Injury primes mutation-bearing astrocytes for dedifferentiation in later life.

Despite their latent neurogenic potential, most normal parenchymal astrocytes fail to dedifferentiate to neural stem cells in response to injury. In contrast, aberrant lineage plasticity is a hallmark of gliomas, and this suggests that tumor suppressors may constrain astrocyte dedifferentiation. Here, we show that p53, one of the most commonly inactivated tumor suppressors in glioma, is a gatekeeper of astrocyte fate. In the context of stab-wound injury, p53 loss destabilized the identity of astrocytes, priming them to dedifferentiate in later life. This resulted from persistent and age-exacerbated neuroinflammation at the injury site and EGFR activation in periwound astrocytes. Mechanistically, dedifferentiation was driven by the synergistic upregulation of mTOR signaling downstream of p53 loss and EGFR, which reinstates stemness programs via increased translation of neurodevelopmental transcription factors. Thus, our findings suggest that first-hit mutations remove the barriers to injury-induced dedifferentiation by sensitizing somatic cells to inflammatory signals, with implications for tumorigenesis.

Tissue CD14+CD8+ T cells reprogrammed by myeloid cells and modulated by LPS.

The liver is bathed in bacterial products, including lipopolysaccharide transported from the intestinal portal vasculature, but maintains a state of tolerance that is exploited by persistent pathogens and tumours1-4. The cellular basis mediating this tolerance, yet allowing a switch to immunity or immunopathology, needs to be better understood for successful immunotherapy of liver diseases. Here we show that a variable proportion of CD8+ T cells compartmentalized in the human liver co-stain for CD14 and other prototypic myeloid membrane proteins and are enriched in close proximity to CD14high myeloid cells in hepatic zone 2. CD14+CD8+ T cells preferentially accumulate within the donor pool in liver allografts, among hepatic virus-specific and tumour-infiltrating responses, and in cirrhotic ascites. CD14+CD8+ T cells exhibit increased turnover, activation and constitutive immunomodulatory features with high homeostatic IL-10 and IL-2 production ex vivo, and enhanced antiviral/anti-tumour effector function after TCR engagement. This CD14+CD8+ T cell profile can be recapitulated by the acquisition of membrane proteins-including the lipopolysaccharide receptor complex-from mononuclear phagocytes, resulting in augmented tumour killing by TCR-redirected T cells in vitro. CD14+CD8+ T cells express integrins and chemokine receptors that favour interactions with the local stroma, which can promote their induction through CXCL12. Lipopolysaccharide can also increase the frequency of CD14+CD8+ T cells in vitro and in vivo, and skew their function towards the production of chemotactic and regenerative cytokines. Thus, bacterial products in the gut-liver axis and tissue stromal factors can tune liver immunity by driving myeloid instruction of CD8+ T cells with immunomodulatory ability.

Starch-Assisted Synthesis of Bi2S3 Nanoparticles for Enhanced Dielectric and Antibacterial Applications.

Starch [(C6H10O5) n ]-stabilized bismuth sulfide (Bi2S3) nanoparticles (NPs) were synthesized in a single-pot reaction using bismuth nitrate pentahydrate (Bi(NO3)3·5H2O) and sodium sulfide (Na2S) as precursors. Bi2S3 NPs were stable over time and a wide band gap of 2.86 eV was observed. The capping of starch on the Bi2S3 NPs prevents them from agglomeration and provides regular uniform shapes. The synthesized Bi2S3 NPs were quasispherical, and the measured average particle size was ∼11 nm. The NPs are crystalline with an orthorhombic structure as determined by powder X-ray diffraction and transmission electron microscopy. The existence and interaction of starch on the NP's surface were analyzed using circular dichroism. Impedance spectroscopy was used to measure the electronic behavior of Bi2S3 NPs at various temperatures and frequencies. The dielectric measurements on the NPs show high dielectric polarizations. Furthermore, it was observed that the synthesized Bi2S3 NPs inhibited bacterial strains (Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus) and demonstrated substantial antibacterial activity.

Targeted non AR mediated smart delivery of abiraterone to the prostate cancer.

