AATF/Che-1 RNA polymerase II binding protein overexpression reduces the anti-tumor NK-cell cytotoxicity through activating receptors modulation.

Introduction: AATF/Che-1 over-expression in different tumors is well known and its effect on tumorigenicity is mainly due to its central role demonstrated in the oncogenic pathways of solid tumors, where it controls proliferation and viability. The effect exerted by tumors overexpressing Che-1 on the immune response has not yet been investigated. Methods: Starting from ChIP-sequencing data we confirmed Che-1 enrichment on Nectin-1 promoter. Several co-cultures experiments between NK-cells and tumor cells transduced by lentiviral vectors carrying Che-1-interfering sequence, analyzed by flow-cytometry have allowed a detailed characterization of NK receptors and tumor ligands expression. Results: Here, we show that Che-1 is able to modulate the expression of Nectin-1 ligand at the transcriptional level, leading to the impairment of killing activity of NK-cells. Nectin-1 down-modulation induces a modification in NK-cell ligands expression able to interact with activating receptors and to stimulate NK-cell function. In addition, NK-cells from Che-1 transgenic mice, confirming a reduced expression of activating receptors, exhibit impaired activation and a preferential immature status. Discussion: The critical equilibrium between NK-cell ligand expression on tumor cells and the interaction with NK cell receptors is affected by Che-1 over-expression and partially restored by Che-1 interference. The evidence of a new role for Che-1 as regulator of anti-tumor immunity supports the necessity to develop approaches able to target this molecule which shows a dual tumorigenic function as cancer promoter and immune response modulator.

Significant enhancement of ferromagnetism above room temperature in epitaxial 2D van der Waals ferromagnet Fe5-δGeTe2/Bi2Te3 heterostructures.

Two-dimensional (2D) van der Waals (vdW) ferromagnetic metals FexGeTe2 with x = 3-5 have raised significant interest in the scientific community. Fe5GeTe2 shows prospects for spintronic applications since the Curie temperature Tc has been reported near or higher than 300 K. In the present work, epitaxial Fe5-δGeTe2 (FGT) heterostructures were grown by Molecular Beam Epitaxy (MBE) on insulating crystalline substrates. The FGT films were combined with Bi2Te3 topological insulator (TI) aiming to investigate the possible beneficial effect of the TI on the magnetic properties of FGT. FGT/Bi2Te3 films were compared to FGT capped only with AlOx to prevent oxidation. SQUID and MOKE measurements revealed that the growth of Bi2Te3 TI on FGT films significantly enhances the saturation magnetization of FGT as well as the Tc well above room temperature (RT) reaching record values of 570 K. First-principles calculations predict a shift of the Fermi level and an associated enhancement of the majority spin (primarily) as well as the total density of states at the Fermi level suggesting that effective doping of FGT from Bi2Te3 could explain the enhancement of ferromagnetism in FGT. It is also predicted that strain induced stabilization of a high magnetic moment phase in FGT/Bi2Te3 could be an alternative explanation of magnetization and Tc enhancement. Ferromagnetic resonance measurements evidence an enhanced broadening in the FGT/Bi2Te3 heterostructure when compared to FGT. We obtain a large spin mixing conductance of g↑↓eff = 4.4 × 1020 m-2, which demonstrates the great potential of FGT/Bi2Te3 systems for spin-charge conversion applications at room temperature.

Clonal KEAP1 mutations with loss of heterozygosity share reduced immunotherapy efficacy and low immune cell infiltration in lung adenocarcinoma.

