SARS-CoV-2 mutations affect antigen processing by the proteasome to alter CD8+ T cell responses.

Mutations within viral epitopes can result in escape from T cells, but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two SARS-CoV-2 nucleoprotein CD8+ epitopes, we investigated the contribution of these flanking mutations to proteasomal processing and T cell activation. We found decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103 N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on proteasomal processing, either contributing to T cell escape or enhancement that may be exploited for future vaccine design.

Evaluation of T cell responses to naturally processed variant SARS-CoV-2 spike antigens in individuals following infection or vaccination.

Most existing studies characterizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell responses are peptide based. This does not allow evaluation of whether tested peptides are processed and presented canonically. In this study, we use recombinant vaccinia virus (rVACV)-mediated expression of SARS-CoV-2 spike protein and SARS-CoV-2 infection of angiotensin-converting enzyme (ACE)-2-transduced B cell lines to evaluate overall T cell responses in a small cohort of recovered COVID-19 patients and uninfected donors vaccinated with ChAdOx1 nCoV-19. We show that rVACV expression of SARS-CoV-2 antigen can be used as an alternative to SARS-CoV-2 infection to evaluate T cell responses to naturally processed spike antigens. In addition, the rVACV system can be used to evaluate the cross-reactivity of memory T cells to variants of concern (VOCs) and to identify epitope escape mutants. Finally, our data show that both natural infection and vaccination could induce multi-functional T cell responses with overall T cell responses remaining despite the identification of escape mutations.

[Prevalence and risk factors of obesity in children with Diamond-Blackfan anemia]. / å ˆå¤©æ€§çº¯çº¢ç»†èƒžå†ç”Ÿéšœç¢æ€§è´«è¡€æ‚£å„¿è‚¥èƒ–å‘ç”Ÿæƒ å†µåŠå½±å“å› ç´ åˆ†æž.

OBJECTIVES: To investigate the distribution of body mass index (BMI) and risk factors for obesity in children with Diamond-Blackfan Anemia (DBA). METHODS: The children with DBA who attended National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, from January 2003 to December 2020 were enrolled as subjects. The related clinical data and treatment regimens were recorded. The height and weight data measured within 1 week before or after follow-up time points were collected to calculate BMI. The risk factors for obesity were determined by multivariate regression analysis in children with DBA. RESULTS: A total of 129 children with DBA were enrolled, among whom there were 80 boys (62.0%) and 49 girls (38.0%), with a median age of 49 months (range 3-189 months). The prevalence rate of obesity was 14.7% (19/129). The multivariate logistic regression analysis showed that the absence of ribosomal protein gene mutation was closely associated with obesity in children with DBA (adjusted OR=3.63, 95%CI: 1.16-11.38, adjusted P=0.027). In children with glucocorticoid-dependent DBA, obesity was not associated with age of initiation of glucocorticoid therapy, duration of glucocorticoid therapy, and maintenance dose of glucocorticoids (P>0.05). CONCLUSIONS: There is a high prevalence rate of obesity in children with DBA, and the absence of ribosomal protein gene mutation is closely associated with obesity in children with DBA.

Probing longitudinal carrier transport in perovskite thin films via modified transient reflection spectroscopy.

Accurate characterization of the longitudinal (along the thickness direction) carrier transport property is of significant importance for evaluating the quality and performance of perovskite thin films. Herein, we report the development of a modified transient reflection (TR) spectroscopy method to realize the direct observation and determination of the longitudinal carrier transport process in MAPbI3 polycrystalline thin films. Unlike the traditional TR spectroscopy, the carrier transport dynamics along the film thickness is resolved by making the pump (excitation) and probe beams spatially separated on each side of the film, so that the carrier transport from the excitation side to the probe side is directly captured. Utilizing this method, the longitudinal carrier diffusion coefficients (D) in various perovskite films with different thicknesses and grain sizes (extracted from SEM images) are determined, showing D values of ∼1.5 to 1.8 cm2 s-1 (∼0.5 to 0.8 cm2 s-1) for films with grain size larger (smaller) than the thickness. This empirical correlation between the longitudinal D and film thickness/grain size provides a reference for quick quality screening and evaluation of perovskite polycrystalline thin films.

Hbxip is essential for murine embryogenesis and regulates embryonic stem cell differentiation through activating mTORC1.

HBXIP, also named LAMTOR5, has been well characterized as a transcriptional co-activator in various cancers. However, the role of Hbxip in normal development remains unexplored. Here, we demonstrated that homozygous knockout of Hbxip leads to embryonic lethality, with retarded growth around E7.5, and that depletion of Hbxip compromises the self-renewal of embryonic stem cells (ESCs), with reduced expression of pluripotency genes, reduced cell proliferation and decreased colony-forming capacity. In addition, both Hbxip-/- ESCs and E7.5 embryos displayed defects in ectodermal and mesodermal differentiation. Mechanistically, Hbxip interacts with other components of the Ragulator complex, which is required for mTORC1 activation by amino acids. Importantly, ESCs depleted of Ragulator subunits, Lamtor3 or Lamtor4, displayed differentiation defects similar to those of Hbxip-/- ESCs. Moreover, Hbxip-/-, p14-/- and p18-/- mice, lacking subunits of the Ragulator complex, also shared similar phenotypes, embryonic lethality and retarded growth around E7-E8. Thus, we conclude that Hbxip plays a pivotal role in the development and differentiation of the epiblast, as well as the self-renewal and differentiation of ESCs, through activating mTORC1 signaling.

Significance of paroxysmal nocturnal hemoglobinuria clone in immunosuppressive therapy for children with severe aplastic anemia. / é˜µå‘æ€§ç¡çœ æ€§è¡€çº¢è›‹ç™½å°¿å ‹éš†åœ¨å„¿ç«¥é‡åž‹å†ç”Ÿéšœç¢æ€§è´«è¡€å ç–«æŠ‘åˆ¶æ²»ç–—ä¸­çš„æ„ä¹‰.

OBJECTIVES: To study the association between paroxysmal nocturnal hemoglobinuria (PNH) clone and immunosuppressive therapy (IST) in children with severe aplastic anemia (SAA). METHODS: A retrospective analysis was performed on the medical data of 151 children with SAA who were admitted and received IST from January 2012 to May 2020. According to the status of PNH clone, these children were divided into a negative PNH clone group (n=135) and a positive PNH clone group (n=16). Propensity score matching was used to balance the confounding factors, and the impact of PNH clone on the therapeutic effect of IST was analyzed. RESULTS: The children with positive PNH clone accounted for 10.6% (16/151), and the median granulocyte clone size was 1.8%. The children with positive PNH clone had an older age and a higher reticulocyte count at diagnosis (P<0.05). After propensity score matching, there were no significant differences in baseline features between the negative PNH clone and positive PNH clone groups (P>0.05). The positive PNH clone group had a significantly lower overall response rate than the negative PNH clone group at 6, 12, and 24 months after IST (P<0.05). The evolution of PNH clone was heterogeneous after IST, and the children with PNH clone showed an increase in the 3-year cumulative incidence rate of aplastic anemia-PNH syndrome (P<0.05). CONCLUSIONS: SAA children with positive PNH clone at diagnosis tend to have poor response to IST and are more likely to develop aplastic anemia-PNH syndrome.

Water-Stable Nickel Metal-Organic Framework Nanobelts for Cocatalyst-Free Photocatalytic Water Splitting to Produce Hydrogen.

Development of water-stable metal-organic frameworks (MOFs) for promising visible-light-driven photocatalytic water splitting is highly desirable but still challenging. Here we report a novel p-type nickel-based MOF single crystal (Ni-TBAPy-SC) and its exfoliated nanobelts (Ni-TBAPy-NB) that can bear a wide range of pH environment in aqueous solution. Both experimental and theoretical results indicate a feasible electron transfer from the H4TBAPy ligand (light-harvesting center) to the Ni-O cluster node (catalytic center), on which water splitting to produce hydrogen can be efficiently driven free of cocatalyst. Compared to the single crystal, the exfoliated two-dimensional (2D) nanobelts show more efficient charge separation due to its shortened charge transfer distance and remarkably enhanced active surface areas, resulting in 164 times of promoted water reduction activity. The optimal H2 evolution rate on the nanobelt reaches 98 µmol h-1 (ca. 5 mmol h-1 g-1) showing benchmarked apparent quantum efficiency (AQE) of 8.0% at 420 nm among water-stable MOFs photocatalysts.

An immunodominant NP105-113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease.

NP105-113-B*07:02-specific CD8+ T cell responses are considered among the most dominant in SARS-CoV-2-infected individuals. We found strong association of this response with mild disease. Analysis of NP105-113-B*07:02-specific T cell clones and single-cell sequencing were performed concurrently, with functional avidity and antiviral efficacy assessed using an in vitro SARS-CoV-2 infection system, and were correlated with T cell receptor usage, transcriptome signature and disease severity (acute n = 77, convalescent n = 52). We demonstrated a beneficial association of NP105-113-B*07:02-specific T cells in COVID-19 disease progression, linked with expansion of T cell precursors, high functional avidity and antiviral effector function. Broad immune memory pools were narrowed postinfection but NP105-113-B*07:02-specific T cells were maintained 6 months after infection with preserved antiviral efficacy to the SARS-CoV-2 Victoria strain, as well as Alpha, Beta, Gamma and Delta variants. Our data show that NP105-113-B*07:02-specific T cell responses associate with mild disease and high antiviral efficacy, pointing to inclusion for future vaccine design.

Short Stature in Patients with Diamond-Blackfan Anemia: A Cross-Sectional Study.

OBJECTIVE: To systematically describe the short stature of patients with Diamond-Blackfan anemia and to explore factors affecting the height development of patients with Diamond-Blackfan anemia. STUDY DESIGN: This cross-sectional study was conducted at the Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, and the height, weight, and clinical data of 129 patients with Diamond-Blackfan anemia were collected from June 2020 to September 2020. RESULTS: The median height-age-z score (HAZ) of children affected by Diamond-Blackfan anemia was -1.54 (-6.36-1.96). Short stature was found in 37.98% of the patients. Specific Diamond-Blackfan anemia growth curves were developed for weight, height, and body mass index, separately for male and female patients. Multivariable logistic regression models showed that female sex (aOR 4.92; 95% CI 1.29-18.71; P = .0195), underweight (aOR 10.41, 95% CI 1.41-76.98, P = .0217), cardiovascular malformations (aOR 216.65; 95% CI 3.29-14279.79; P = .0118), and RPL11(aOR 29.14; 95% CI 1.18-719.10; P = .0392) or RPS26 (aOR 53.49; 95% CI 1.40-2044.30; P = .0323) mutations were independent risk factors for short stature. In the subgroup of patients who were steroid-dependent, patients with a duration of steroid therapy over 2 years (OR 2.95; 95% CI 1.00-8.66; P = .0494) or maintenance dose of prednisone >0.1 mg/kg per day (OR 3.30; 95% CI 1.02-10.72; P = .0470) had a higher incidence of short stature. CONCLUSIONS: Patients with Diamond-Blackfan anemia had a high prevalence of short stature. The risk of short stature increased with age and was associated with sex, underweight, congenital malformations, and RPL11 or RPS26 mutations. The duration of steroid therapy and maintenance dose of steroid was significantly associated with the incidence of short stature in steroid-dependent patients with Diamond-Blackfan anemia.

Ultrafast and High-Yield Polaronic Exciton Dissociation in Two-Dimensional Perovskites.

Layered two-dimensional (2D) lead halide perovskites are a class of quantum well (QW) materials, holding dramatic potentials for optical and optoelectronic applications. However, the thermally activated exciton dissociation into free carriers in 2D perovskites, a key property that determines their optoelectronic performance, was predicted to be weak due to large exciton binding energy (Eb, about 100-400 meV). Herein, in contrast to the theoretical prediction, we discover an ultrafast (<1.4 ps) and highly efficient (>80%) internal exciton dissociation in (PEA)2(MA)n-1PbnI3n+1 (PEA = C6H5C2H4NH3+, MA = CH3NH3+, n = 2-4) 2D perovskites despite the large Eb. We demonstrate that the exciton dissociation activity in 2D perovskites is significantly promoted because of the formation of exciton-polarons with considerably reduced exciton binding energy (down to a few tens of millielectronvolts) by the polaronic screening effect. This ultrafast and high-yield exciton dissociation limits the photoluminescence of 2D perovskites but on the other hand well explains their exceptional performance in photovoltaic devices. The finding should represent a common exciton property in the 2D hybrid perovskite family and provide a guideline for their rational applications in light emitting and photovoltaics.

Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2.

Immunodominance is a complex and highly debated topic of T cell biology. The current SARS-CoV-2 pandemic has provided the opportunity to profile adaptive immune responses and determine molecular factors contributing to emerging responses towards immunodominant viral epitopes. Here, we discuss parameters that alter the dynamics of CD8 viral epitope processing, generation and T-cell responses, and how immunodominance counteracts viral immune escape mechanisms that develop in the context of emerging SARS-CoV-2 variants.

Auger-Assisted Electron Transfer between Adjacent Quantum Wells in Two-Dimensional Layered Perovskites.

Two-dimensional (2D) layered perovskites are naturally formed multiple quantum-well (QW) materials, holding great promise for applications in many optoelectronic devices. However, the further use of 2D layered perovskites in some devices is limited by the lack of QW-to-QW carrier transport/transfer due to the energy barrier formed by the insulating ligands between QWs. Herein, we report an Auger-assisted electron transfer between adjacent QWs in (CmH2m+1NH3)2PbI4 2D perovskites particularly with m = 12 and 18, where the electron energy barrier (Eb) is similar to the QW band gap energy (Eg). This Auger-assisted QW-to-QW electron transfer mechanism is established by the observation of a long-lived and derivative-like transient absorption feature, which is a signature of the quantum confined Stark effect induced by the electron-hole separation (thus an internal electric field) between different QW layers. Our finding provides a new guideline to design 2D perovskites with an optically tunable QW-to-QW charge transport property, advancing their applications in optoelectronics and optical modulations.

Defect-Induced Inhomogeneous Phase Transition in 2D Perovskite Single Crystals at Low Temperatures.

The temperature-induced phase transition in two-dimensional (2D) layered perovskites was recently found to be incomplete even if the temperature dropped to tens of kelvin. However, its intrinsic cause still remains unclear, and the information on the phase transition in individual single crystals (SCs) is also limited. Herein, we study the phase transition process in individual (n-C4H9NH3)2PbI4 SCs using a home-built photoluminescence (PL)-scanned image microscope. At 83 K, the phase transition is indeed incomplete, leading to the coexistence and inhomogeneous distributions of room-temperature and low-temperature phases. We map the distribution of phase transition degree on individual SCs at 83 K, which exhibits a strong positive (negative) correlation with the distribution of local defects (PL lifetimes) at 293 K, indicating that the phase transition is enhanced by initial defects. Our findings might provide new insight into the phase transition of (n-C4H9NH3)2PbI4 crystals, which is of potential value for applications based on 2D layered perovskites.

IFITM3-specific antibody reveals IFN preferences and slow IFN induction of the antiviral factor IFITM3 in humans.

Using a specific antibody, we found that expression of the viral restriction factor IFITM3 differs across cell types within the immune compartment with higher expression in myeloid rather than lymphoid cells. IFITM3 expression was increased following IFN stimulation, mostly type I, in immune cells, with the exception of T cells.

Long-Range Exciton Transport in Perovskite-Metal Organic Framework Solid Composites.

The encapsulation of perovskite quantum dots (PQDs) in metal organic frameworks (MOFs) is a promising strategy for fabricating stable and functional perovskite solid composites (denoted as PQDs@MOF), which have exhibited great potential for optoelectronics, catalysis, and luminesce applications. However, the exciton diffusion distance, one of the key factors determining the performance of PQDs@MOF in these applications, remains unknown. Herein, by using time-resolved and photoluminescence-scanned imaging microscopy, we report the observation of long-distance exciton transport (278 ± 12.6 nm) and high diffusion coefficient (0.0428 ± 0.0039 cm2/s) in MAPbBr3 PQDs@MOF microcrystals. We show that the long exciton diffusion length, which is seven times longer than that in colloid MAPbBr3 PQD solid films, can be attributed to the strong dipole-dipole coupling between adjacent PQDs embedded in the MOF matrix and their long carrier lifetimes. These findings demonstrate the great potential of PQDs@MOF crystals for optoelectronic applications.

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19.

The development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and therapeutics will depend on understanding viral immunity. We studied T cell memory in 42 patients following recovery from COVID-19 (28 with mild disease and 14 with severe disease) and 16 unexposed donors, using interferon-γ-based assays with peptides spanning SARS-CoV-2 except ORF1. The breadth and magnitude of T cell responses were significantly higher in severe as compared with mild cases. Total and spike-specific T cell responses correlated with spike-specific antibody responses. We identified 41 peptides containing CD4+ and/or CD8+ epitopes, including six immunodominant regions. Six optimized CD8+ epitopes were defined, with peptide-MHC pentamer-positive cells displaying the central and effector memory phenotype. In mild cases, higher proportions of SARS-CoV-2-specific CD8+ T cells were observed. The identification of T cell responses associated with milder disease will support an understanding of protective immunity and highlights the potential of including non-spike proteins within future COVID-19 vaccine design.

Trap-Enabled Long-Distance Carrier Transport in Perovskite Quantum Wells.

Layered two-dimensional (2D) hybrid perovskites are naturally formed multiple quantum well (QW) materials with promising applications in quantum and optoelectronic devices. In principle, the transport of excitons in 2D perovskites is limited by their short lifetime and small mobility to a distance within a few hundred nanometers. Herein, we report an observation of long-distance carrier transport over 2 to 5 µm in 2D perovskites with various well thicknesses. Such a long transport distance is enabled by trap-induced exciton dissociation into long-lived and nonluminescent electron-hole separated state, followed by a trap-mediated charge transport process. This unique property makes 2D perovskites comparable with 3D perovskites and other traditional semiconductor QWs in terms of a carrier transport property and highlights their potential application as an efficient energy/charge-delivery material.

Broad and strong memory CD4 + and CD8 + T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients.

COVID-19 is an ongoing global crisis in which the development of effective vaccines and therapeutics will depend critically on understanding the natural immunity to the virus, including the role of SARS-CoV-2-specific T cells. We have conducted a study of 42 patients following recovery from COVID-19, including 28 mild and 14 severe cases, comparing their T cell responses to those of 16 control donors. We assessed the immune memory of T cell responses using IFNγ based assays with overlapping peptides spanning SARS-CoV-2 apart from ORF1. We found the breadth, magnitude and frequency of memory T cell responses from COVID-19 were significantly higher in severe compared to mild COVID-19 cases, and this effect was most marked in response to spike, membrane, and ORF3a proteins. Total and spike-specific T cell responses correlated with the anti-Spike, anti-Receptor Binding Domain (RBD) as well as anti-Nucleoprotein (NP) endpoint antibody titre (p<0.001, <0.001 and =0.002). We identified 39 separate peptides containing CD4 + and/or CD8 + epitopes, which strikingly included six immunodominant epitope clusters targeted by T cells in many donors, including 3 clusters in spike (recognised by 29%, 24%, 18% donors), two in the membrane protein (M, 32%, 47%) and one in the nucleoprotein (Np, 35%). CD8+ responses were further defined for their HLA restriction, including B*4001-restricted T cells showing central memory and effector memory phenotype. In mild cases, higher frequencies of multi-cytokine producing M- and NP-specific CD8 + T cells than spike-specific CD8 + T cells were observed. They furthermore showed a higher ratio of SARS-CoV-2-specific CD8 + to CD4 + T cell responses. Immunodominant epitope clusters and peptides containing T cell epitopes identified in this study will provide critical tools to study the role of virus-specific T cells in control and resolution of SARS-CoV-2 infections. The identification of T cell specificity and functionality associated with milder disease, highlights the potential importance of including non-spike proteins within future COVID-19 vaccine design.

Stacking Effects on Electron-Phonon Coupling in Layered Hybrid Perovskites via Microstrain Manipulation.

Organic-inorganic hybrid halide perovskites (ABX3), especially layered 2D perovskites, have been recognized as promising semiconductors due to their tunable crystal structure and unique optoelectronic properties. A-site cations, as spacers, allow various metal halide assemblies, but the stacking pattern and the influence of their collective behavior on the properties of the resultant materials remain ambiguous. Here, the cation-stacking effects in the 2D perovskite single crystals, with a focus on the electron-phonon interaction, are investigated. We reveal the different photoluminescence from the surface region and the interior of the crystal, which is due to the residual strain induced by A-site cation stacking. We also examine the cation-stacking effects on the electron-phonon interaction, which is further employed to tailor the optoelectronic properties of the resultant 2D crystals. By reducing the microstrain, we reduce the electron-phonon coupling to improve the mobility and their stability against electric field in the corresponding crystals. Our study suggests a way to manipulate the optoelectronic properties in 2D perovskite materials by rational design of cation stacking.

Simple Meets Single: The Application of CRISPR/Cas9 in Haploid Embryonic Stem Cells.

The CRISPR/Cas9 system provides a powerful method for the genetic manipulation of the mammalian genome, allowing knockout of individual genes as well as the generation of genome-wide knockout cell libraries for genetic screening. However, the diploid status of most mammalian cells restricts the application of CRISPR/Cas9 in genetic screening. Mammalian haploid embryonic stem cells (haESCs) have only one set of chromosomes per cell, avoiding the issue of heterozygous recessive mutations in diploid cells. Thus, the combination of haESCs and CRISPR/Cas9 facilitates the generation of genome-wide knockout cell libraries for genetic screening. Here, we review recent progress in CRISPR/Cas9 and haPSCs and discuss their applications in genetic screening.