Prostate cancer is the second-deadliest tumor in men all over the world. Different types of drugs with various delivery systems and pathways were developed, but no one showed prominent results against cancer. Meanwhile, nanoparticles have shown good results against cancer. Therefore, in the given study, citrate mediated synthesized gold nanoparticles (CtGNPs) with immobilized survivin antibodies (SvGNPs) were bioconjugated to the substantially potent drug abiraterone (AbSvGNPs) to develop as a combinatorial therapeutic against prostate cancer. The AbSvGNPs are made up of CtGNPs, survivin antibodies, and abiraterone. The selected drug abiraterone (Abira) possesses exceptionally good activity against prostate cancer, but cancer cells develop resistance against this drug and it also poses several severe side effects. Meanwhile, survivin antibodies were used to deliver AbSvGNPs specifically into cancer cells by considering survivin, an anti-apoptotic overexpressed protein in cancer cells, as a marker. The survivin antibodies have also been used to inhibit cancer cells as an immunotherapeutic agent. Similarly, CtGNPs were discovered to inhibit cancer cell proliferation via several transduction pathways. The given bioconjugated nanoparticles (AbSvGNPs) were found to be substantially effective against prostate cancer with an IC50 of 11.8 and 7.3 µM against DU145 and PC-3 cells, respectively. However, it was found safe against NRK and showed less than 25% cytotoxicity up to 20µM concentration. The as-synthesized nanoparticles CtGNPs, SvGNPs, and AbSvGNPs were characterized by several physical techniques to confirm their synthesis, whereas the immobilization of survivin antibodies and bioconjugation of Abira was confirmed by UV-visible spectroscopy, DLS, TEM, FTIR, and zeta-potential. The anticancer potential of AbSvGNPs was determined by MTT, DAPI, ROS, MITO, TUNEL ASSAY, and caspase-3 activity against DU145 and PC3 cells.

Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma.

ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.

Persistent T Cell Repertoire Perturbation and T Cell Activation in HIV After Long Term Treatment.

Objective: In people living with HIV (PLHIV), we sought to test the hypothesis that long term anti-retroviral therapy restores the normal T cell repertoire, and investigate the functional relationship of residual repertoire abnormalities to persistent immune system dysregulation. Methods: We conducted a case-control study in PLHIV and HIV-negative volunteers, of circulating T cell receptor repertoires and whole blood transcriptomes by RNA sequencing, complemented by metadata from routinely collected health care records. Results: T cell receptor sequencing revealed persistent abnormalities in the clonal T cell repertoire of PLHIV, characterized by reduced repertoire diversity and oligoclonal T cell expansion correlated with elevated CD8 T cell counts. We found no evidence that these expansions were driven by cytomegalovirus or another common antigen. Increased frequency of long CDR3 sequences and reduced frequency of public sequences among the expanded clones implicated abnormal thymic selection as a contributing factor. These abnormalities in the repertoire correlated with systems level evidence of persistent T cell activation in genome-wide blood transcriptomes. Conclusions: The diversity of T cell receptor repertoires in PLHIV on long term anti-retroviral therapy remains significantly depleted, and skewed by idiosyncratic clones, partly attributable to altered thymic output and associated with T cell mediated chronic immune activation. Further investigation of thymic function and the antigenic drivers of T cell clonal selection in PLHIV are critical to efforts to fully re-establish normal immune function.

Silk Cocoon-Derived Protein Bioinspired Gold Nanoparticles as a Formidable Anticancer Agent.

We synthesized bioinspired sericin encapsulated gold nanoparticles (SGNPs) using HAuCl4 as the starting material in a bottom-up approach. Further, two-dimensional (2D) and three-dimensional (3D) conformational changes (folding and unfolding) in sericin were studied using circular dichroism (CD) and fluorescence spectroscopy, respectively, during and after the synthesis of particles. Finally, the synthesized SGNPs were characterized using several physical techniques to ensure their correct synthesis and study the size, stability, and charge over the surface of particles. At the beginning of the reaction, when gold was in the ionic form (Au+³), sericin exhibited maximum electrostatic interaction and underwent unfolding. Au+³ reduced to Au during the reaction, and sericin regained its 3D confirmation due to a decrease in its native electrostatic interactions. However, CD revealed the same patterns of unfolding and folding; a decrease in α helix and an increase inß3 pleated sheets were noticed. Although the 3D structure of sericin was restored after the synthesis of SGNPs, it was substantially altered. In addition, certain changes in the 2D structure were observed; however, these did not alter the activity of sericin. Furthermore, Fourier-transform infrared spectroscopy (FTIR) confirmed these findings. The SGNPs were found to be effective against lung cancer (A549 cells), with an IC50 of 145.49 ßM, without exerting any toxic effects on normal cells (NRK cells). The effectiveness of SGNPs was examined by MTT cytotoxicity and nuclear fragmentation assays. Furthermore, we assessed their ability to produce excessive ROS and release Cyt-c from the mitochondria for caspase-3-mediated apoptosis.

Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases.

Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor ß (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.

Role of MgO nanoparticles in the suppression of Meloidogyne incognita, infecting cowpea and improvement in plant growth and physiology.

Root-knot disease, caused by Meloidogyne spp., alters histology as well as physiology of the roots thus influencing metabolism of vegetative and reproductive parts leading to huge losses in crop productivity. The experimental plant, Vigna unguiculata L. (cowpea of Fabaceae family) var. Gomti is an economically important pulse crop plant. An experiment was conducted to evaluate the effects of different concentrations (0, 25, 50 or 100 ppm) and various modes of applications (root dip, soil drench or foliar spray) of MgO nanoparticles on cowpea infected with M. incognita. The MgO nanoparticles were synthesized chemically and characterized by transmission and scanning electron microscopy (TEM, SEM), UV-Vis spectroscopy, X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The scanning electron microscopy images of second stage juveniles of M. incognita treated with MgO nanoparticles (50 and 100 ppm) exhibited indentations, roughness and distortions in the cuticular surface, in comparison to the control untreated juveniles. MgO nanoparticles, in varying concentrations (50, 100 and 200 ppm), were dispensed into the plants by root dip, soil drench and foliar spray methods and their efficacy was assessed in terms of morphological characteristics, yield parameters and biochemical attributes of M. incognita infected plants. In planta trials revealed that 100 ppm dose of MgO nanoparticles, as root dip application, demonstrated reduced nematode fecundity, decreased number and smaller size of galls; enhanced plant growth, increased chlorophyll, carotenoid, seed protein, and root and shoot nitrogen contents. From these findings it could be inferred that MgO nanoparticles played twin roles, first as a nematicidal agent and the other as growth promotion inducer.

The T cell differentiation landscape is shaped by tumour mutations in lung cancer.

Tumour mutational burden (TMB) predicts immunotherapy outcome in non-small cell lung cancer (NSCLC), consistent with immune recognition of tumour neoantigens. However, persistent antigen exposure is detrimental for T cell function. How TMB affects CD4 and CD8 T cell differentiation in untreated tumours, and whether this affects patient outcomes is unknown. Here we paired high-dimensional flow cytometry, exome, single-cell and bulk RNA sequencing from patients with resected, untreated NSCLC to examine these relationships. TMB was associated with compartment-wide T cell differentiation skewing, characterized by loss of TCF7-expressing progenitor-like CD4 T cells, and an increased abundance of dysfunctional CD8 and CD4 T cell subsets, with significant phenotypic and transcriptional similarity to neoantigen-reactive CD8 T cells. A gene signature of redistribution from progenitor-like to dysfunctional states associated with poor survival in lung and other cancer cohorts. Single-cell characterization of these populations informs potential strategies for therapeutic manipulation in NSCLC.

Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Ultrasmall aqueous starch-capped CuS quantum dots with tunable localized surface plasmon resonance and composition for the selective and sensitive detection of mercury(ii) ions.

Ultrasmall starch-capped CuS quantum dots (QDs) with controllable size were chemically fabricated in an aqueous medium. The phase of the CuS QDs was confirmed via X-ray diffraction (XRD), whereas the characteristic localized surface plasmon resonance (LSPR) peak in the near-infrared (NIR) region was measured using UV-Vis spectroscopy. Transmission electron microscopy and high bandgap analysis confirmed the formation of ultrasmall CuS QDs in the size range of 4-8 nm. CuS QDs have been used for the selective and sensitive detection of Hg2+ ions through colorimetric and spectroscopic techniques. The selective sensing of Hg2+ ions from various metal ions was detected via a remarkable change in color, damping in LSPR intensity, significant change in the Fourier-transform infrared spectra and X-ray photoelectron spectroscopic measurements. The mechanism of interaction between the CuS QDs and Hg2+ ions has been deeply explored in terms of the role played by the starch and the reorganization of sulfide and disulfide bonds to facilitate the access of Hg2+ ions into the CuS lattice. Finally, an intermediate Cu2-x Hg x S nanostructure resulted in the leaching of Cu+ ions into the solution, which were further recovered and reused for the formation of fluorescent Cu2S nanoparticles. Thus, the entire process of synthesis, sensing and reuse paves the way for sustainable nanotechnology.

