Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.

Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8+ T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8+ T cells and Tregs and represses the CD8+ T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers.

Neoantigen T-Cell Receptor Gene Therapy in Pancreatic Cancer.

A patient with progressive metastatic pancreatic cancer was treated with a single infusion of 16.2×109 autologous T cells that had been genetically engineered to clonally express two allogeneic HLA-C*08:02-restricted T-cell receptors (TCRs) targeting mutant KRAS G12D expressed by the tumors. The patient had regression of visceral metastases (overall partial response of 72% according to the Response Evaluation Criteria in Solid Tumors, version 1.1); the response was ongoing at 6 months. The engineered T cells constituted more than 2% of all the circulating peripheral-blood T cells 6 months after the cell transfer. In this patient, TCR gene therapy targeting the KRAS G12D driver mutation mediated the objective regression of metastatic pancreatic cancer. (Funded by the Providence Portland Medical Foundation.).

Determining Surface Shape of Translucent Objects with the Combination of Laser-Beam-Based Structured Light and Polarization Technique.

In this study, we focus on the 3D surface measurement and reconstruction of translucent objects. The proposed approach of surface-shape determination of translucent objects is based on the combination of the projected laser-beam-based sinusoidal structured light and the polarization technique. The theoretical analyses are rigorously completed in this work, including the formation, propagation, and physical features of the generated sinusoidal signal by the designed optical system, the reflection and transmission of the projected monochromatic fringe pattern on the surface of the translucent object, and the formation and the separation of the direct-reflection and the global components of the surface radiance of the observed object. The results of experimental investigation designed in accordance with our theoretical analyses have confirmed that accurate reconstructions can be obtained using the one-shot measurement based on the proposed approach of this study and Fourier transform profilometry, while the monochromaticity and the linearly-polarized characteristic of the projected sinusoidal signal can be utilized by using a polarizer and an optical filter simultaneously for removing the global component, i.e., the noised signal contributed by multiply-scattered photons and the background illuminance in the frame of our approach. Moreover, this study has also revealed that the developed method is capable of getting accurate measurements and reconstructions of translucent objects when the background illumination exists, which has been considered as a challenging issue for 3D surface measurement and reconstruction of translucent objects.

Photo-Switchable Aggregation-Induced Emission of Bisthienylethene-Dipyrimido[2,1-b][1,3]benzothiazole Triad.

A bisthienylethene-dipyrimido[2,1-b][1,3]benzothiazole (BTE-2PBT) triad has been designed and synthesized based on our recent discovery of PBTs as atypical propeller-shaped novel AIEgens. The triad not only maintains the photochromic properties of BTE moiety in solution, film, and solid state but also exhibits remarkable AIE properties. Moreover, the fluorescence of BTE-2PBT PMMA film could be modulated with high contrast by alternate UV and visible light irradiation. Photoerasing, rewriting, and non-destructive readout of fluorescent images on BTE-2PBT PMMA film well demonstrate its potential application as optical memory media.

Microfluidic Device for Studying Controllable Hydrodynamic Flow Induced Cellular Responses.

Hydrodynamic flow is an essential stimulus in many cellular functions, regulating many mechanical sensitive pathways and closely associating with human health status and diseases. The flow pattern of blood in vessels is the key factor in causing atherosclerosis. Hemodynamics has great effect on endothelial cells' gene expression and biological functions. There are various tools that can be used for studying flow-induced cellular responses but most of them are either bulky or lack precise controllability. We develop an integrated microfluidic device that can precisely generate different flow patterns to human endothelial cells cultured on-chip. We monitored cell morphology and used small-input RNA-seq technology to depict the transcriptome profiles of human umbilical vein endothelial cells under uni- or bidirectional flow. Such integrated and miniatured device has greatly facilitated our understanding of endothelial functions with shear stimulus, not only providing new data on the transcriptomic scale but also building the connection between cell phenotypic changes and expression alternations.

A highly selective fluorescent chemosensor for Cu2+ : synthesis and properties of a rhodamine B-containing diarylethene.

