Loss of the TRPM4 channel in humans causes immune dysregulation with defective monocyte migration.

BACKGROUND: TRPM4 is a broadly expressed, calcium-activated, monovalent cation channel that regulates immune cell function in mice and cell lines. Clinically, however, partial loss- or gain-of-function mutations in TRPM4 lead to arrhythmia and heart disease, with no documentation of immunologic disorders. OBJECTIVE: To characterize functional cellular mechanisms underlying the immune dysregulation phenotype in a proband with a mutated TRPM4 gene. METHODS: We employed a combination of biochemical, cell biological, imaging, omics analyses, flow cytometry, and gene editing approaches. RESULTS: We report the first human cases to our knowledge with complete loss of the TRPM4 channel, leading to immune dysregulation with frequent bacterial and fungal infections. Single-cell and bulk RNA sequencing point to altered expression of genes affecting cell migration, specifically in monocytes. Inhibition of TRPM4 in T cells and the THP-1 monocyte cell line reduces migration. More importantly, primary T cells and monocytes from TRPM4 patients migrate poorly. Finally, CRISPR knockout of TRPM4 in THP-1 cells greatly reduces their migration potential. CONCLUSION: Our results demonstrate that TRPM4 plays a critical role in regulating immune cell migration, leading to increased susceptibility to infections.

Modulation of SLFN11 induces changes in DNA Damage response in breast cancer.

BACKGROUND: Lack of Schlafen family member 11 (SLFN11) expression has been recently identified as a dominant genomic determinant of response to DNA damaging agents in numerous cancer types. Thus, several strategies aimed at increasing SLFN11 are explored to restore chemosensitivity of refractory cancers. In this study, we examined various approaches to elevate SLFN11 expression in breast cancer cellular models and confirmed a corresponding increase in chemosensitivity with using the most successful efficient one. As oncogenic transcriptomic downregulation is often driven by methylation of the promotor region, we explore the demethylation effect of 5-aza-2'-deoxycytidine (decitabine), on the SLFN11 gene. Since SLFN11 has been reported as an interferon inducible gene, and interferon is secreted during an active anti-tumor immune response, we investigated the in vitro effect of IFN-γ on SLFN11 expression in breast cancer cell lines. As a secondary approach to pick up cross talk between immune cells and SLFN11 expression we used indirect co-culture of breast cancer cells with activated PBMCs and evaluated if this can drive SLFN11 upregulation. Finally, as a definitive and specific way to modulate SLFN11 expression we implemented SLFN11 dCas9 (dead CRISPR associated protein 9) systems to specifically increase or decrease SLFN11 expression. RESULTS: After confirming the previously reported correlation between methylation of SLFN11 promoter and its expression across multiple cell lines, we showed in-vitro that decitabine and IFN-γ could increase moderately the expression of SLFN11 in both BT-549 and T47D cell lines. The use of a CRISPR-dCas9 UNISAM and KRAB system could increase or decrease SLFN11 expression significantly (up to fivefold), stably and specifically in BT-549 and T47D cancer cell lines. We then used the modified cell lines to quantify the alteration in chemo sensitivity of those cells to treatment with DNA Damaging Agents (DDAs) such as Cisplatin and Epirubicin or DNA Damage Response (DDRs) drugs like Olaparib. RNAseq was used to elucidate the mechanisms of action affected by the alteration in SLFN11 expression. In cell lines with robust SLFN11 promoter methylation such as MDA-MB-231, no SLFN11 expression could be induced by any approach. CONCLUSION: To our knowledge this is the first report of the stable non-lethal increase of SLFN11 expression in a cancer cell line. Our results show that induction of SLFN11 expression can enhance DDA and DDR sensitivity in breast cancer cells and dCas9 systems may represent a novel approach to increase SLFN11 and achieve higher sensitivity to chemotherapeutic agents, improving outcome or decreasing required drug concentrations. SLFN11-targeting therapies might be explored pre-clinically to develop personalized approaches.

Solid-State 19F NMR Chemical Shift in Square-Planar Nickel-Fluoride Complexes Linked by Halogen Bonds.