Quantitative analysis of the T cell receptor repertoire.

The T cell receptor repertoire provides a window into the cellular adaptive immune response. In the context of cancer, determining the repertoire within a tumor can give important insights into the evolution of the T cell anti-cancer response, and has the potential to identify specific personalized biomarkers for tracking host responses during cancer therapy, including immunotherapy. We describe a protocol for amplifying, sequencing and analyzing T cell receptors which is economical, robust, sensitive and versatile. The key experimental step is the ligation of a single stranded oligonucleotide to the 3' end of the T cell receptor cDNA, which allows easy amplification of all possible rearrangements using only a single set of primers per locus, while simultaneously introducing a unique molecular identifier to label each starting cDNA molecule. After sequencing, this molecular identifier can be used to correct both sequence errors and the effects of differential PCR amplification efficiency, thus producing a more accurate measure of the true T cell receptor frequency within the sample. We describe a detailed protocol describing this method to create libraries of T cell receptors from in vitro T cell cultures, blood or tissue samples. We combine this with a computational pipeline, which incorporates sample multiplexing, T cell receptor annotation and error correction to provide accurate counts of individual T cell receptor sequences within samples. The integrated experimental and computational pipeline should be of value to researchers interested in documenting and understanding the T cell immune response to cancer, and in manipulating it for therapeutic purposes.

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer.

Somatic mutations together with immunoediting drive extensive heterogeneity within non-small-cell lung cancer (NSCLC). Herein we examine heterogeneity of the T cell antigen receptor (TCR) repertoire. The number of TCR sequences selectively expanded in tumors varies within and between tumors and correlates with the number of nonsynonymous mutations. Expanded TCRs can be subdivided into TCRs found in all tumor regions (ubiquitous) and those present in a subset of regions (regional). The number of ubiquitous and regional TCRs correlates with the number of ubiquitous and regional nonsynonymous mutations, respectively. Expanded TCRs form part of clusters of TCRs of similar sequence, suggestive of a spatially constrained antigen-driven process. CD8+ tumor-infiltrating lymphocytes harboring ubiquitous TCRs display a dysfunctional tissue-resident phenotype. Ubiquitous TCRs are preferentially detected in the blood at the time of tumor resection as compared to routine follow-up. These findings highlight a noninvasive method to identify and track relevant tumor-reactive TCRs for use in adoptive T cell immunotherapy.

In vitro anthelmintic effect of biologically synthesized silver nanoparticles on liver amphistome, Gigantocotyle explanatum.

In order to ensure global food security a rationale approach is required to control all those factors which directly or indirectly affect the food productivity. The neglected helminthic diseases alone are responsible for huge economic losses to the agrarian stakeholders. The problem is further compounded by the emerging drug resistance in flukes against the commonly used anthelmintics like triclabendazole. Therefore, the search for alternatives including the nano-based approaches has become a necessity to develop future control strategies. In the present study the effect of biologically synthesized silver nanoparticles (AgNPs) was investigated on an economically important amphistome parasite, Gigantocotyle explanatum, obtained from the infected liver of the Indian water buffaloes, Bubalus bubalis. In vitro treatment of the adult worms with different doses of AgNPs severely affected the worm motility and caused ROS mediated damages in the treated flukes. The antioxidant system and the detoxification ability of the worms appeared to be disrupted along with pronounced DNA damage in the treated worms as compared to the controls. Following the treatment of worms with different concentrations of AgNPs there was a significant (p < 0.05) increase in lipid peroxidation and protein carbonylation levels which are the key oxidative stress markers. The tegumental surface which is metabolically active, was severely damaged as evident from the loss of papillae, severe blebbing, shearing and erosion of the surface structures. Such topographical disruptions would facilitate the penetration of the nanoparticles deep within the tissues that might greatly reduce the invasive potential of the flukes as evident from the decreased motility. Taken together our findings suggest that the AgNPs posses great anthelmintic potential and could be further exploited for the development of anthelmintic formulations which may be tested in vivo.

An Economical, Quantitative, and Robust Protocol for High-Throughput T Cell Receptor Sequencing from Tumor or Blood.