A diarylethene bearing a triazole-linked rhodamine B unit was synthesized. Its fluorescent emission was significantly enhanced in the presence of protons or Cu2+ due to transformation from the pirocyclic form to open-ring form. The fluorescence was quenched sequentially upon irradiation with 297 nm light based on the intramolecular fluorescence resonance energy transfer mechanism. In an acetonitrile: water binary solvent (1: 1 v/v), the compound showed significant fluorescent enhancement for Cu2+ compared with a wide range of tested metal ions with a fast response and a limit of detection of 2.86 × 10-8  mol L-1 . Using Cu2+ and UV light as the chemical inputs, and fluorescence intensity at 597 nm as the output, a logic gate was developed at the molecular level. Moreover, the compound can be used with a high accuracy to detect Cu2+ in a natural water sample.

Evaluation of microcirculation in asymptomatic cerebral infarction with multi-parameter imaging of spectral CT.

OBJECTIVE: To investigate the role of spectral CT multiparametric imaging in the evaluation of cerebral microcirculatory perfusion. METHODS: The imaging data of 145 patients with asymptomatic cerebral infarction confirmed by MR were retrospectively analyzed, and all cases underwent head CTA and cranial CT perfusion imaging (CTP) on double-layer detector spectral CT. Single energy level images (MonoE45 keV), iodine density maps, and effective atomic number maps were reconstructed based on spectral CTA data, and CT values, iodine density values, and effective atomic number values were measured in the infarcted area, healthy control area, centrum semiovale and posterior limb of the internal capsule, respectively; perfusion values, such as cerebral blood volume (CBV) values, cerebral blood flow (CBF) values, time to peak (TTP) values, and mean passage time, were measured in the above-mentioned areas on CTP images. (TTP) values, and mean time to passage (MTT) values. CT values, iodine density values, effective atomic number values, and perfused CBV, CBF, TTP, and MTT values were compared between the infarcted area and the healthy side, the center of the hemianopia, and the posterior limb of the internal capsule. The role of spectral CT parameters and perfusion parameters in the evaluation of asymptomatic cerebral infarction was analyzed. RESULTS: CT values, iodine density values, and effective atomic number values were statistically different between the infarcted area and the healthy side; CT values, iodine density values, and effective atomic number values were not statistically different between the infarcted side and the healthy side of the hemispheric centrum and the posterior limb of the internal capsule; CBV and CBF were statistically different between the infarcted side and the healthy side, and MTT and TTP were not statistically different. There were statistically significant differences in TTP between the infarcted area and the healthy side of the hemiaxial center, and no statistically significant differences in CBV, CBF, and MTT. There were no statistical differences in CBV, CBF, TTP, and MTT in the inner capsule area. ROC curve analysis of spectral CT-related parameters and CT perfusion parameters for the diagnosis of asymptomatic cerebral infarction: area under the curve of MonoE 45Kv 0.71, area under the curve of iodine density values 0.76, area under the curve of effective atomic number values 0.74; area under the curve of CBV value 0.64, area under the curve of CBF value 0.61, area under the curve of MTT value 0.50, The area under the TTP curve was 0.52. The area under the ROC curve of the multivariate logistic regression model based on spectral parameters is 0.76, which is higher than that of the logistic regression model with perfusion parameters (P < 0.05). CONCLUSION: Spectral CT can better demonstrate small intracranial ischemic lesions, and iodine density values have a better evaluation of microcirculation in asymptomatic cerebral infarcts.

Quantitative study of the dynamic tumor-endothelial cell interactions through an integrated microfluidic coculture system.

The interaction between tumor and endothelial cells is crucial to cancer metastasis and angiogenesis. We developed a novel microfluidic device to assess the cell-cell interaction quantitatively at the single cell resolution. This integrated chip offers 16 coculture experiments in parallel with controllable microenvironments to study interactions between cells dynamically. We applied this approach to model the tumor invasion using Hela cells and human umbilical vein endothelial cells (HUVECs) and monitored the migration of both. We observed the retreatment of HUVECs upon the approach of Hela cells during coculture, indicating that the interaction between two cells was mediated by soluble factors. This interaction was further analyzed through quantitatively processing the phase-contrast microscopic time-lapse images of each individual coculture chamber. We also confirmed this paracrine effect by varying the frequency of medium change. This microfluidic technique is highly controllable, contamination free, fully automatic, and inexpensive. This approach not only offers a unique way to quantitatively study the interaction between cells but also provides accurate spatial-temporal tunability of microenvironments for cell coculture. We believe this method, intrinsically high-throughput and quantitative, will greatly facilitate the study of cell-cell interactions and communications.

