Targeted therapy for non-small-cell lung cancer: New insights into regulated cell death combined with immunotherapy.

Non-small-cell lung cancer (NSCLC), which has a high rate of metastatic spread and drug resistance, is the most common subtype of lung cancer. Therefore, NSCLC patients have a very poor prognosis and a very low chance of survival. Human cancers are closely linked to regulated cell death (RCD), such as apoptosis, autophagy, ferroptosis, pyroptosis, and necroptosis. Currently, small-molecule compounds targeting various types of RCD have shown potential as anticancer treatments. Moreover, RCD appears to be a specific part of the antitumor immune response; hence, the combination of RCD and immunotherapy might increase the inhibitory effect of therapy on tumor growth. In this review, we summarize small-molecule compounds used for the treatment of NSCLC by focusing on RCD and pharmacological systems. In addition, we describe the current research status of an immunotherapy combined with an RCD-based regimen for NSCLC, providing new ideas for targeting RCD pathways in combination with immunotherapy for patients with NSCLC in the future.

Annotation of cell types (ACT): a convenient web server for cell type annotation.

BACKGROUND: The advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital importance to this process, allowing for the analysis and interpretation of enormous single-cell datasets. At present, however, manual cell annotation which is the predominant approach remains limited by both speed and the requirement of expert knowledge. METHODS: To address these challenges, we constructed a hierarchically organized marker map through manually curating over 26,000 cell marker entries from about 7000 publications. We then developed WISE, a weighted and integrated gene set enrichment method, to integrate the prevalence of canonical markers and ordered differentially expressed genes of specific cell types in the marker map. Benchmarking analysis suggested that our method outperformed state-of-the-art methods. RESULTS: By integrating the marker map and WISE, we developed a user-friendly and convenient web server, ACT ( http://xteam.xbio.top/ACT/ or http://biocc.hrbmu.edu.cn/ACT/ ), which only takes a simple list of upregulated genes as input and provides interactive hierarchy maps, together with well-designed charts and statistical information, to accelerate the assignment of cell identities and made the results comparable to expert manual annotation. Besides, a pan-tissue marker map was constructed to assist in cell assignments in less-studied tissues. Applying ACT to three case studies showed that all cell clusters were quickly and accurately annotated, and multi-level and more refined cell types were identified. CONCLUSIONS: We developed a knowledge-based resource and a corresponding method, together with an intuitive graphical web interface, for cell type annotation. We believe that ACT, emerging as a powerful tool for cell type annotation, would be widely used in single-cell research and considerably accelerate the process of cell type identification.

Computational Quantification of Cancer Immunoediting.

The remarkable success of cancer immunotherapy has revolutionized cancer treatment, emphasizing the importance of tumor-immune interactions in cancer evolution and treatment. Cancer immunoediting describes the dual effect of tumor-immune interactions: inhibiting tumor growth by destroying tumor cells and facilitating tumor escape by shaping tumor immunogenicity. To better understand tumor-immune interactions, it is critical to develop computational methods to measure the extent of cancer immunoediting. In this review, we provide a comprehensive overview of the computational methods for quantifying cancer immunoediting. We focus on describing the basic ideas, computational processes, advantages, limitations, and influential factors. We also summarize recent advances in quantifying cancer immunoediting studies and highlight future research directions. As the methods for quantifying cancer immunoediting are continuously improved, future research will further help define the role of immunity in tumorigenesis and hopefully provide a basis for the design of new personalized cancer immunotherapy strategies.

Status and associated factors of gerontological nurse specialists' core competency: a national cross-sectional study.

