Crosstalk between tumor cells and other cells within the tumor microenvironment (TME) plays a crucial role in tumor progression, metastases, and therapy resistance. We present iTALK, a computational approach to characterize and illustrate intercellular communication signals in the multicellular tumor ecosystem using single-cell RNA sequencing data. iTALK can in principle be used to dissect the complexity, diversity, and dynamics of cell-cell communication from a wide range of cellular processes.The TME has emerged as a key modulator of tumor progression, immune evasion, and emergence of the anti-tumor therapy resistance mechanisms 1, 2 . The TME includes a diversity of cell types such as tumor cells, a heterogeneous group of immune cells, and the nonimmune stromal components. Tumor cells orchestrate and interact dynamically with these non-tumor components, and the crosstalk between them is thought to provide key signals that can direct and promote tumor cell growth and migration. Through this intercellular communication, tumor cells can elicit profound phenotypic changes in other TME cells such as tumor-associated fibroblasts, macrophages and T cells, and reprogram the TME, in order to escape from immune surveillance to facilitate survival. Therefore, a better understanding of the cell-cell communication signals may help identify novel modulating therapeutic strategies for better patient advantage. However, this has been hampered by the lack of bioinformatics tools for efficient data analysis and visualization.Here, we present iTALK (identifying and illustrating alterations in intercellular signaling network; https://github.com/Coolgenome/iTALK), an open source R package designed to profile and visualize the ligand-receptor mediated intercellular cross-talk signals from singlecell RNA sequencing data (scRNA-seq) ( Fig. 1 and Online Methods). We demonstrated that iTALK can be successfully applied to scRNA-seq data to capture highly abundant ligandreceptor gene (or transcript) pairs, identify gains or losses of cellular interactions by comparative analysis, and track the dynamic changes of intercellular communication signals in longitudinal samples. Notably, functional annotation of ligand-receptor genes is automatically added with our curated iTALK ligand-receptor database, and the output can be visualized in different formats with our efficient data visualization tool, which is implemented as part of iTALK. This approach can be applied to data sets ranging from hundreds to hundreds of thousands of cells and is not limited by sequencing platforms. It is also noteworthy that, in addition to studying the TME, iTALK can also be applied to a wide range of biomedical research fields that involve cell-cell communication.

SignificanceTumor cells reprogram their metabolism to support cell growth, proliferation, and differentiation, thus driving cancer progression. Profiling of the metabolic signatures in heterogeneous tumors facilitates the understanding of tumor metabolism and introduces potential metabolic vulnerabilities that might be targeted therapeutically. We proposed a spatially resolved metabolomics method for high-throughput discovery of tumor-associated metabolite and enzyme alterations using ambient mass spectrometry imaging. Metabolic pathway-related metabolites and metabolic enzymes that are associated with tumor metabolism were efficiently discovered and visualized in heterogeneous esophageal cancer tissues. Spatially resolved metabolic alterations hold the key to defining the dependencies of metabolism that are most limiting for cancer growth and exploring metabolic targeted strategies for better cancer treatment.

Capacity degradation by phase changes and oxygen evolution has been the largest obstacle for the ultimate commercialization of high‐capacity LiNiO2‐based cathode materials. The ultimate thermodynamic and kinetic reasons of these limitations are not yet systematically studied, and the fundamental mechanisms are still poorly understood. In this work, both phenomena are studied by density functional theory simulations and validation experiments. It is found that during delithiation of LiNiO2, decreased oxygen reduction induces a strong thermodynamic driving force for oxygen evolution in bulk. However, oxygen evolution is kinetically prohibited in the bulk phase due to a large oxygen migration kinetic barrier (2.4 eV). In contrast, surface regions provide a larger space for oxygen migration leading to facile oxygen evolution. These theoretical results are validated by experimental studies, and the kinetic stability of bulk LiNiO2 is clearly confirmed. Based on these findings, a rational design strategy for protective surface coating is proposed.

