Polymorphisms within autophagy-related genes as susceptibility biomarkers for multiple myeloma: a meta-analysis of three large cohorts and functional characterization

Functional data used in this project have been meticulously catalogued and archived in the BBMRI-NL data infrastructure (https://hfgp.bbmri.nl/, accessed on 12 February 2020) using the MOLGENIS open-source platform for scientific data.Multiple myeloma (MM) arises following malignant proliferation of plasma cells in the bone marrow, that secrete high amounts of specific monoclonal immunoglobulins or light chains, resulting in the massive production of unfolded or misfolded proteins. Autophagy can have a dual role in tumorigenesis, by eliminating these abnormal proteins to avoid cancer development, but also ensuring MM cell survival and promoting resistance to treatments. To date no studies have determined the impact of genetic variation in autophagy-related genes on MM risk. We performed meta-analysis of germline genetic data on 234 autophagy-related genes from three independent study populations including 13,387 subjects of European ancestry (6863 MM patients and 6524 controls) and examined correlations of statistically significant single nucleotide polymorphisms (SNPs; p < 1 × 10−9) with immune responses in whole blood, peripheral blood mononuclear cells (PBMCs), and monocyte-derived macrophages (MDM) from a large population of healthy donors from the Human Functional Genomic Project (HFGP). We identified SNPs in six loci, CD46, IKBKE, PARK2, ULK4, ATG5, and CDKN2A associated with MM risk (p = 4.47 × 10−4−5.79 × 10−14). Mechanistically, we found that the ULK4rs6599175 SNP correlated with circulating concentrations of vitamin D3 (p = 4.0 × 10−4), whereas the IKBKErs17433804 SNP correlated with the number of transitional CD24+CD38+ B cells (p = 4.8 × 10−4) and circulating serum concentrations of Monocyte hemoattractant Protein (MCP)-2 (p = 3.6 × 10−4). We also found that the CD46rs1142469 SNP corre lated with numbers of CD19+ B cells, CD19+CD3− B cells, CD5+ IgD− cells, IgM− cells, IgD−IgM− cells, and CD4−CD8− PBMCs (p = 4.9 × 10−4−8.6 × 10−4 ) and circulating concentrations of interleukin (IL)-20 (p = 0.00082). Finally, we observed that the CDKN2Ars2811710 SNP correlated with levels of CD4+EMCD45RO+CD27− cells (p = 9.3 × 10−4 ). These results suggest that genetic variants within these six loci influence MM risk through the modulation of specific subsets of immune cells, as well as vitamin D3−, MCP-2−, and IL20-dependent pathways.This work was supported by the European Union’s Horizon 2020 research and innovation program, N° 856620 and by grants from the Instituto de Salud Carlos III and FEDER (Madrid, Spain; PI17/02256 and PI20/01845), Consejería de Transformación Económica, Industria, Conocimiento y Universidades and FEDER (PY20/01282), from the CRIS foundation against cancer, from the Cancer Network of Excellence (RD12/10 Red de Cáncer), from the Dietmar Hopp Foundation and the German Ministry of Education and Science (BMBF: CLIOMMICS [01ZX1309]), and from National Cancer Institute of the National Institutes of Health under award numbers: R01CA186646, U01CA249955 (EEB).This work was also funded d by Portuguese National funds, through the Foundation for Science and Technology (FCT)—project UIDB/50026/2020 and UIDP/50026/2020 and by the project NORTE-01-0145-FEDER-000055, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF)

Familial hypercholesterolaemia in children and adolescents from 48 countries: a cross-sectional study