The halogen bond (XB) is a highly directional class of noncovalent interactions widely explored by experimental and computational studies. However, the NMR signature of the XB has attracted limited attention. The prediction and analysis of the solid-state NMR (SSNMR) chemical shift tensor provide useful strategies to better understand XB interactions. In this work, we employ a computational protocol for modeling and analyzing the 19F SSNMR chemical shifts previously measured in a family of square-planar trans NiII-L2-iodoaryl-fluoride (L = PEt3) complexes capable of forming self-complementary networks held by a NiF···I(C) halogen bond [Thangavadivale, V.; Chem. Sci. 2018, 9, 3767-3781]. To understand how the 19F NMR resonances of the nickel-bonded fluoride are affected by the XB, we investigate the origin of the shielding in trans-[NiF(2,3,5,6-C6F4I)(PEt3)2], trans-[NiF(2,3,4,5-C6F4I)(PEt3)2], and trans-[NiF(C6F5)(PEt3)2] in the solid state, where a XB is present in the two former systems but not in the last. We perform the 19F NMR chemical shift calculations both in periodic and molecular models. The results show that the crystal packing has little influence on the NMR signatures of the XB, and the NMR can be modeled successfully with a pair of molecules interacting via the XB. Thus, the observed difference in chemical shift between solid-state and solution NMR can be essentially attributed to the XB interaction. The very high shielding of the fluoride and its driving contributor, the most shielded component of the chemical shift tensor, are well reproduced at the 2c-ZORA level. Analysis of the factors controlling the shielding shows how the highest occupied Ni/F orbitals shield the fluoride in the directions perpendicular to the Ni-F bond and specifically perpendicular to the coordination plane. This shielding arises from the magnetic coupling of the Ni(3d)/F(2p lone pair) orbitals with the vacant σNi-F* orbital, thereby rationalizing the very highly upfield (shielded) resonance of the component (δ33) along this direction. We show that these features are characteristic of square-planar nickel-fluoride complexes. The deshielding of the fluoride in the halogen-bonded systems is attributed to an increase in the energy gap between the occupied and vacant orbitals that are mostly responsible for the paramagnetic terms, notably along the most shielded direction.

Calcium-catalysed synthesis of amines through imine hydrosilylation: an experimental and theoretical study.

A method to reduce aldimines through hydrosilylation is reported. The catalytic system involves calcium triflimide (Ca(NTf2)2) and potassium hexafluorophosphate (KPF6) which have been shown to act in a synergistic manner. The expected amines are obtained in fair to very high yields (40-99%) under mild conditions (room temperature in most cases). To illustrate the potential of this method, a bioactive molecule with antifungal properties was prepared on the gram scale and in high yield in environmentally friendly 2-methyltetrahydrofuran. Moreover, it is shown in this example that the imine can be prepared in situ from the aldehyde and the amine without isolating the imine. The mechanism involved has been explored experimentally and through DFT calculations, and the results are in accordance with an electrophilic activation of the silane by the calcium catalyst.

Carbon-13 NMR Chemical Shift: A Descriptor for Electronic Structure and Reactivity of Organometallic Compounds.