Generation of three-dimensional entangled state between a single atom and a Bose-Einstein condensate via adiabatic passage.

Inspired by a recently experiment by M. Lettner et al. [Phys. Rev. Lett. 106, 210503 (2011)], we propose a robust scheme to prepare three-dimensional entanglement state between a single atom and a Bose-Einstein condensate (BEC) via stimulated Raman adiabatic passage (STIRAP) technique. The atomic spontaneous radiation, the cavity decay, and the fiber loss are efficiently suppressed by the engineering adiabatic passage. Our strictly numerical simulation shows our proposal is good enough to demonstrate the generation of three-dimensional entanglement with high fidelity and within the current experimental technology.

L-histidine functionalized ZiF-8 with aggregation-induced emission for detection of tetracycline.

In this study, we constructed zinc based metal-organic framework functionalized by L-histidine (His@ZiF-8). The His@ZiF-8 had high porosity, large surface area, abundant carboxyl and amino group, which has been found to greatly enhance the aggregation-induced emission (AIE) of tetracycline (TC). After the His@ZiF-8 enrichment with TC, the TC exhibited strong fluorescence emission peak at 565 nm based on AIE. Under the optimal conditions, the fluorescence intensity of TC exhibited a good linear relationship with TC concentration within 0.1-80 µM with a low limit of detection of 28.6 nM. Antibiotic analogs such as neomycin, chloramphenico, ampicillin, kanamycin, and erythromycin have no obvious interference. In addition, the developed method was successfully used to the detection of TC in milk, river water, and honey.

Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers.

Tumor-infiltrating neoantigen-reactive T cells can mediate regression of metastatic gastrointestinal cancers yet remain poorly characterized. We performed immunological screening against personalized neoantigens in combination with single-cell RNA sequencing on tumor-infiltrating lymphocytes from bile duct and pancreatic cancer patients to characterize the transcriptomic landscape of neoantigen-reactive T cells. We found that most neoantigen-reactive CD8+ T cells displayed an exhausted state with significant CXCL13 and GZMA co-expression compared with non-neoantigen-reactive bystander cells. Most neoantigen-reactive CD4+ T cells from a patient with bile duct cancer also exhibited an exhausted phenotype but with overexpression of HOPX or ADGRG1 while lacking IL7R expression. Thus, neoantigen-reactive T cells infiltrating gastrointestinal cancers harbor distinct transcriptomic signatures, which may provide new opportunities for harnessing these cells for therapy.

A highly selective fluorescent probe for visualization of organic hydroperoxides in living cells.

The transcriptional regulatory protein OhrR is converted into a fluorescent bioprobe capable of detecting organic hydroperoxides in living cells with high sensitivity and selectivity.

An ionic liquid-modified diarylethene: Synthesis, properties and sensing cyanide ions.

An ionic liquid-modified diarylethene was synthesized and characterized. Its photochromic properties in a variety of solutions were studied. Compared to the neutral diarylethene, the closed-ring isomer of the ionic liquid-modified diarylethene exhibits obvious solvent-dependence. The closed-ring isomer showed solvatochromism depending on the solvent dielectric constants. More importantly, a dual colorimetric cyanide sensor with high selectivity has been achieved based on this ionic liquid-modified diarylethene derivative. Both the open-ring and closed-ring isomers recognized the strongly nucleophilic cyanide by forming of C4-cyano adducts. This study provides a novel design strategy for the development of photochromic diarylethenes for the colorimetric recognition of CN-.

Publisher Correction: Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing.

In the version of this article originally published, the P statistic described in Fig. 3d was incorrect. It was described as "P < 22 × 10-16". It should have been "P < 2.2 × 10-16". Also, the "CD8+ Treg" label in Fig. 4f was incorrect. It should have been "CD4+ Treg". The errors have been corrected in the HTML and PDF versions of this article.

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing.