Background: Approximately 450 000 children are born with familial hypercholesterolaemia worldwide every year, yet only 2·1% of adults with familial hypercholesterolaemia were diagnosed before age 18 years via current diagnostic approaches, which are derived from observations in adults. We aimed to characterise children and adolescents with heterozygous familial hypercholesterolaemia (HeFH) and understand current approaches to the identification and management of familial hypercholesterolaemia to inform future public health strategies. Methods: For this cross-sectional study, we assessed children and adolescents younger than 18 years with a clinical or genetic diagnosis of HeFH at the time of entry into the Familial Hypercholesterolaemia Studies Collaboration (FHSC) registry between Oct 1, 2015, and Jan 31, 2021. Data in the registry were collected from 55 regional or national registries in 48 countries. Diagnoses relying on self-reported history of familial hypercholesterolaemia and suspected secondary hypercholesterolaemia were excluded from the registry; people with untreated LDL cholesterol (LDL-C) of at least 13·0 mmol/L were excluded from this study. Data were assessed overall and by WHO region, World Bank country income status, age, diagnostic criteria, and index-case status. The main outcome of this study was to assess current identification and management of children and adolescents with familial hypercholesterolaemia. Findings: Of 63 093 individuals in the FHSC registry, 11 848 (18·8%) were children or adolescents younger than 18 years with HeFH and were included in this study; 5756 (50·2%) of 11 476 included individuals were female and 5720 (49·8%) were male. Sex data were missing for 372 (3·1%) of 11 848 individuals. Median age at registry entry was 9·6 years (IQR 5·8-13·2). 10 099 (89·9%) of 11 235 included individuals had a final genetically confirmed diagnosis of familial hypercholesterolaemia and 1136 (10·1%) had a clinical diagnosis. Genetically confirmed diagnosis data or clinical diagnosis data were missing for 613 (5·2%) of 11 848 individuals. Genetic diagnosis was more common in children and adolescents from high-income countries (9427 [92·4%] of 10 202) than in children and adolescents from non-high-income countries (199 [48·0%] of 415). 3414 (31·6%) of 10 804 children or adolescents were index cases. Familial-hypercholesterolaemia-related physical signs, cardiovascular risk factors, and cardiovascular disease were uncommon, but were more common in non-high-income countries. 7557 (72·4%) of 10 428 included children or adolescents were not taking lipid-lowering medication (LLM) and had a median LDL-C of 5·00 mmol/L (IQR 4·05-6·08). Compared with genetic diagnosis, the use of unadapted clinical criteria intended for use in adults and reliant on more extreme phenotypes could result in 50-75% of children and adolescents with familial hypercholesterolaemia not being identified. Interpretation: Clinical characteristics observed in adults with familial hypercholesterolaemia are uncommon in children and adolescents with familial hypercholesterolaemia, hence detection in this age group relies on measurement of LDL-C and genetic confirmation. Where genetic testing is unavailable, increased availability and use of LDL-C measurements in the first few years of life could help reduce the current gap between prevalence and detection, enabling increased use of combination LLM to reach recommended LDL-C targets early in life

Combining Static and Dynamical Approaches for Infrared Spectra Calculations of Gas Phase Molecules and Clusters

International audienceFour models for the calculation of the IR spectrum of gas phase molecules and clusters from molecular dynamics simulations are presented with the aim to reduce the computational cost of the usual Fourier transform (FT) of the time correlation function of the dipole moment. These models are based on the VDOS, FT of time correlation function of velocities, and atomic polar tensors (APT). The models differ from each other by the number of APTs inserted into the velocities correlation function. Excellent accuracy is achieved by the model adopting a weighted linear combination of a few selected APTs adapted for the rotation of the molecule (model D). The achieved accuracy relates to band positions, band shapes, and band intensities. Depending on the degree of actual dynamics of the molecule, rotational motion, conformational isomerization, and large amplitude motions that can be seen during the finite temperature trajectory, one could also apply one of the other models (models A, B, or C), but with caution. Model D is therefore found simple and accurate, with appealing computational cost and should be systematically applied. Its generalization to condensed phase systems should be straightforward

Influence of argon and D₂ tagging on the hydrogen bond network in Cs⁺(H₂O)₃; kinetic trapping below 40 K