Metal-bonded carbon atoms in metal-alkyl, metal-carbene/alkylidene, and metal-carbyne/alkylidyne species often show significantly more deshielded isotropic chemical shifts than their organic counterparts (alkanes, alkenes, and alkynes). While isotropic chemical shift is universally used to characterize a chemical compound in solution, it is an average value of the three principal components of the chemical shift tensor (δ11 > δ22 > δ33). The tensor components, which are accessible by solid-state NMR spectroscopy, can provide detailed information about the electronic structure (frontier molecular orbitals) at the observed nuclei. This information can be accessed in detail by quantum chemical calculations, most notably by an analysis of the paramagnetic contribution to the NMR shielding tensor. The paramagnetic term mainly results from the coupling of occupied and empty molecular orbitals close in energy-the frontier molecular orbitals-under the effect of the external magnetic field (B0). In organometallic compounds, a large deshielding of the isotropic carbon-13 chemical shift of the metal-bonded carbon atom is commonly related to the coupling between the occupied σM-C orbital and low-lying vacant orbitals of πM═C* character. The deshielding at the α-carbon hence probes the extent of σM-C and πM═C* interactions. This molecular orbital view readily explains the strong deshielding and large anisotropy (evidenced by the span Ω = δ11 - δ33) observed in metal alkylidenes and alkylidynes (200 < δiso < 400 ppm). Fischer carbenes are generally more deshielded than Schrock or Grubbs alkylidenes due to their low-lying πM═C* orbital. Chemical shift hence shows their higher electrophilic character, connecting NMR spectroscopy to reactivity patterns. Similarly, the α-carbon of metal-alkyls display deshielded chemical shifts in specific coordination environments. This deshielding, which is often prominently pronounced for cationic species, indicates the presence of partial π-bond character in the metal-carbon bond, making these bonds topologically equivalent to alkylidene π-bonds. The π-character in metal-alkyl bonds favors (i) α-H abstraction processes in metal bis-alkyl compounds yielding metal alkylidenes, (ii) [2 + 2]-retrocyclization of metallacyclobutanes that participate in olefin metathesis, (iii) olefin insertion in cationic metal alkyls thus explaining polymerization activity trends and the importance of α-H agostic interactions, and (iv) C-H bond activation on metal-alkyls via σ-bond metathesis. The presence of π-character in the metal-carbon bonds involved in these processes rationalizes the parallel reactivity patterns of metal-alkyls toward olefin insertion and σ-bond metathesis and the fact that σ-bond metathesis, olefin insertion, and olefin metathesis are commonly observed with metal atoms in the same ligand field. Because of the similarities in the frontier molecular orbitals involved in these processes, these reactions can be viewed as isolobal. This explains why certain fragments, such as bent metallocenes (d0 Cp2M) or T-shaped L3M, are ubiquitous in these reactions.

31P Chemical Shifts in Ru(II) Phosphine Complexes. A Computational Study of the Influence of the Coordination Sphere.

The NMR chemical shift has been the most versatile marker of chemical structures, by reflecting global and local electronic structures, and is very sensitive to any change within the chemical species. In this work, Ru(II) complexes with the same five ligands and a variable sixth ligand L (none, H2O, H2S, CH3SH, H2, N2, N2O, NO+, C═CHPh, and CO) are studied by using as the NMR reporter the phosphorus PA of a coordinated bidentate PA-N ligand (PA-N = o-diphenylphosphino-N,N'-dimethylaniline). The chemical shift of PA in RuCl2(PA-N)(PR3)(L) (R = phenyl, p-tolyl, or p-FC6H4) was shown to increase as the Ru-PA bond distance decreases, an observation that was not rationalized. This work, using density functional theory (DFT) calculations, reproduces reasonably well the observed 31P chemical shifts for these complexes and the correlation between the shifts and the Ru-PA bond distance as L varies. An interpretation of this correlation is proposed by using a natural chemical shift (NCS) analysis based on the natural bonding orbital (NBO) method. This analysis of the principal components of the chemical shift tensors shows how the σ-donating properties of L have a particularly high influence on the phosphine chemical shifts.

Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH3)3-x(CF3)x}3] (MoF0, x = 0; MoF3, x = 1; MoF6, x = 2; MoF9, x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF0 < MoF3 < MoF6 before sharply decreasing for MoF9, with a similar effect for the supported systems (MoF0 ≈ MoF9 < MoF6 < MoF3). This is consistent with the different kinetic behavior (zeroth order in alkyne for MoF9 derivatives instead of first order for the others) and the isolation of stable metallacyclobutadiene intermediates of MoF9 for both molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF6, prior to a sharp decrease in reactivity for MoF9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13C NMR chemical shift tensors.

Orbital Analysis of Carbon-13 Chemical Shift Tensors Reveals Patterns to Distinguish Fischer and Schrock Carbenes.

Fischer and Schrock carbenes display highly deshielded carbon chemical shifts (>250 ppm), in particular Fischer carbenes (>300 ppm). Orbital analysis of the principal components of the chemical shift tensors determined by solid-state NMR spectroscopy and calculated by a 2-component DFT method shows specific patterns that act as fingerprints for each type of complex. The calculations highlight the role of the paramagnetic term in the shielding tensor especially in the two most deshielded components (σ11 and σ22 ). The paramagnetic term of σ11 is dominated by coupling σ(M=C) with π*(M=C) through the angular momentum operator perpendicular to the σ and π M=C bonds. The highly deshielded carbon of Fischer carbenes results from the particularly low-lying π*(M=C) associated with the CO ligand. A contribution of the coupling of π(M=C) with σ*(M=C) is found for Schrock and Ru-based carbenes, indicating similarities between them, despite their different electronic configurations (d0 vs. d6 ).

Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso).

Tailoring Novel PTFE Surface Properties: Promoting Cell Adhesion and Antifouling Properties via a Wet Chemical Approach.

Many biomaterials used for tissue engineering applications lack cell-adhesiveness and, in addition, are prone to nonspecific adsorption of proteins. This is especially important for blood-contacting devices such as vascular grafts and valves where appropriate surface properties should inhibit the initial attachment of platelets and promote endothelial cell colonization. As a consequence, the long-term outcome of the implants would be improved and the need for anticoagulation therapy could be reduced or even abolished. Polytetrafluoroethylene (PTFE), a frequently used polymer for various medical applications, was wet-chemically activated and subsequently modified by grafting the endothelial cell (EC) specific peptide arginine-glutamic acid-aspartic acid-valine (REDV) using a bifunctional polyethylene glycol (PEG)-spacer (known to reduce platelet and nonspecific protein adhesion). Modified and control surfaces were both evaluated in terms of EC adhesion, colonization, and the attachment of platelets. In addition, samples underwent bacterial challenges. The results strongly suggested that PEG-mediated peptide immobilization renders PTFE an excellent substrate for cellular growth while simultaneously endowing the material with antifouling properties.

Donor-Promoted 1,2-Hydrogen Migration from Silicon to a Saturated Ruthenium Center and Access to Silaoxiranyl and Silaiminyl Complexes.

Masked silylene complexes Cp*(IXy-H)(H)RuSiH2R (R = Mes (3) and Trip (4); IXy = 1,3-bis(2,6-dimethylphenyl)imidazol-2-ylidene; "IXy-H" is the deprotonated form of IXy) exhibit metallosilylene-like (LnM-Si-R) reactivity, as observed in reactions of nonenolizable ketones, enones, and tosyl azides, to give unprecedented silaoxiranyl, oxasilacyclopentenyl, and silaiminyl complexes, respectively. Notably, these silicon-containing complexes are derived from the primary silanes MesSiH3 and TripSiH3 via activation of all three Si-H bonds. DFT calculations suggest that the mechanism of formation for the silaoxiranyl complex Cp*(IXy)(H)2Ru-Si(OCPh2)Trip (6) involves coordination of benzophenone to a silylene silicon atom, followed by a single-electron transfer in which Si-bonded, non-innocent benzophenone accepts an electron from the reactive, electron-rich ruthenium center. Importantly, this electron transfer promotes an unusual 1,2-hydrogen migration to the resulting, more electron-deficient ruthenium center via a diradicaloid transition state.

Cyclometalated N-heterocyclic carbene complexes of ruthenium for access to electron-rich silylene complexes that bind the Lewis acids CuOTf and AgOTf.