Cancer immunotherapies have shown sustained clinical responses in treating non-small-cell lung cancer1-3, but efficacy varies and depends in part on the amount and properties of tumor infiltrating lymphocytes4-6. To depict the baseline landscape of the composition, lineage and functional states of tumor infiltrating lymphocytes, here we performed deep single-cell RNA sequencing for 12,346 T cells from 14 treatment-naïve non-small-cell lung cancer patients. Combined expression and T cell antigen receptor based lineage tracking revealed a significant proportion of inter-tissue effector T cells with a highly migratory nature. As well as tumor-infiltrating CD8+ T cells undergoing exhaustion, we observed two clusters of cells exhibiting states preceding exhaustion, and a high ratio of "pre-exhausted" to exhausted T cells was associated with better prognosis of lung adenocarcinoma. Additionally, we observed further heterogeneity within the tumor regulatory T cells (Tregs), characterized by the bimodal distribution of TNFRSF9, an activation marker for antigen-specific Tregs. The gene signature of those activated tumor Tregs, which included IL1R2, correlated with poor prognosis in lung adenocarcinoma. Our study provides a new approach for patient stratification and will help further understand the functional states and dynamics of T cells in lung cancer.

A multi-state fluorescent switch based on a diarylethene with an acridine unit.

A new asymmetrical fluorescent diarylethene derivative with an acridine unit was synthesized by Schiff base condensation. The derivative was sensitive to lights and special metal ions. Stimulated by UV/vis lights and Zn2+, distinct changes were observed in UV-vis and fluorescent spectra. Upon addition of Zn2+, the derivative emission peak was blue-shifted by 34nm and the emission intensity was enhanced by 16 fold, accompanied by the fluorescent color changed from red to light yellow, due to the formation of a 1:1 metal/ligand complex. The complex exhibited excellent fluorescence switching upon irradiation with UV light. Taking advantage of the lights and Zn2+ stimuli (inputs), and fluorescence intensity at 580nm (output), a molecular logic gate was constructed. Moreover, a new absorption band centered at 420-450nm emerged upon exposure to Zn2+. The dramatic color change of the solution made the 'naked-eyes' detection of Zn2+ possible.

Detection of circulating tumour cells in patients with epithelial ovarian cancer by a microfluidic system.

Ovarian cancer is a gynaecological cancer with a high mortality rate. In recent years, circulating tumour cells (CTCs) have attracted attention from scientists because of their significant association with metastasis. However, due to the low CTC enrichment rate of the conventional CellSearch system and limited clinical sample sizes, only a small number of studies have focused on CTCs and epithelial ovarian cancer (EOC). Here, we apply a microfluidic system with immunomagnetic beads preconjugated with an anti-EpCAM antibody to enrich CTCs from whole blood and then analyse the enriched cells by immunofluorescence staining and automatic fluorescence microscope scanning. The average recovery rate of SK-OV-3 EOC cells was 70.2%±13.3%. When using blood samples from EOC patients and healthy volunteers, CTC counts of more than 8 cells were detected in 20 of 23 EOC patients (87.0%) but in none of the 16 healthy volunteers (0%). Total CTC counts were found to be significantly (P<0.05) elevated in the EOC group (median =55.0 [29.5, 123.0] CTCs/7.5 mL) compared with the healthy control group (median =0.5 [0,3.5] CTCs/7.5 mL). In conclusion, this is the first study to use the IsoFlux system on ovarian cancer samples. This system can efficiently capture EOC CTCs from a majority of patients and may provide a potential tool for further biological studies and for the development of in vitro EOC diagnostic products.

Fish in chips: an automated microfluidic device to study drug dynamics in vivo using zebrafish embryos.

Interference of the Hedgehog (Hh) signaling pathway by cyclopamine leads to abnormal embryonic development. We monitor this dynamical drug effect in zebrafish embryos with highly precise microenvironment control using an integrated microfluidic device. This chip-based platform, which is programmable and automated, greatly facilitates the accuracy and reproducibility of the in vivo assays.

Enhancement of cyclization quantum yields of perfluorodiarylethenes via weak intramolecular interactions.

The weak intramolecular F∙∙∙N and S∙∙∙N interactions in the novel pyridine-containing perfluorodiarylethenes achieved high cyclization quantum yields in solutions. While the F∙∙∙N interactions stabilize the photoreactive conformation, the S∙∙∙N contacts contribute from the energetic aspect.