International audienceThe influence of enthalpic and entropic effects as well as of kinetic trapping processes on the structure of Ar/D2-tagged Cs+(H2O)3 clusters is studied by temperature-dependent infrared photodissociation spectroscopy combined with harmonic vibrational spectra calculations and anharmonic free energy profiles from finite temperature metadynamics molecular dynamics simulations. Each tag favors a different hydrogen bond network of water molecules, with Ar-tagging (vs. D2-tagging) of Cs+(H2O)3 leading to the lower energy conformation. The relative population of these conformers can be tuned over a temperature range of 12 to 21 K. The formation mechanisms of these tagged clusters can be deduced from the free energy profiles. This investigation demonstrates that a variety of factors, both thermodynamic and kinetic, play a role in the structure of flexible molecular species, even at cryogenic temperatures

Intermolecular modulation of IR intensities in the solid state. The role of weak interactions in polyethylene crystal: A computational DFT study

Density functional theory calculations with periodic boundary conditions are exploited to study the infrared spectrum of crystalline polyethylene. Spectral changes lead by the intermolecular packing in the orthorhombic three-dimensional crystal are discussed by means of a careful comparison with calculations carried out for an isolated polymer chain in the all-trans conformation, described as an ideal one-dimensional crystal. The results are analyzed in the framework of the "oligomer approach" through the modelling of the IR spectrum of n-alkanes of different lengths. The study demonstrates that a relevant absorption intensity modulation of CH2 deformation transitions takes place in the solid state. This finding suggests a new interpretation for the experimental evidences collected in the past by means of IR intensity measurement during thermal treatment. Moreover, the comparison between calculations for 3-D crystal and for the isolated polyethylene chain (1-D crystal) allows to put in evidence the effect of the local electric field on the computed infrared intensities. This observation provides guidelines for the comparison between infrared absorption intensities predicted for an isolated unit and for a molecule belonging to a crystal, through the introduction of suitable correction factors based on the refraction index of the material and depending on the dimensionality of such units (0D - molecule; 1D - polymer; 2D - slab)

Molecular hydrophobicity at a macroscopically hydrophilic surface

International audienceInterfaces between water and silicates are ubiquitous and relevant for, among others, geochemistry, atmospheric chemistry, and chromatography. The molecular-level details of water organization at silica surfaces are important for a fundamental understanding of this interface. While silica is hydrophilic, weakly hydrogen-bonded OH groups have been identified at the surface of silica, characterized by a high O-H stretch vibrational frequency. Here, through a combination of experimental and theoretical surface-selective vibrational spectroscopy, we demonstrate that these OH groups originate from very weakly hydrogen-bonded water molecules at the nominally hydrophilic silica interface. The properties of these OH groups are very similar to those typically observed at hydrophobic surfaces. Molecular dynamics simulations illustrate that these weakly hydrogen-bonded water OH groups are pointing with their hydrogen atom toward local hydrophobic sites consisting of oxygen bridges of the silica. An increased density of these molecular hydrophobic sites, evident from an increase in weakly hydrogen-bonded water OH groups, correlates with an increased macroscopic contact angle

Crystal Structure and Vibrational Spectra of Poly(trimethylene terephthalate) from Periodic Density Functional Theory Calculations

The crystal structure and the IR spectrum of crystalline poly(trimethylene terephthalate), PTT, have been investigated by means of periodic density functional theory calculations including Grimme’s correction for dispersion interactions. Both structural and spectroscopic results have been critically compared to the experimental data taken from the literature, showing very good agreement between theory and the experiments. The previous spectral assignments, based only on experimental investigations, have been revised, and further insights have been obtained. Furthermore, spectroscopic markers of crystallinity or regularity (i.e., of the regular conformation of the polymer chain) have been proposed. In addition to the analysis of the IR spectra, the effect of computational parameters on the crystal structure determination (basis sets and parameters for Grimme’s correction) have been analyzed. This work demonstrates that state of-the-art computational methods can provide an unambiguous description of the structural and vibrational properties of crystalline polymers on the basis of the peculiar intra- and intermolecular interactions occurring in different macromolecular materials