The T cell receptor repertoire provides a window to the cellular adaptive immune response within a tumor, and has the potential to identify specific and personalized biomarkers for tracking host responses during cancer therapy, including immunotherapy. We describe a protocol for amplifying, sequencing, and analyzing T cell receptors which is economical, robust, sensitive, and versatile. The key experimental step is the ligation of a single-stranded oligonucleotide to the 3' end of the T cell receptor cDNA, which allows easy amplification of all possible rearrangements using only a single set of primers per locus, while simultaneously introducing a unique molecular identifier to label each starting cDNA molecule. After sequencing, this molecular identifier can be used to correct both sequence errors and the effects of differential PCR amplification efficiency, thus producing a more accurate measure of the true T cell receptor frequency within the sample. This method has been applied to the analysis of unfractionated human tumor lysates, subpopulations of tumor-infiltrating lymphocytes, and peripheral blood samples from patients with a variety of solid tumors.

Tunable porous silica nanoparticles as a universal dye adsorbent.

Here, we report selective adsorption of cationic dyes methylene blue (MB) and rhodamine B (RB) and anionic dyes methyl orange (MO) and bromo cresol green (BCG) by modifying the surface of cetyl trimethyl ammonium bromide (CTAB) coated porous silica nanoparticles (PSN). We used a top down approach to synthesize PSN (porous silica nanoparticles) without high temperature calcination. X-ray diffraction study confirms the formation of pure phase silica nanoparticles. SEM analysis reveals that the particle morphology is spherical and the size range lies in-between 150-200 nm. We have studied the dye adsorption properties for three cases of PSN at varying calcination temperatures of 100 °C, 250 °C and 500 °C, respectively. Thermal study has been performed in the temperature range of 50-800 °C to check the calcination temperature. In this report, we have tuned the surface properties for selective adsorption of cationic and anionic dyes in water. In the first case, 100 °C calcined PSN selectively adsorb only anionic dyes, whereas in the second case, 500 °C calcined PSN adsorb only cationic dyes and finally, an optimized calcination temperature ≈250 °C could be used for all types of dye to be adsorbed irrespective of charges on the dyes. The mode of interaction of dyes with PSN has been explained with a proper mechanism in all three cases. The adsorptions of dyes are confirmed by UV-Vis spectroscopy. Adsorption capacity and regenerable performance of adsorbents have also been studied.

Urine-derived lymphocytes as a non-invasive measure of the bladder tumor immune microenvironment.

Despite the advances in cancer immunotherapy, only a fraction of patients with bladder cancer exhibit responses to checkpoint blockade, highlighting a need to better understand drug resistance and identify rational immunotherapy combinations. However, accessibility to the tumor prior and during therapy is a major limitation in understanding the immune tumor microenvironment (TME). Herein, we identified urine-derived lymphocytes (UDLs) as a readily accessible source of T cells in 32 patients with muscle invasive bladder cancer (MIBC). We observed that effector CD8+ and CD4+ cells and regulatory T cells within the urine accurately map the immune checkpoint landscape and T cell receptor repertoire of the TME. Finally, an increased UDL count, specifically high expression of PD-1 (PD-1hi) on CD8+ at the time of cystectomy, was associated with a shorter recurrence-free survival. UDL analysis represents a dynamic liquid biopsy that is representative of the bladder immune TME that may be used to identify actionable immuno-oncology (IO) targets with potential prognostic value in MIBC.

Mechanistic approach to study conjugation of nanoparticles for biomedical applications.

Interaction of nanoparticles with biological systems turns out to be vibrant for their efficient application in biomedical field. Here, we have shown antibiotic amakicin loaded nanoparticles are responsible for the dual role as reducing and stabilizing the silver nanoparticles without the use of any undesired chemicals. Synthesized nanoparticles are well-dispersed having quasi spherical morphology with an average particle size around 10-11 nm. Crystallinity of nanoparticles was measured using selected area electron diffraction (SAED) and powder XRD analysis which show that particles are perfectly crystalline with cubic phase of geometry. UV-Vis, FTIR and circular dichroism (CD) analysis explained the presence and interaction of antibiotic on the nanoparticle's surface. Amakicin functionalized Ag nanoparticles used in this study have shown enhanced antibacterial activity against E. coli. These studies will help in designing an in-depth understanding that how nanostructures can possibly interact with biological systems.

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile.

The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3' end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts.