Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations.

Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs). We identify numerous cis-eQTLs that contribute to the marked differences in immune responses detected within and between populations and a strong trans-eQTL hotspot at TLR1 that decreases expression of pro-inflammatory genes in Europeans only. We find that immune-responsive regulatory variants are enriched in population-specific signals of natural selection and show that admixture with Neandertals introduced regulatory variants into European genomes, affecting preferentially responses to viral challenges. Together, our study uncovers evolutionarily important determinants of differences in host immune responsiveness between human populations.

SCF-ChemBio: Chemical Biology Tour de France.

Chemical biology is a steadily growing field that has traditionally struggled to clearly define its boundaries in a short sentence. However, it can be stated that through the development of chemical and physicochemical tools, concepts and methods, chemical biology aims to address or stimulate biological questions at the molecular level in living organisms. Chemical biologists design and develop molecular tools that can probe or modulate biological processes, in order to understand their function, and sometimes to modify it for specific applications, but also to observe and analyze these tools in complex biological environments. Essentially positioned as a fundamental approach, chemical biology often remains very close to potential applications as it builds molecular objects capable of reacting to a significant biological stimulus. Chemical biology therefore finds natural development in fields such as health for the design of drugs and diagnostic systems or the environment for applications in crop science and ecology.

PSL Chemical Biology Symposia Third Edition: A Branch of Science in its Explosive Phase.

This symposium is the third PSL (Paris Sciences & Lettres) Chemical Biology meeting (2016, 2019, 2023) held at Institut Curie. This initiative originally started at Institut de Chimie des Substances Naturelles (ICSN) in Gif-sur-Yvette (2013, 2014), under the directorship of Professor Max Malacria, with a strong focus on chemistry. It was then continued at the Institut Curie (2015) covering a larger scope, before becoming the official PSL Chemical Biology meeting. This latest edition was postponed twice for the reasons that we know. This has given us the opportunity to invite additional speakers of great standing. This year, Institut Curie hosted around 300 participants, including 220 on site and over 80 online. The pandemic has had, at least, the virtue of promoting online meetings, which we came to realize is not perfect but has its own merits. In particular, it enables those with restricted time and resources to take part in events and meetings, which can now accommodate unlimited participants. We apologize to all those who could not attend in person this time due to space limitation at Institut Curie.

Na6Li4MO4(CO3)4 (M = W and Mo): An Alternative Electrolyte for High-Temperature Electrochemical Cells.

Two new acentric oxycarbonates Na6Li4MO4(CO3)4 (M = W and Mo) were synthesized via a conventional solid-state route. Their structure was determined from X-ray diffraction data on single crystals. Na6Li4MO4(CO3)4 (M = W and Mo) crystallizes in the acentric cubic P-43m space group (a ≈ 7.15 Å). It is composed of MLi4O16 units built from MO4 and LiO4 tetrahedra and linked by CO32- groups to form a three-dimensional framework in which Na+ ions are inserted. We showed from differential scanning calorimetry and powder X-ray diffraction experiments that the melting is congruent (T ∼525 °C). In the solid and molten forms, conductivity was measured for both oxycarbonates by electrochemical impedance spectroscopy with three various gas compositions (CO2 100 vol %, CO2-air 70-30 vol %, and CO2-air 20-80 vol %). Each time, the stability of the electrical behavior was checked via heating and cooling cycles. The conductivity of both solid and molten phases is purely ionic and in the same order of magnitude as for the classical molten alkali electrolyte made of Li-Na or Li-K carbonates. As activation energies are also comparable, those new oxycarbonates appear to be promising electrolytes for electrochemical devices.

A CDH23 missense variant in Beauceron dogs with non-syndromic deafness.

Congenital coat-colour-related deafness is common among certain canine breeds especially those exhibiting extreme white spotting or merle patterning. We identified a non-syndromic deafness in Beauceron dogs characterised by a bilateral hearing loss in puppies that is not linked to coat colour. Pedigree analysis suggested an autosomal recessive transmission. By combining homozygosity mapping with whole genome sequencing and variant filtering in affected dogs we identified a CDH23:c.700C>T variant. The variant, located in the CHD23 (cadherin related 23) gene, was predicted to induce a CDH23:p.(Pro234Ser) change in the protein. Proline-234 of CDH23 protein is highly conserved across different vertebrate species. In silico tools predicted the CDH23:p.(Pro234Ser) change to be deleterious. CDH23 encodes a calcium-dependent transmembrane glycoprotein localised near the tips of hair-cell stereocilia in the mammalian inner ear. Intact function of these cilia is mandatory for the transformation of the acoustical wave into a neurological signal, leading to sensorineural deafness when impaired. By genotyping a cohort of 90 control Beauceron dogs sampled in France, we found a 3.3% carrier frequency. The CDH23:c.[700C>T] allele is easily detectable with a genetic test to avoid at-risk matings.

Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes.

Humans homozygous or hemizygous for variants predicted to cause a loss of function (LoF) of the corresponding protein do not necessarily present with overt clinical phenotypes. We report here 190 autosomal genes with 207 predicted LoF variants, for which the frequency of homozygous individuals exceeds 1% in at least one human population from five major ancestry groups. No such genes were identified on the X and Y chromosomes. Manual curation revealed that 28 variants (15%) had been misannotated as LoF. Of the 179 remaining variants in 166 genes, only 11 alleles in 11 genes had previously been confirmed experimentally to be LoF. The set of 166 dispensable genes was enriched in olfactory receptor genes (41 genes). The 41 dispensable olfactory receptor genes displayed a relaxation of selective constraints similar to that observed for other olfactory receptor genes. The 125 dispensable nonolfactory receptor genes also displayed a relaxation of selective constraints consistent with greater redundancy. Sixty-two of these 125 genes were found to be dispensable in at least three human populations, suggesting possible evolution toward pseudogenes. Of the 179 LoF variants, 68 could be tested for two neutrality statistics, and 8 displayed robust signals of positive selection. These latter variants included a known FUT2 variant that confers resistance to intestinal viruses, and an APOL3 variant involved in resistance to parasitic infections. Overall, the identification of 166 genes for which a sizeable proportion of humans are homozygous for predicted LoF alleles reveals both redundancies and advantages of such deficiencies for human survival.

The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm.

Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modeled in human populations.

Structural Characterization and Influence of Defects on the Optical Properties of the Oxygen-Deficient Perovskite Ba3LiNb2O8.5□0.5.

A new oxygen-deficient perovskite Ba3LiNb2O8.5□0.5 was synthesized via a conventional solid-state route and compared to the already known perovskite Ba3Li0.75Nb2.25O9. The structure of Ba3LiNb2O8.5□0.5 was investigated by means of X-ray and neutron diffraction, TEM, NMR, and XPS. The study of its thermal behavior revealed an unexpected color change when heated to 1400 °C in a sealed platinum tube, with conservation of the initial X-ray structure. First-principles calculations have been performed in order to better understand these observations. The geometry optimizations and the optical spectra simulations highlight the role of both Nb/Li distribution and oxygen-vacancy location.

Inhibitors of DNA Methylation.

DNA methylation is involved in numerous biological processes and is deregulated in human diseases. The modulation of the activity of the enzymes and proteins in charge of DNA methylation, for example, DNA methyltransferases (DNMTs), can represent a powerful strategy to alter DNA methylation patterns and restore biological processes that are aberrant in diseases. In this chapter, we present examples of inhibitors of DNMTs (DNMTi). We review their fields of application either as therapeutic molecules, for example, in cancers, cardiovascular, neurological, and infectious diseases or as bioengineering tools. Finally, novel strategies to target DNA methylation and overcome the limits of single DNMT inhibitors will be described. These strategies consist in either targeting the methyl group reader proteins rather than targeting directly DNMTs or to combine within the same molecule a DNMT inhibitor with an additional active moiety, e.g., HDAC inhibitor, to improve efficacy and lower secondary effect of such drug.

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis.

Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis.

Polygenic adaptation and convergent evolution on growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers.

Different human populations facing similar environmental challenges have sometimes evolved convergent biological adaptations, for example, hypoxia resistance at high altitudes and depigmented skin in northern latitudes on separate continents. The "pygmy" phenotype (small adult body size), characteristic of hunter-gatherer populations inhabiting both African and Asian tropical rainforests, is often highlighted as another case of convergent adaptation in humans. However, the degree to which phenotypic convergence in this polygenic trait is due to convergent versus population-specific genetic changes is unknown. To address this question, we analyzed high-coverage sequence data from the protein-coding portion of the genomes of two pairs of populations: Batwa rainforest hunter-gatherers and neighboring Bakiga agriculturalists from Uganda and Andamanese rainforest hunter-gatherers and Brahmin agriculturalists from India. We observed signatures of convergent positive selection between the rainforest hunter-gatherers across the set of genes with "growth factor binding" functions ([Formula: see text]). Unexpectedly, for the rainforest groups, we also observed convergent and population-specific signatures of positive selection in pathways related to cardiac development (e.g., "cardiac muscle tissue development"; [Formula: see text]). We hypothesize that the growth hormone subresponsiveness likely underlying the adult small body-size phenotype may have led to compensatory changes in cardiac pathways, in which this hormone also plays an essential role. Importantly, in the agriculturalist populations, we did not observe similar patterns of positive selection on sets of genes associated with growth or cardiac development, indicating our results most likely reflect a history of convergent adaptation to the similar ecology of rainforests rather than a more general evolutionary pattern.

CO2 Capture by Na2TeO4: Structure of Na2- xH xTeO4 and Kinetic Aspects.

ß-Na2TeO4 is able to trap CO2 in a humid atmosphere due to a partial Na+/H+ exchange and the formation of NaHCO3. The RT powder X-ray diffraction pattern of the resulting Na2- xH xTeO4 shows broad and narrow hkl lines preventing the structural study. We show by the DIFFaX program that Na+/H+ exchange is topotactic since the structure, as in the mother form, consists of [TeO4] n2 n- chains of TeO6 octahedra. We also show that the broadening of some hkl lines is due to stacking faults which result from the weakness of H-O···H bonds connecting the [TeO4] n2 n- chains. Upon heating, a progressive structural organization takes place which has been followed by powder X-ray diffraction, Raman, and NMR spectroscopies. Around 300 °C, a well organized structure can be described from powder X-ray diffraction refinements in the monoclinic P21/ n space group while ab initio computations allowed location of the hydrogen atoms with satisfactory H-O bonds. In addition, we present the CO2 sorption/desorption by Na2TeO4 and compare its performance to that of Na2SiO3. Finally, the existence of a Na2- xLi xTeO4 solid solution (0 ≤ x ≤ 0.9) is evidenced, and we show that the presence of lithium in the structure leads to the disappearance of the structural transition observed for ß-Na2TeO4 and to a progressive decrease of the CO2 capture ability.

Natural Products and Chemical Biology Tools: Alternatives to Target Epigenetic Mechanisms in Cancers.

DNA methylation and histone acetylation are widely studied epigenetic modifications. They are involved in numerous pathologies such as cancer, neurological disease, inflammation, obesity, etc. Since the discovery of the epigenome, numerous compounds have been developed to reverse DNA methylation and histone acetylation aberrant profile in diseases. Among them several were inspired by Nature and have a great interest as therapeutic molecules. In the quest of finding new ways to target epigenetic mechanisms, the use of chemical tools is a powerful strategy to better understand epigenetic mechanisms in biological systems. In this review we will present natural products reported as DNMT or HDAC inhibitors for anticancer treatments. We will then discuss the use of chemical tools that have been used in order to explore the epigenome.

ß-Na2TeO4: Phase Transition from an Orthorhombic to a Monoclinic Form. Reversible CO2 Capture.

The present work concerns the tellurate Na2TeO4 which has a 1D structure and could then present a CO2 capture ability. It has been synthesized in a powder form via a solid-state reaction and structurally characterized by thermal X-ray diffraction experiments, Raman spectroscopy, and differential scanning calorimetry. The room temperature structure corresponds to the ß-Na2TeO4 orthorhombic form, and we show that it undergoes a reversible structural transition near 420 °C toward a monoclinic system. Ab initio computations were also performed on the room temperature structure, the Raman vibration modes calculated, and a normal mode attribution proposed. In agreement with our expectations, this sodium oxide is able to trap CO2 by a two-step mechanism: Na+/H+ exchange and carbonation of the released sodium as NaHCO3. This capture is reversible since CO2 can be released upon heating by recombination of the mother phase.

IP3 signalling regulates exogenous RNAi in Caenorhabditis elegans.

RNA interference (RNAi) is a widespread and widely exploited phenomenon. Here, we show that changing inositol 1,4,5-trisphosphate (IP3) signalling alters RNAi sensitivity in Caenorhabditis elegans. Reducing IP3 signalling enhances sensitivity to RNAi in a broad range of genes and tissues. Conversely up-regulating IP3 signalling decreases sensitivity. Tissue-specific rescue experiments suggest IP3 functions in the intestine. We also exploit IP3 signalling mutants to further enhance the sensitivity of RNAi hypersensitive strains. These results demonstrate that conserved cell signalling pathways can modify RNAi responses, implying that RNAi responses may be influenced by an animal's physiology or environment.

Instability of the Ionic Conductor Li6BaLa2B2O12 (B = Nb, Ta): Barium Exsolution from the Garnet Network Leading to CO2 Capture.

The instability of the two garnets Li6BaLa2B2O12 (B = Nb, Ta) has been studied on samples prepared in powder form by solid-state reaction. For this study, we coupled different techniques: powder X-ray diffraction, IR spectrometry, thermal analysis, transmission electron microscopy, and complex impedance spectroscopy. We showed that in ambient air and at low temperature (<150 °C), a spontaneous Li+/H+ exchange occurs. At higher temperature (500-700 °C), a progressive exsolution of the barium from the garnet framework is observed, leading to the formation of a second garnet, BaCO3, and a 3D cubic perovskite. To conclude this work, we studied the impact of barium exsolution on the ionic conductivity measured by complex impedance spectroscopy. We observed a significant decrease in the starting bulk conductivity (60%) when the pellet is heated at 500 °C for 5 h.

Phase Transitions in the Ruddlesden-Popper Phase Li2CaTa2O7: X-ray and Neutron Powder Thermodiffraction, TEM, Raman, and SHG Experiments.

The structure of the Ruddlesden-Popper layered perovskite Li2CaTa2O7, known for its high photocatalytic water activity since its discovery in 2008, is reinvestigated. This oxide has been characterized by powder X-ray and neutron thermodiffraction, TEM, second harmonic generation (SHG), and Raman experiments on powders and single crystals. It is shown that it undergoes two structural phase transitions (i) around 220 °C, mainly characterized by the progressive emergence of SHG signal at low temperatures, and (ii) at 660 °C, mainly characterized by changes of the temperature behavior of lattice parameters and by the emergence of Raman signals that linearly increase on decreasing temperature. It is shown by powder neutron diffraction profile refinements at RT, 400, and 800 °C that the space groups of the successive phases of Li2CaTa2O7 are the acentric Pna21 (RT ≤ T ≤ 220 °C), Pnma (220 °C ≤ T ≤ 660 °C), and Cmcm (T ≥ 660 °C). A soft mode associated with the transition to the highest symmetry for this structural arrangement (I4/mmm) is also found in the Raman spectra. All these transitions appear continuous: the high temperature ones can be attributed to progressive vanishings of the octahedra tiltings (displacives) while the transition in the vicinity of 220 °C from Pna21 to Pnma exhibits order-disorder character.

DNA Methyltransferase Inhibitors: Development and Applications.

As described in previous chapters of this book, DNA methylation is involved in numerous biological processes, and modulation of the activity of DNA methyltransferases (DNMTs) is a powerful strategy to modulate, restore, or reduce DNA methylation. In this chapter, we will present examples of inhibitors of DNMTs (DNMTi) and review the fields of applications of DNMTi mainly as therapeutic molecules, for example, in cancers, cardiovascular or neurological diseases, but also as bioengineering tools. Finally, the limits of currently available inhibitors will be discussed and the perspectives to discover improved DNMTi will be presented.

Suppression of Hedgehog signalling promotes pro-tumourigenic integrin expression and function.

Aberrant Hedgehog (Hh) signalling has been reported in a number of malignancies, particularly basal cell carcinoma (BCC) of the skin. Clinical trials of Hh inhibitors are underway in many cancers, and these have produced significant clinical benefit in BCC patients, although regrowth of new, or clinically aggressive, variants, as well as development of secondary malignancies, has been reported. αvß6 integrin is expressed in many cancers, where it has been shown to correlate with an aggressive tumour phenotype and poor prognosis. We have previously reported αvß6 up-regulation in aggressive, morphoeic BCC variants, where it modulates the stromal response and induces invasion. To examine a possible link between Hh and αvß6 function, we generated BCC models, overexpressing Gli1 in immortalized keratinocytes (NTert1, HaCaT). Unexpectedly, we found that suppressing Gli1 significantly increased αvß6 expression. This promoted tumour cell motility and also stromal myofibroblast differentiation through integrin-dependent TGF-ß1 activation. Gli1 inhibited αvß6 expression by suppressing TGF-ß1-induced Smad2/3 activation, blocking a positive feedback loop maintaining high αvß6 levels. A similar mechanism was observed in AsPC1 pancreatic cancer cells expressing endogenous Gli1, suggesting a common mechanism across tumour types. In vitro findings were supported using human clinical samples, where we showed an inverse correlation between αvß6 and Gli1 expression in different BCC subtypes and pancreatic cancers. In summary, we show that expression of Gli1 and αvß6 inversely correlates in tumours in vivo, and Hh targeting up-regulates TGF-ß1/Smad2/3-dependent αvß6 expression, promoting pro-tumourigenic cell functions in vitro. These results have potential clinical significance, given the reported recurrence of BCC variants and secondary malignancies in patients treated by Hh targeting.

Behavioural Repertoires and Time Budgets of Semi-Free-Ranging and Captive Groups of Wedge-Capped Capuchin Monkeys, Cebus olivaceus, in Zoo Exhibits in Venezuela.

The behavioural repertoires and time budgets of 2 captive groups and 1 semi-free-ranging group of Cebus olivaceus were determined with the aim to assess the impact of the zoo environment on behaviour. The repertoires were qualitatively similar between groups and to those reported for wild troops, but the captive groups showed self-directed and stereotyped behaviours not reported in the wild. The differences in repertoires between groups were easily associated with the opportunity to interact directly with the visitors, with particularities of the enclosure and with the severity of confinement. Overall, females spent more time foraging than males in the 2 captive groups, and adults rested and watched more than subadults in all the groups. Time budgets were dominated by foraging, resting, movement and affiliative interactions, but their relative importance varied between groups, with foraging being especially prominent in the most confined group. The time budgets also varied qualitatively from those reported for wild troops. We conclude the species is behaviourally able to adjust to captivity, but the slight differences along the continuum from wild to semi-free to captive are suggestive of mild stress or social tension probably due to unstimulating environmental conditions, high visitor pressure and deviations from typical sex-age group composition.