The synthesis of the cyclometalated complexes Cp*Ru(IXy-H) (2) [IXy = 1,3-bis(2,6-dimethylphenyl)imidazol-2-ylidene; IXy-H = 1-(2-CH2C6H3-6-methyl)-3-(2,6-dimethylphenyl)imidazol-2-ylidene-1-yl (the deprotonated form of IXy); Cp* = η(5)-C5Me5] and Cp*Ru(IXy-H)(N2) (3) was achieved by dehydrochlorination of Cp*Ru(IXy)Cl (1) with KCH2Ph. Complexes 2 and 3 activate primary silanes (RSiH3) to afford the silyl complexes Cp*(IXy-H)(H)RuSiH2R [R = p-Tol (4), Mes (5), Trip (6)]. Density functional theory studies indicated that these complexes are close in energy to the corresponding isomeric silylene species Cp*(IXy)(H)Ru═SiHR. Indeed, reactivity studies indicated that various reagents trap the silylene isomer of 6, Cp*(IXy)(H)Ru═SiHTrip (6a). Thus, benzaldehyde reacts with 6 to give the [2 + 2] cycloaddition product 7, while 4-bromoacetophenone reacts via C-H bond cleavage and formation of the enolate Cp*(IXy)(H)2RuSiH[OC(═CH2)C6H4Br]Trip (8). Addition of the O-H bond of 2,6-dimethylphenol across the Ru═Si bond of 6a gives Cp*(IXy)(H)2RuSiH(2,6-Me2C6H3O)Trip (9). Interestingly, CuOTf and AgOTf also react with 6 to provide unusual Lewis acid-stabilized silylene complexes in which MOTf bridges the Ru-Si bond. The AgOTf complex, which was crystallographically characterized, exhibits a structure similar to that of [Cp*((i)Pr3P)Ru(µ-H)2SiHMes](+), with a three-center, two-electron Ru-Ag-Si interaction. Natural bond orbital analysis of the MOTf complexes supported this type of bonding and characterized the donor interaction with Ag (or Cu) as involving a delocalized interaction with contributions from the carbene, silylene, and hydride ligands of Ru.

1,2-hydrogen migration to a saturated ruthenium complex via reversal of electronic properties for tin in a stannylene-to-metallostannylene conversion.

An intramolecular 1,2(α)-H migration in a saturated ruthenium stannylene complex, to form a ruthenostannylene complex, involves a reversal of the role for a coordinated stannylene ligand, from that of an electron donor to an acceptor in the transition state. This change in the bonding properties for a stannylene group, with a simple molecular motion, lifts the usual requirement for generation of an unsaturated metal center in migration chemistry.

B-H, C-H, and B-C bond activation: the role of two adjacent agostic interactions.

Tuning the nature of the linker in a L~BHR phosphinoborane compound led to the isolation of a ruthenium complex stabilized by two adjacent, δ-C-H and ε-B(sp2)-H, agostic interactions. Such a unique coordination mode stabilizes a 14-electron "RuH2P2" fragment through connected σ-bonds of different polarity, and affords selective B-H, C-H, and B-C bond activation as illustrated by reactivity studies with H2 and boranes.

Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture.

Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151.

Mesenchymal stem cells enhance ovarian cancer cell infiltration through IL6 secretion in an amniochorionic membrane based 3D model.

BACKGROUND: The early peritoneal invasion of epithelial ovarian cancer (EOC) by tumoral aggregates presents in ascites is a major concern. The role of the microenvironment seems to be important in this process but the lack of adequate models to study cellular interactions between cancer cells and stromal cells does not allow to uncover the molecular pathways involved. Our goal was to study the interactions between ovarian cancer cells (OCC) and mesenchymal stem cells (MSC) using a 3D model. METHODS: We used millimetric pieces of amniochorionic membrane - referred to as amniotic membrane scaffold (AMS) - to create 3D peritoneal nodules mimicking EOC early invasion. We were able to measure the distribution and the depth of infiltration using confocal microsopy. We extracted MSC from the amniochorionic membrane using the markers CD34-, CD45-, CD73+, CD90+, CD105+ and CD29+ at the Fluorescence Activated Cell Sorting (FACS) analysis. We used transwell and wound healing tests to test OCC migration and invasion in vitro. RESULTS: Here we show that OCC tumors were located in regions rich in MSC (70%). The tumors infiltrated deeper within AMS in regions rich in MSC (p<0.001). In vitro tests revealed that higher IL6 secretion in a context of MSC-OCC co-culture could enhance migration and invasion of OCC. After IL6 receptor antagonism, OCC infiltration was significantly decreased, mostly in regions rich in MSCs, indicating that recruitment and tridimensional invasion of OCC was dependent of IL6 secretion. CONCLUSIONS: The use of tridimensional models using AMS could be a useful tool to decipher early molecular events in ovarian cancer metastasis. Cytokine inhibitors interrupting the cross-talk between OCCs and MSCs such as IL6 should be investigated as a new therapeutic approach in ovarian cancer.

