem repeat loci in the population of Carloforte were analyzed, these representing a linguistic and genetic isolate located on the island of Sardinia (Italy). The markers span the entire length of chromosomes 19, 20, 21 and 22. Allele frequencies and statistical parameters were presented for all loci. Observed heterozygosity ranged from 0.279 to 0.884, and polymorphism information content from 0.552 to 0.886. All but two loci showed Hardy-Weinberg equilibrium after Bonferroni correction. The 31 short tandem repeat loci examined in the present work provide additional data on the genetic structure of the Carloforte population.