BACKGROUND: KEAP1 mutations have been associated with reduced survival in lung adenocarcinoma (LUAD) patients treated with immune checkpoint inhibitors (ICIs), particularly in the presence of STK11/KRAS alterations. We hypothesized that, beyond co-occurring genomic events, clonality prediction may help identify deleterious KEAP1 mutations and their counterparts with retained sensitivity to ICIs. PATIENTS AND METHODS: Beta-binomial modelling of sequencing read counts was used to infer KEAP1 clonal inactivation by combined somatic mutation and loss of heterozygosity (KEAP1 C-LOH) versus partial inactivation [KEAP1 clonal diploid-subclonal (KEAP1 CD-SC)] in the Memorial Sloan Kettering Cancer Center (MSK) MetTropism cohort (N = 2550). Clonality/LOH prediction was compared to a streamlined clinical classifier that relies on variant allele frequencies (VAFs) and tumor purity (TP) (VAF/TP ratio). The impact of this classification on survival outcomes was tested in two independent cohorts of LUAD patients treated with immunotherapy (MSK/Rome N = 237; DFCI N = 461). Immune-related features were studied by exploiting RNA-sequencing data (TCGA) and multiplexed immunofluorescence (DFCI mIF cohort). RESULTS: Clonality/LOH inference in the MSK MetTropism cohort overlapped with a clinical classification model defined by the VAF/TP ratio. In the ICI-treated MSK/Rome discovery cohort, predicted KEAP1 C-LOH mutations were associated with shorter progression-free survival (PFS) and overall survival (OS) compared to KEAP1 wild-type cases (PFS log-rank P = 0.001; OS log-rank P < 0.001). Similar results were obtained in the DFCI validation cohort (PFS log-rank P = 0.006; OS log-rank P = 0.014). In both cohorts, we did not observe any significant difference in survival outcomes when comparing KEAP1 CD-SC and wild-type tumors. Immune deconvolution and multiplexed immunofluorescence revealed that KEAP1 C-LOH and KEAP1 CD-SC differed for immune-related features. CONCLUSIONS: KEAP1 C-LOH mutations are associated with an immune-excluded phenotype and worse clinical outcomes among advanced LUAD patients treated with ICIs. By contrast, survival outcomes of patients whose tumors harbored KEAP1 CD-SC mutations were similar to those with KEAP1 wild-type LUADs.

Radial Spin Texture of the Weyl Fermions in Chiral Tellurium.

Trigonal tellurium, a small-gap semiconductor with pronounced magneto-electric and magneto-optical responses, is among the simplest realizations of a chiral crystal. We have studied by spin- and angle-resolved photoelectron spectroscopy its unconventional electronic structure and unique spin texture. We identify Kramers-Weyl, composite, and accordionlike Weyl fermions, so far only predicted by theory, and show that the spin polarization is parallel to the wave vector along the lines in k space connecting high-symmetry points. Our results clarify the symmetries that enforce such spin texture in a chiral crystal, thus bringing new insight in the formation of a spin vectorial field more complex than the previously proposed hedgehog configuration. Our findings thus pave the way to a classification scheme for these exotic spin textures and their search in chiral crystals.

KEAP1-driven co-mutations in lung adenocarcinoma unresponsive to immunotherapy despite high tumor mutational burden.

BACKGROUND: Immune checkpoint inhibitors (ICIs) have demonstrated significant overall survival (OS) benefit in lung adenocarcinoma (LUAD). Nevertheless, a remarkable interpatient heterogeneity characterizes immunotherapy efficacy, regardless of programmed death-ligand 1 (PD-L1) expression and tumor mutational burden (TMB). KEAP1 mutations are associated with shorter survival in LUAD patients receiving chemotherapy. We hypothesized that the pattern of KEAP1 co-mutations and mutual exclusivity may identify LUAD patients unresponsive to immunotherapy. PATIENTS AND METHODS: KEAP1 mutational co-occurrences and somatic interactions were studied in the whole MSKCC LUAD dataset. The impact of coexisting alterations on survival outcomes in ICI-treated LUAD patients was verified in the randomized phase II/III POPLAR/OAK trials (blood-based sequencing, bNGS cohort, N = 253). Three tissue-based sequencing studies (Rome, MSKCC and DFCI) were used for independent validation (tNGS cohort, N = 289). Immunogenomic features were analyzed using The Cancer Genome Atlas (TCGA) LUAD study. RESULTS: On the basis of KEAP1 mutational co-occurrences, we identified four genes potentially associated with reduced efficacy of immunotherapy (KEAP1, PBRM1, SMARCA4 and STK11). Independent of the nature of co-occurring alterations, tumors with coexisting mutations (CoMut) had inferior survival as compared with single-mutant (SM) and wild-type (WT) tumors (bNGS cohort: CoMut versus SM log-rank P = 0.048, CoMut versus WT log-rank P < 0.001; tNGS cohort: CoMut versus SM log-rank P = 0.037, CoMut versus WT log-rank P = 0.006). The CoMut subset harbored higher TMB than the WT disease and the adverse significance of coexisting alterations was maintained in LUAD with high TMB. Significant immunogenomic differences were observed between the CoMut and WT groups in terms of core immune signatures, T-cell receptor repertoire, T helper cell signatures and immunomodulatory genes. CONCLUSIONS: This study indicates that coexisting alterations in a limited set of genes characterize a subset of LUAD unresponsive to immunotherapy and with high TMB. An immune-cold microenvironment may account for the clinical course of the disease.