AMOEBA Polarizable Force Field for Molecular Dynamics Simulations of Glyme Solvents.

Classical molecular dynamics (MD) simulations of electrolyte systems are important to gain insight into the atom-scale properties that determine the battery-relevant performance. The recent Tinker-HP software release enables efficient and accurate MD simulations with the AMOEBA polarizable force field. In this work, we developed a procedure to construct a universal AMOEBA model for the solvent family of glymes (glycol methyl ethers), which involves a refinement scheme for valence parameters by fitting the AMOEBA-derived atomic forces to those computed at the DFT level. The refined AMOEBA model provides a good description of both local and nonlocal properties in terms of the spectroscopic response of glyme molecules, as well as the liquid glyme density and dielectric constant. In addition, the complexation energies of alkali and alkaline-earth metal cations with tetraglyme molecules obtained from AMOEBA calculations are in good agreement with DFT results, demonstrating the suitability of the developed AMOEBA model for an accurate simulation of glyme-based battery electrolytes. We also expect the procedure to be transferable to the development of AMOEBA models for other battery electrolyte systems.

An integrated tumor, immune and microbiome atlas of colon cancer.

The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.

Gene expression analysis of matched ovarian primary tumors and peritoneal metastasis.

BACKGROUND: Ovarian cancer is the most deadly gynecological cancer due to late diagnosis at advanced stage with major peritoneal involvement. To date most research has focused on primary tumor. However the prognosis is directly related to residual disease at the end of the treatment. Therefore it is mandatory to focus and study the biology of metastatic disease that is most frequently localized to the peritoneal cavity in ovarian cancer. METHODS: We used high-density gene expression arrays to investigate gene expression changes between matched primary and metastatic (peritoneal) lesions. RESULTS: Here we show that gene expression profiles in peritoneal metastasis are significantly different than their matched primary tumor and these changes are affected by underlying copy number variation differences among other causes. We show that differentially expressed genes are enriched in specific pathways including JAK/STAT pathway, cytokine signaling and other immune related pathways. We show that underlying copy number variations significantly affect gene expression. Indeed patients with important differences in copy number variation displayed greater gene expression differences between their primary and matched metastatic lesions. CONCLUSIONS: Our analysis shows a very specific targeting at both the genomic and transcriptomic level to upregulate certain pathways in the peritoneal metastasis of ovarian cancer. Moreover, while primary tumors use certain pathways we identify distinct differences with metastatic lesions. The variation between primary and metastatic lesions should be considered in personalized treatment of ovarian cancer.

Structures of d4 MH3X: a computational study of the influence of the metal and the ligands.

Density functional theory (DFT, PBE0, and range separated DFT, RSH + MP2) and coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) calculations have been used to probe the structural preference of d(4) MH(3)X(q) (M = Ru, Os, Rh(+), Ir(+), and Re(-); X = H, F, CH(3), CF(3), SiH(3), and SiF(3)) and of MX(4) (M = Ru; X = H, F, CH(3), CF(3), SiH(3), and SiF(3)). Landis et al. have shown that complexes in which the metal is sd(3) hybridized have tetrahedral and non-tetrahedral structures with shapes of an umbrella or a 4-legged piano stool. In this article, the influence of the metal and ligands on the energies of the three isomeric structures of d(4) MH(3)X and MX(4) is established and rationalized. Fluoride and alkyl ligands stabilize the tetrahedral relative to non-tetrahedral structures while hydride and silyl ligands stabilize the non-tetrahedral structures. For given ligands and charge, 4d metal favors more the non-tetrahedral structures than 5d metals. A positive charge increases the preference for the non-tetrahedral structures while a negative charge increases the preference for the tetrahedral structure. The factors that determine these energy patterns are discussed by means of a molecular orbital analysis, based on Extended Hückel (EHT) calculations, and by means of Natural Bond Orbital (NBO) analyses of charges and resonance structures (NRT analysis). These analyses show the presence of through-space interactions in the non-tetrahedral structures that can be sufficiently stabilizing, for specific metals and ligands, to stabilize the non-tetrahedral structures relative to the tetrahedral isomer.