Risk for Hereditary Neoplastic Syndromes in Women with Mismatch Repair-Proficient Endometrial Cancer.

Endometrial cancer (EC) is a prevalent malignancy in women, and those who are proficient in the DNA mismatch repair (pMMR) pathway may have a family history (FH) that meets the criteria for a hereditary neoplastic condition (HNS). This study aimed to estimate the risk of HNS in women with pMMR endometrial tumors by analyzing their FH. To achieve this, we collaborated with a primary study and collected FH information by telephone. The final sample comprised 42 women who responded to the Primary Screening Questionnaire. Their family pedigrees were drawn and categorized according to internationally standardized criteria for the risk of HNS. Results showed that 26 women (61%) were found to be at risk for HNS, with Bethesda criteria being met by 23%, Amsterdam criteria by 15%, and 4% met the attenuated familial adenomatous polyposis criteria. Our results emphasize the importance of FH and the need to encourage healthcare professionals to collect and document FH more frequently, even if it is self-reported. By identifying individuals with HNS, we can improve their outcomes and reduce the burden of cancer in families with a predisposition to cancer.

Genetic diversity of the LILRB1 and LILRB2 coding regions in an admixed Brazilian population sample.

Leukocyte immunoglobulin (Ig)-like receptors (LILR) LILRB1 and LILRB2 may play a pivotal role in maintaining self-tolerance and modulating the immune response through interaction with classical and nonclassical HLA molecules. Although both diversity and natural selection patterns over HLA genes have been extensively evaluated, little information is available concerning the genetic diversity and selection signatures on the LILRB1/2 regions. Therefore, we identified the LILRB1/2 genetic diversity using next-generation sequencing in a population sample from São Paulo State, Brazil. We identified 58 LILRB1 Single Nucleotide Variants (SNVs), which gave rise to 13 haplotypes, and 41 LILRB2 SNVs arranged into 11 haplotypes. Although we may not exclude as a possible effect of population structure, we found evidence of either positive or purifying selection on LILRB1/2 coding regions. Some residues in both proteins showed to be under the effect of positive selection, suggesting that amino acid replacements in these proteins resulted in beneficial functional changes. Finally, we have revealed that allelic variation (six and five amino acid exchanges in LILRB1 and LILRB2, respectively) affects the structure and/or stability of both molecules. Nonetheless, LILRB2 has shown higher average stability, with no D1/D2 residue affecting protein structure. Overall, our findings demonstrate that LILRB1 and LILRB2 are as polymorphic as HLA class Ib genes and provide strong evidence supporting the directional selection regime hypothesis.

Elephant bones for the Middle Pleistocene toolmaker.

The use of bone as raw material for implements is documented since the Early Pleistocene. Throughout the Early and Middle Pleistocene bone tool shaping was done by percussion flaking, the same technique used for knapping stone artifacts, although bone shaping was rare compared to stone tool flaking. Until recently the generally accepted idea was that early bone technology was essentially immediate and expedient, based on single-stage operations, using available bone fragments of large to medium size animals. Only Upper Paleolithic bone tools would involve several stages of manufacture with clear evidence of primary flaking or breaking of bone to produce the kind of fragments required for different kinds of tools. Our technological and taphonomic analysis of the bone assemblage of Castel di Guido, a Middle Pleistocene site in Italy, now dated by 40Ar/39Ar to about 400 ka, shows that this general idea is inexact. In spite of the fact that the number of bone bifaces at the site had been largely overestimated in previous publications, the number of verified, human-made bone tools is 98. This is the highest number of flaked bone tools made by pre-modern hominids published so far. Moreover the Castel di Guido bone assemblage is characterized by systematic production of standardized blanks (elephant diaphysis fragments) and clear diversity of tool types. Bone smoothers and intermediate pieces prove that some features of Aurignacian technology have roots that go beyond the late Mousterian, back to the Middle Pleistocene. Clearly the Castel di Guido hominids had done the first step in the process of increasing complexity of bone technology. We discuss the reasons why this innovation was not developed. The analysis of the lithic industry is done for comparison with the bone industry.

Environmental evolution, faunal and human occupation since 2 Ma in the Anagni basin, central Italy.

We present the study of a composite, yet continuous sedimentary succession covering the time interval spanning 2.6-0.36 Ma in the intramontane basin of Anagni (central Italy) through a dedicated borecore, field surveys, and the review of previous data at the three palaeontological and archaeological sites of Colle Marino, Coste San Giacomo and Fontana Ranuccio. By combining the magneto- and chronostratigraphic data with sedimentologic and biostratigraphic analysis, we describe the palaeogeographic and tectonic evolution of this region during this entire interval. In this time frame, starting from 0.8 Ma, the progressive shallowing and temporary emersion of the large lacustrine basins and alluvial plains created favorable conditions for early hominin occupation of the area, as attested by abundant tool industry occurrences and fossils. This study provides new constraints to better interpret the hominin migratory dynamics and the factors that influenced the location and spatial distribution during the early occupation of this region.

The origin of early Acheulean expansion in Europe 700 ka ago: new findings at Notarchirico (Italy).

Notarchirico (Southern Italy) has yielded the earliest evidence of Acheulean settlement in Italy and four older occupation levels have recently been unearthed, including one with bifaces, extending the roots of the Acheulean in Italy even further back in time. New 40Ar/39Ar on tephras and ESR dates on bleached quartz securely and accurately place these occupations between 695 and 670 ka (MIS 17), penecontemporaneous with the Moulin-Quignon and la Noira sites (France). These new data demonstrate a very rapid expansion of shared traditions over Western Europe during a period of highly variable climatic conditions, including interglacial and glacial episodes, between 670 and 650 (i.e., MIS17/MIS16 transition). The diversity of tools and activities observed in these three sites shows that Western Europe was populated by adaptable hominins during this time. These conclusions question the existence of refuge areas during intense glacial stages and raise questions concerning understudied migration pathways, such as the Sicilian route.

Correction: A biface production older than 600 ka ago at Notarchirico (Southern Italy) contribution to understanding early Acheulean cognition and skills in Europe.

[This corrects the article DOI: 10.1371/journal.pone.0218591.].

HLA-G Polymorphisms Are Associated with Non-segmental Vitiligo among Brazilians.

(1) Background: Vitiligo is characterized by white patches on the skin caused by loss of melanocyte activity or the absence of these cells. The available treatments minimize the symptoms by retarding the process of skin depigmentation or re-pigmenting the affected regions. New studies are required for a better comprehension of the mechanisms that trigger the disease and for the development of more efficient treatments. Studies have suggested an autoimmune feature for vitiligo, based on the occurrence of other autoimmune diseases in vitiligo patients and their relatives, and on the involvement of genes related to the immune response. (2) Methods: We evaluated, by massive parallel sequencing, polymorphisms of the HLA-G gene in vitiligo patients and control samples, to verify if variants of this gene could influence the susceptibility to vitiligo. (3) Results: We detected an association with non-segmental vitiligo regarding the haplotype Distal-010101a/G*01:01:01:01/UTR-1, adjusting for population stratification by using ancestry-informative markers (AIMs). (4) Conclusions: It remains unclear whether the HLA-G variants associated with vitiligo were detected because of the high linkage disequilibrium (LD) with HLA-A*02, or if the HLA-A variants previously reported as associated with vitiligo were detected because of the high LD with HLA-G*01:01:01:01/UTR-1, or if both genes jointly contribute to vitiligo susceptibility.

A biface production older than 600 ka ago at Notarchirico (Southern Italy) contribution to understanding early Acheulean cognition and skills in Europe.

For the past decade, debates on the earliest evidence of bifacial shaping in Western Europe have focused on several key issues, such as its origin (i.e., local or introduced), or on what should define the Acheulean culture. Whatever hypotheses are proposed for its origin, the onset and technological strategies for making Large Cutting Tools (LCTs), including biface production, are key issues and are often associated with other behavioural changes, such as increased core technology complexity. Current archaeological patterns do not support the existence of transitional industries. Rather, the scant evidence suggests that biface production associated with the management of bifacial volume was widespread around 700 ka. Among the earliest sites, the site of Notarchirico in Southern Italy stands out as one of the most significant examples. 40Ar/39Ar ages and ESR dates recently provided a revised chronology for the whole sedimentary sequence and constrained the archaeological levels between ca. 610 and 670 ka. Five archaeosurfaces (A, A1, B, D and F) yielded LCTs, including bifaces, during Marcello Piperno's excavations from 1980 to 1995. In light of this new chronological framework, which is much shorter than previously thought, we propose in this contribution a revision of the bifaces by applying the "chaine opératoire" method for the first time (analysis of reduction processes). Our goals are to assess biface production in this early Western European locality and to characterize the strategies applied at the site throughout the sequence. A corpus of 32 tools was selected from the A-A1, B, D and F archaeosurfaces. The technological analysis shows that hominins had the capacity to manage bifacial volumes, when raw material quality was adequate. Clear differences do not emerge between the different levels in terms of shaping modes or final forms. However, we demonstrate that the oldest level (level F), with the richest corpus, lacks flint and displays a higher diversity of bifaces. This ability to manage bifacial and bilateral equilibrium, as well as the diversity of the morphological results, is observed in a few penecontemporaneous sites (700-600 ka), both in the north-western and southern parts of Western Europe. These patterns suggest that hominins mastered well-controlled and diversified biface production, combining intense shaping and minimal shaping, and shared a common technological background regardless of the geographical area, and applied this technology regardless of the available raw materials. The degree of skill complexity of hominins in Western Europe between 700 and 600 ka, the current lack of evidence suggesting "gradual industries" between core-and-flake series and Acheulean techno-complexes, raise numerous questions on the origin of new behaviours in Western Europe, their mode of diffusion, and their association with Homo heidelbergensis or other Middle Pleistocene populations.

Applicability of the SNPforID 52-plex panel for human identification and ancestry evaluation in a Brazilian population sample by next-generation sequencing.

SNP analysis is of paramount importance in forensic genetics. The development of new technologies in next-generation sequencing allowed processing a large number of markers in various samples simultaneously. Although SNPs are less informative than STRs, they present lower mutation rates and perform better when using degraded samples. Some SNP systems were developed for forensic usage, such as the SNPforID 52-plex, from the SNPforID Consortium, containing 52 bi-allelic SNPs for human identification. In this paper we evaluated the informativeness of this system in a Brazilian population sample (n = 340). DNA libraries were prepared using a customized HaloPlex Target Enrichment System kit (Agilent Technologies, Inc.) and sequenced in the MiSeq Personal Sequencer platform (Illumina Inc.). The methodology presented here allowed the analysis of 51 out of 52 SNPforID markers. Allele frequencies and forensic parameters were estimated, revealing high informativeness: the combined match probability and power of exclusion were 6.48 × 10-21 and 0.9997, respectively. Population admixture analysis indicates high European contribution (more than 70%) and low Amerindian contribution (less than 10%) in our population, while individual admixture analyses were consistent with the majority of individuals presenting high European contribution. This study demonstrates that the 52-plex kit is suitable for forensic cases in a Brazilian population, presenting results comparable with those obtained using a 16 STR panel.

Extended HLA-G genetic diversity and ancestry composition in a Brazilian admixed population sample: Implications for HLA-G transcriptional control and for case-control association studies.

Human leukocyte antigen-G (HLA-G) is a nonclassical Major Histocompatibility Complex (MHC) molecule with immunomodulatory function and restricted tissue expression. The genetic diversity of HLA-G has been extensively studied in several populations, however, the segment located upstream -1406 has not yet been evaluated. We characterized the nucleotide variation and haplotype structure of an extended distal region (-2635), all exons and the 3'UTR segment of HLA-G by next-generation sequencing (NGS) in a sample of 335 Brazilian individuals. We detected 29 variants at the HLA-G distal promoter region, arranged into 19 haplotypes, among which we identified sites that may influence transcription factor targeting. Although the variation pattern in the distal region resembled the one observed in the conventional promoter segment, molecular signature for balancing selection was observed in the promoter segment from -1406 to -1 (Tajima's D = 2.315, P = 0.017), but not in this distal segment (D = 1.049, P = 0.118). Furthermore, the ancestry composition of this Brazilian population sample was determined by the analysis of SNPforID 34-plex ancestry informative marker (AIM) SNP panel. The distribution of HLA-G haplotypes was ancestry-dependent, corroborating previous findings and emphasizing the importance of considering the ancestry information in association studies.

Molecular modeling and statistical analysis in the design of derivatives of human dipeptidyl peptidase IV.