Atomic-scale study of the amorphous-to-crystalline phase transition mechanism in GeTe thin films.

The underlying mechanism driving the structural amorphous-to-crystalline transition in Group VI chalcogenides is still a matter of debate even in the simplest GeTe system. We exploit the extreme sensitivity of 57Fe emission Mössbauer spectroscopy, following dilute implantation of 57Mn (T½ = 1.5 min) at ISOLDE/CERN, to study the electronic charge distribution in the immediate vicinity of the 57Fe probe substituting Ge (FeGe), and to interrogate the local environment of FeGe over the amorphous-crystalline phase transition in GeTe thin films. Our results show that the local structure of as-sputtered amorphous GeTe is a combination of tetrahedral and defect-octahedral sites. The main effect of the crystallization is the conversion from tetrahedral to defect-free octahedral sites. We discover that only the tetrahedral fraction in amorphous GeTe participates to the change of the FeGe-Te chemical bonds, with a net electronic charge density transfer of ~ 1.6 e/a0 between FeGe and neighboring Te atoms. This charge transfer accounts for a lowering of the covalent character during crystallization. The results are corroborated by theoretical calculations within the framework of density functional theory. The observed atomic-scale chemical-structural changes are directly connected to the macroscopic phase transition and resistivity switch of GeTe thin films.

Selective Probing of Hidden Spin-Polarized States in Inversion-Symmetric Bulk MoS_{2}.

Spin- and angle-resolved photoemission spectroscopy is used to reveal that a large spin polarization is observable in the bulk centrosymmetric transition metal dichalcogenide MoS_{2}. It is found that the measured spin polarization can be reversed by changing the handedness of incident circularly polarized light. Calculations based on a three-step model of photoemission show that the valley and layer-locked spin-polarized electronic states can be selectively addressed by circularly polarized light, therefore providing a novel route to probe these hidden spin-polarized states in inversion-symmetric systems as predicted by Zhang et al. [Nat. Phys. 10, 387 (2014).NPAHAX1745-247310.1038/nphys2933].

Entanglement and manipulation of the magnetic and spin-orbit order in multiferroic Rashba semiconductors.

Entanglement of the spin-orbit and magnetic order in multiferroic materials bears a strong potential for engineering novel electronic and spintronic devices. Here, we explore the electron and spin structure of ferroelectric α-GeTe thin films doped with ferromagnetic Mn impurities to achieve its multiferroic functionality. We use bulk-sensitive soft-X-ray angle-resolved photoemission spectroscopy (SX-ARPES) to follow hybridization of the GeTe valence band with the Mn dopants. We observe a gradual opening of the Zeeman gap in the bulk Rashba bands around the Dirac point with increase of the Mn concentration, indicative of the ferromagnetic order, at persistent Rashba splitting. Furthermore, subtle details regarding the spin-orbit and magnetic order entanglement are deduced from spin-resolved ARPES measurements. We identify antiparallel orientation of the ferroelectric and ferromagnetic polarization, and altering of the Rashba-type spin helicity by magnetic switching. Our experimental results are supported by first-principles calculations of the electron and spin structure.

Electrochemotherapy as First Line Cancer Treatment: Experiences from Veterinary Medicine in Developing Novel Protocols.

Tumor microenvironment is one of the major obstacles to the efficacy of chemotherapy in cancer patients. The abnormal blood flow within the tumor results in uneven drug distribution. Electrochemotherapy (ECT) is a tumor treatment that adopts the systemic or local delivery of anticancer drugs with the application of permeabilizing electric pulses having appropriate amplitude and waveforms. This allows the use of lipophobic drugs that frequently have a narrow therapeutic index maintaining at the same time a reduced patient morbidity and preserving appropriate anticancer efficacy. Its use in humans is addressed to the treatment of cutaneous neoplasms or the palliation of skin tumor metastases, and a standard operating procedure has been devised. On the other hand, in veterinary oncology this approach is gaining popularity, thus becoming a first line treatment for different cancer histotypes, in a variety of clinical conditions due to its high efficacy and low toxicity. This review summarizes the state of the art in veterinary oncology as a preclinical model and reports the new protocols in terms of drugs and therapy combination that have been developed.

Electroporation Enhances Bleomycin Efficacy in Cats with Periocular Carcinoma and Advanced Squamous Cell Carcinoma of the Head.

BACKGROUND: Advanced carcinoma of the head represents a substantial health problem in cats for local control and overall survival. OBJECTIVES: Evaluate the capability of electrochemotherapy (ECT) to improve bleomycin efficacy in cats with periocular carcinoma and advanced carcinoma of the head. ANIMALS: Twenty-one cats with periocular carcinoma (17 squamous cell carcinoma [SCC] and 4 anaplastic carcinoma) and 26 cats with advanced SCC of the head. METHODS: Nonrandomized prospective controlled study. Periocular carcinoma cohorts: 12 cats were treated with bleomycin (15 mg/m(2) i.v.) coupled with ECT under anesthesia; 9 cats were treated with bleomycin alone. Advanced head SCC cohorts: 14 cats were treated with bleomycin (15 mg/m(2) i.v.) coupled with ECT administered under sedation; 12 control cats were treated with bleomycin alone. ECT treatments (2-8) were performed every other week until complete remission (CR) or tumor progression occurred. RESULTS: Toxicities were minimal and mostly treated symptomatically. Overall response rate in the ECT treated animals was 89% (21 Complete Response [CR] and 2 Partial Response [PR]) whereas controls had response rate of 33% (4 CR and 3 PR). Median time to progression in ECT group was 30.5 months, whereas in controls it was 3.9 months (P < .0001). Median time to progression for ECT cohorts was 24.2 months for periocular cohort and 20.6 in advanced head SCC cohort, respectively. CONCLUSIONS: Electrochemotherapy is well tolerated for advanced SCC of the head in cats; its use may be considered among loco-regional strategies for cancer therapy in sensitive body regions such as periocular region.

Nucleation and temperature-driven phase transitions of silicene superstructures on Ag(1 1 1).

Silicene grown on Ag(1 1 1) is characterized by several critical parameters. Among them, the substrate temperature plays a key role in determining the morphology during growth. However, an unexpected important role is also equally played by the post-deposition annealing temperature which determines the self-organization of silicene domains even in the submonolayer coverage regime and consecutive transitions between silicene with different periodicity. These temperature-driven phase transitions can be exploited to select the desired majority silicene phase, thus allowing for the manipulation of silicene properties.

Che-1 modulates the decision between cell cycle arrest and apoptosis by its binding to p53.

The tumor suppressor p53 is mainly involved in the transcriptional regulation of a large number of growth-arrest- and apoptosis-related genes. However, a clear understanding of which factor/s influences the choice between these two opposing p53-dependent outcomes remains largely elusive. We have previously described that in response to DNA damage, the RNA polymerase II-binding protein Che-1/AATF transcriptionally activates p53. Here, we show that Che-1 binds directly to p53. This interaction essentially occurs in the first hours of DNA damage, whereas it is lost when cells undergo apoptosis in response to posttranscriptional modifications. Moreover, Che-1 sits in a ternary complex with p53 and the oncosuppressor Brca1. Accordingly, our analysis of genome-wide chromatin occupancy by p53 revealed that p53/Che1 interaction results in preferential transactivation of growth arrest p53 target genes over its pro-apoptotic target genes. Notably, exposure of Che-1(+/-) mice to ionizing radiations resulted in enhanced apoptosis of thymocytes, compared with WT mice. These results confirm Che-1 as an important regulator of p53 activity and suggest Che-1 to be a promising yet attractive drug target for cancer therapy.

HIPK2 sustains apoptotic response by phosphorylating Che-1/AATF and promoting its degradation.

Che-1/AATF is an RNA polymerase II-binding protein that is involved in the regulation of gene transcription, which undergoes stabilization and accumulation in response to DNA damage. We have previously demonstrated that following apoptotic induction, Che-1 protein levels are downregulated through its interaction with the E3 ligase HDM2, which leads to Che-1 degradation by ubiquitylation. This interaction is mediated by Pin1, which determines a phosphorylation-dependent conformational change. Here we demonstrate that HIPK2, a proapoptotic kinase, is involved in Che-1 degradation. HIPK2 interacts with Che-1 and, upon genotoxic stress, phosphorylates it at specific residues. This event strongly increases HDM2/Che-1 interaction and degradation of Che-1 protein via ubiquitin-dependent proteasomal system. In agreement with these findings, we found that HIPK2 depletion strongly decreases Che-1 ubiquitylation and degradation. Notably, Che-1 overexpression strongly counteracts HIPK2-induced apoptosis. Our results establish Che-1 as a new HIPK2 target and confirm its important role in the cellular response to DNA damage.

Evidence of trigonal dangling bonds at the Ge(111)/oxide interface by electrically detected magnetic resonance.

Despite a renewed interest in Ge as a competitor with Si for a broad range of electronic applications, the microstructure and the electronic properties of the dangling bonds that, in analogy with Si, are expected at the Ge/oxide interface have escaped a firm spectroscopy observation and characterization. Clear evidence based on contactless electrically detected magnetic resonance spectroscopy of a dangling bond at the Ge(111)/GeO(2) interface is reported in this Letter. This result supports the similarity between dangling bonds at the Si(111)/oxide and Ge(111)/oxide interfaces, both showing C(3v) trigonal point symmetry with the main axis oriented along the ⟨111⟩ direction. In contrast, at the Ge(001)/oxide interface the absence of the trigonal center in favor of a lower symmetry dangling bond marks the difference with the Si(001)/oxide interface, where both centers are present and the one having higher point symmetry prevails. This fact is rationalized in terms of suboxide interface rearrangement and oxide viscoelasticity, which promote the generation of the nonaxial centers at distorted dimers. The unambiguous identification of the centers at the Ge/oxide interfaces yields a deeper insight into the physical properties of the suboxide interface structure and offers a valid indicator for the evaluation of different surface capping and passivation techniques, with the potential to boost the Ge-related technology.

Fe charge state adjustment in ZnO upon ion implantation.

The influence of the ion implantation process on the charge state of dilute (57)Fe impurities implanted as radioactive (57)Mn in ZnO is investigated by (57)Fe emission Mössbauer spectroscopy. One sample is additionally implanted with stable (23)Na impurities. Both Fe(2+) and Fe(3+) charge states are observed, and the Fe(3+)/Fe(2+) ratio is found to increase with the fluence of both (57)Mn/(57)Fe and (23)Na ions, demonstrating that the build-up of Fe(3+) is not related to the chemical nature of the implanted ions. The results are interpreted in terms of radiation damage induced changes of the Fermi level, and illustrate that the Fe(3+)/Fe(2+) ratio can be adjusted by ion implantation. The spin-lattice relaxation time for Fe(3+) in ZnO is found to be independent of the implantation fluence, and is evidently an intrinsic property of the system.

LGI1 microdeletion in autosomal dominant lateral temporal epilepsy.

OBJECTIVES: To characterize clinically and genetically a family with autosomal dominant lateral temporal epilepsy (ADLTE) negative to LGI1 exon sequencing test. METHODS: All participants were personally interviewed and underwent neurologic examination. Most affected subjects underwent EEG and neuroradiologic examinations (CT/MRI). Available family members were genotyped with the HumanOmni1-Quad v1.0 single nucleotide polymorphism (SNP) array beadchip and copy number variations (CNVs) were analyzed in each subject. LGI1 gene dosage was performed by real-time quantitative PCR (qPCR). RESULTS: The family had 8 affected members (2 deceased) over 3 generations. All of them showed GTC seizures, with focal onset in 6 and unknown onset in 2. Four patients had focal seizures with auditory features. EEG showed only minor sharp abnormalities in 3 patients and MRI was unremarkable in all the patients examined. Three family members presented major depression and anxiety symptoms. Routine LGI1 exon sequencing revealed no point mutation. High-density SNP array CNV analysis identified a genomic microdeletion about 81 kb in size encompassing the first 4 exons of LGI1 in all available affected members and in 2 nonaffected carriers, which was confirmed by qPCR analysis. CONCLUSIONS: This is the first microdeletion affecting LGI1 identified in ADLTE. Families with ADLTE in which no point mutations are revealed by direct exon sequencing should be screened for possible genomic deletion mutations by CNV analysis or other appropriate methods. Overall, CNV analysis of multiplex families may be useful for identifying microdeletions in novel disease genes.

Electronic properties of pristine and Se doped [001] silicon nanowires: an ab initio study.

We report the results of first-principles density functional theory calculations of the properties of pristine and Se doped hydrogen passivated silicon nanowires oriented along the [001] direction. We show that the effect of confinement in the orthogonal directions is to increase the bandgap as the diameter of the nanowire is progressively reduced, as expected from the simple quantum confinement model. Moreover, we observe that the introduction of surface reconstruction before H passivation can lead to an indirect bandgap due to a shift of the valence band maximum away from the convergence point. We also study the formation energy and hyperfine parameters of Se located in different positions in a nanowire with diameter of 0.8 nm. Our results confirms a tendency to surface segregation for Se atoms, probably driven by deformations close to the nanowire surface. These deformations cause also a steep decrease in the hyperfine contact term of Se in surface positions compared to the situation when Se is placed near the axis of the nanowire. The latter values of the hyperfine contact term are instead much greater than the corresponding bulk values.

The fabrication of tunable nanoporous oxide surfaces by block copolymer lithography and atomic layer deposition.

Patterned nanoscale materials with controllable characteristic feature sizes and periodicity are of considerable interest in a wide range of fields, with various possible applications ranging from biomedical to nanoelectronic devices. Block-copolymer (BC)-based lithography is a powerful tool for the fabrication of uniform, densely spaced nanometer-scale features over large areas. Following this bottom-up approach, nanoporous polymeric films can be deposited on any type of substrate. The nanoporous periodic template can be transferred to the underlying substrate by dry anisotropic etching. Nevertheless the physical sizes of the polymeric mask represent an important limitation in the implementation of suitable lithographic protocols based on BC technology, since the diameter and the center-to-center distance of the pores cannot be varied independently in this class of materials. This problem could be overcome by combining block copolymer technology with atomic layer deposition (ALD): by means of BC-based lithography a nanoporous SiO2 template, with well-reproducible characteristic dimensions, can be fabricated and subsequently used as a backbone for the growth of perfectly conformal thin oxide films by ALD. In this work polystyrene-b-poly(methylmethacrylate) (PS-b-PMMA) BC and reactive ion etching are used to fabricate hexagonally packed 23 nm wide nanopores in a 50 nm thick SiO2 matrix. By ALD deposition of Al2O3 thin films onto the nanoporous SiO2 templates, nanostructured Al2O3 surfaces are obtained. By properly adjusting the thickness of the Al2O3 film the dimension of the pores in the oxide films is progressively reduced, with nanometer precision, from the original size down to complete filling of the pores, thus providing a simple and fast strategy for the fabrication of nanoporous Al2O3 surfaces with well-controllable feature size.

Si nanocrystal synthesis in HfO2/SiO/HfO2 multilayer structures.

The synthesis of two-dimensional arrays of Si nanocrystals in an HfO2 matrix has been achieved by deposition of HfO2/SiO/HfO2 multilayer structures followed by high temperature (1100 degrees C) thermal treatment in nitrogen atmosphere. Silicon out-diffusion from the SiO layer through the HfO2 films has been shown to be the limiting factor in the formation of the Si nanocrystals. Suitable strategies have been identified in order to overcome this limitation. Si nanocrystal formation has been achieved by properly adjusting the thickness of the SiO layer.

Gene copy number variation and common human disease.

Variation in gene copy number is increasingly recognized as a common, heritable source of inter-individual differences in genomic sequence. The role of copy number variation is well established in the pathogenesis of rare genomic disorders. More recently, germline and somatic copy number variation have been shown to be important pathogenic factors in a range of common diseases, including infectious, autoimmune and neuropsychiatric diseases and cancer. In this review, we describe the range of methods available for measuring copy number variants (CNVs) in individuals and populations, including the limitations of presently available assays, and highlight some key examples of common diseases in which CNVs have been shown clearly to have a pathogenic role. Although there has been major progress in this field in the last 5 years, understanding the full contribution of CNVs to the genetic basis of common diseases will require further studies, with more accurate CNV assays and larger cohorts than have presently been completed.