IMPORTANCEThe role of postoperative radiotherapy (PORT) has not been well defined in resected pIIIA-N2 non-small cell lung cancer (NSCLC).OBJECTIVE To evaluate the effect of PORT using modern techniques on survival and safety in patients with pIIIA-N2 NSCLC after complete resection and adjuvant chemotherapy. DESIGN, SETTING, AND PARTICIPANTS The PORT-C randomized clinical trial was conducted in 394 patients with pIIIA-N2 NSCLC treated with complete resection and 4 cycles of platinum-based chemotherapy between January 2009 and December 2017. Data were analyzed between March 2019 and December 2020. INTERVENTIONS Patients were randomized equally into the PORT arm (n = 202) or the observation arm (n = 192). The total dose of PORT was 50 Gy. MAIN OUTCOMES AND MEASURESThe primary end point was disease-free survival (DFS). Secondary end points included overall survival (OS), locoregional recurrence-free survival (LRFS), distant metastasis-free survival, and toxic effects.RESULTS In total, 394 patients were enrolled and 364 were eligible, with a median (range) age of 55 (25-70) years. There were 202 (55.5%) male and 162 (44.5%) female patients. The median follow-up was 46.0 (95% CI, 41.9-51.4) months, and 230 DFS events were reported. There were 184 patients in the PORT arm and 180 patients in the observation arm. The 3-year DFS rates were 40.5% with PORT vs 32.7% with observation (median, 22.1 vs 18.6 months), and the difference in DFS was not statistically significant without adjustment (hazard ratio [HR], 0.84; 95% CI, 0.65-1.09; P = .20), though it was significant with preplanned yet exploratory analysis (stratified analysis by the number of detected lymph nodes and positive lymph nodes, HR, 0.75; log-rank P = .04). The 3-year OS rates were 78.3% vs 82.8% (HR, 1.02; P = .93), and LRFS was 66.5% vs 59.7% (HR, 0.71; 95% CI, 0.51-0.97; P = .03), respectively. For 310 per-protocol patients (140 with PORT and 170 with observation), PORT significantly improved DFS (42.8% vs 30.6%; HR, 0.75; 95% CI, 0.57-1.00; P = .05) but not OS (HR, 0.83; 95% CI, 0.53-1.30; P = .41). The 3-year local recurrence only rates were 9.5% and 18.3% in the 2 arms, respectively (Fine-Gray HR, 0.55; Gray test P = .04). No radiotherapy-related grade 4 or 5 adverse event was observed. CONCLUSIONS AND RELEVANCEIn this phase 3 randomized clinical trial of patients with pIIIA-N2 NSCLC after complete resection and adjuvant chemotherapy, PORT did not improve DFS. Further studies exploring patients who might best benefit from PORT are needed.TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT00880971

Small cell lung cancer (SCLC) is one of the most aggressive types of cancer, yet the pathologic mechanisms underlying its devastating clinical outcome remain elusive. In this report, we surveyed 924 miRNA (miR) for their expressions in the formalin-fixed paraffin-embedded specimens from 42 patients with SCLC, and found that the downregulated miR-886-3p is closely correlated with the shorter survival of SCLC. This correlation was validated with another 40 cases. It was further discovered that loss of miR-886-3p expression was mediated by DNA hypermethylation of its promoter in both cultured SCLC cells and tumor samples. Moreover, miR-886-3p potently repressed cell proliferation, migration, and invasion of NCI-H446 cell in cell culture via suppression of the expression of its target genes: PLK1 and TGF-b1 at posttranscription levels. Forced upregulation of miR-886-3p greatly inhibited in vivo tumor growth, bone/muscle invasion, and lung metastasis of NCI-H446 cells. This newly identified miR-886-3p-PLK1/TGF-b1 nexus that modulates SCLC aggression suggests that both loss of miR-886-3p expression and hypermethylation of the miR-886 promoter are the promising indicators for poor outcome of as well as new therapeutic targets for SCLC. Cancer Res; 73(11); 3326-35. Ó2013 AACR.