Human dipeptidyl peptidase IV (hDDP-IV) has a considerable importance in inactivation of glucagon-like peptide-1, which is related to type 2 diabetes. One approach for the treatment is the development of small hDDP-IV inhibitors. In order to design better inhibitors, we analyzed 5-(aminomethyl)-6-(2,4-dichlrophenyl)-2-(3,5-dimethoxyphenyl)pyrimidin-4-amine and a set of 24 molecules found in the BindingDB web database for model designing. The analysis of their molecular properties allowed the design of a multiple linear regression model for activity prediction. Their docking analysis allowed visualization of the interactions between the pharmacophore regions and hDDP-IV. After both analyses were performed, we proposed a set of nine molecules in order to predict their activity. Four of them displayed promising activity, and thus, had their docking performed, as well as, the pharmacokinetic and toxicological study. Two compounds from the proposed set showed suitable pharmacokinetic and toxicological characteristics, and therefore, they were considered promising for future synthesis and in vitro studies.

The Acheulian and Early Middle Paleolithic in Latium (Italy): Stability and Innovation.

We present here the results of a technological and typological analysis of the Acheulian and early Middle Paleolithic assemblages from Torre in Pietra (Latium, Italy) together with comparisons with the Acheulian small tools of Castel di Guido. The assemblages were never chronometrically dated before. We have now 40Ar/39Ar dates and ESR-U-series dates, within a geomorphological framework, which support correlations to marine isotope stages. The Acheulian (previously correlated to MIS 9) is now dated to MIS 10 while the Middle Paleolithic is dated to MIS 7. Lithic analyses are preceded by taphonomic evaluations. The Levallois method of the Middle Paleolithic assemblage is an innovation characterized by the production of thin flake blanks without cortex. In contrast, the small tool blanks of the Acheulian were either pebbles or thick flakes with some cortex. They provided a relatively easy manual prehension. The choice of Levallois thin flake blanks in the Middle Paleolithic assemblage suggest that the new technology is most likely related to the emergence of hafting. Accordingly, the oldest direct evidence of hafting technology is from the site of Campitello Quarry in Tuscany (Central Italy) where birch-bark tar, found on the proximal part of two flint flakes, is dated to the end of MIS 7. Nevertheless, a peculiar feature of the Middle Paleolithic at Torre in Pietra is the continuous presence of small tool blanks on pebbles and cores and on thick flake albeit at a much lower frequency than in the older Acheulian industries. The adoption of the new technology is thus characterized by innovation combined with a degree of stability. The persistence of these habits in spite of the introduction of an innovative technique underlies the importance of cultural transmission and conformity in the behavior of Neandertals.

A Human Deciduous Tooth and New 40Ar/39Ar Dating Results from the Middle Pleistocene Archaeological Site of Isernia La Pineta, Southern Italy.

Isernia La Pineta (south-central Italy, Molise) is one of the most important archaeological localities of the Middle Pleistocene in Western Europe. It is an extensive open-air site with abundant lithic industry and faunal remains distributed across four stratified archaeosurfaces that have been found in two sectors of the excavation (3c, 3a, 3s10 in sect. I; 3a in sect. II). The prehistoric attendance was close to a wet environment, with a series of small waterfalls and lakes associated to calcareous tufa deposits. An isolated human deciduous incisor (labelled IS42) was discovered in 2014 within the archaeological level 3 coll (overlying layer 3a) that, according to new 40Ar/39Ar measurements, is dated to about 583-561 ka, i.e. to the end of marine isotope stage (MIS) 15. Thus, the tooth is currently the oldest human fossil specimen in Italy; it is an important addition to the scanty European fossil record of the Middle Pleistocene, being associated with a lithic assemblage of local raw materials (flint and limestone) characterized by the absence of handaxes and reduction strategies primarily aimed at the production of small/medium-sized flakes. The faunal assemblage is dominated by ungulates often bearing cut marks. Combining chronology with the archaeological evidence, Isernia La Pineta exhibits a delay in the appearance of handaxes with respect to other European Palaeolithic sites of the Middle Pleistocene. Interestingly, this observation matches the persistence of archaic morphological features shown by the human calvarium from the Middle Pleistocene site of Ceprano, not far from Isernia (south-central Italy, Latium). In this perspective, our analysis is aimed to evaluate morphological features occurring in IS42.