BACKGROUND: Nurses' core competency directly affects patients' safety and health outcomes. Gerontological nurse specialists play an essential role in improving older adults' health status. However, little is known about their core competency level and the factors influencing core competency. Therefore, this study aimed to investigate the status of core competency and factors influencing the core competency of gerontological nurse specialists in China. METHODS: A multicenter cross-sectional study was conducted on gerontological nurse specialists certified by province-level or above organizations across China between March 2019 and January 2020. The Revised Core Competency Evaluation Instrument for Gerontological Nurse Specialists was used to measure participants' core competency. The median, frequencies, and percentages were used to describe participants' characteristics and level of core competency. Multivariate stepwise regression analysis was applied to analyze the factors influencing core competency. RESULTS: The median score of gerontological nurse specialists' core competency was 3.84, and professional development skills and research and analysis decision-making skills had the lowest scores among the dimensions. The multivariate stepwise regression analysis showed that individual-level factors (i.e., working experience length of geriatric nursing and attitudes toward caring for older adults), employer-level factors (i.e., departments, job responsibilities, the degree of satisfaction toward the attention and support and the promotion rules provided by the hospital or department), and training-associated factors (i.e., economic zone where training organizations are located and the degree to which the training content met clinical needs) are independently associated with gerontological nurse specialists' core competency level (P < 0.05). CONCLUSIONS: This study showed that gerontological nurse specialists' core competency needs further improvements, especially regarding professional development skills and research and analysis decision-making skills. Additionally, individual-, training-, and employer-level factors could influence their core competency level, indicating that interventions targeting these factors could be applied to improve the core competency of gerontological nurse specialists.

A rationally designed fluorescence probe achieves highly specific and long-term detection of senescence in vitro and in vivo.

Senescent cells (SnCs) are implicated in aging and various age-related pathologies. Targeting SnCs can treat age-related diseases and extend health span. However, precisely tracking and visualizing of SnCs is still challenging, especially in in vivo environments. Here, we developed a near-infrared (NIR) fluorescent probe (XZ1208) that targets ß-galactosidase (ß-Gal), a well-accepted biomarker for cellular senescence. XZ1208 can be cleaved rapidly by ß-Gal and produces a strong fluorescence signal in SnCs. We demonstrated the high specificity and sensitivity of XZ1208 in labeling SnCs in naturally aged, total body irradiated (TBI), and progeroid mouse models. XZ1208 achieved a long-term duration of over 6 days in labeling senescence without causing significant toxicities and accurately detected the senolytic effects of ABT263 on eliminating SnCs. Furthermore, XZ1208 was applied to monitor SnCs accumulated in fibrotic diseases and skin wound healing models. Overall, we developed a tissue-infiltrating NIR probe and demonstrated its excellent performance in labeling SnCs in aging and senescence-associated disease models, indicating great potential for application in aging studies and diagnosis of senescence-associated diseases.

Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears.

Background: Rotator cuff tears (RCT) is the most common cause of shoulder dysfunction, however, its molecular mechanisms remain unclear. Non-coding RNAs(ncRNAs), such as long ncRNA (lncRNA), microRNA (miRNA) and circular RNA (circRNA), are involved in a variety of diseases, but little is known about their roles in RCT. Therefore, the purpose of this study is to identify dysregulated ncRNAs and understand how they influence RCT. Methods: We performed RNA sequencing and miRNA sequencing on five pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. To better comprehend the fundamental biological processes, we carried out enrichment analysis of these dysregulated mRNAs or the co-expressed genes of dysregulated ncRNAs. According to the competing endogenous RNA (ceRNA) theory, we finally established ceRNA networks to explore the relationship among dysregulated RNAs in RCT. Results: A total of 151 mRNAs, 38 miRNAs, 20 lncRNAs and 90 circRNAs were differentially expressed between torn supraspinatus muscles and matched unharmed subscapularis muscles, respectively. We found that these dysregulated mRNAs, the target mRNAs of these dysregulated miRNAs or the co-expressed mRNAs of these dysregulated ncRNAs were enriched in muscle structure development, actin-mediated cell contraction and actin binding. Then we constructed and analyzed the ceRNA network and found that the largest module in the ceRNA network was associated with vasculature development. Based on the topological properties of the largest module, we identified several important ncRNAs including hsa_circ_0000722, hsa-miR-129-5p and hsa-miR-30c-5p, whose interacting mRNAs related to muscle diseases, fat and inflammation. Conclusion: This study presented a systematic dissection of the expression profile of mRNAs and ncRNAs in RCT patients and revealed some important ncRNAs which may contribute to the development of RCT. Such results could provide new insights for further research on RCT.

Decoding the associations between cell functional states in head and neck cancer based on single-cell transcriptome.

OBJECTIVES: Systematically identifying cancer cell functional states, especially their associations, is key to understanding the pathogenesis of cancers. MATERIALS AND METHODS: Here, we systematically identified six cancer-related states, including epithelial-mesenchymal transition (EMT), immune response, epithelial differentiation, stress, G1/S and G2/M phases, in head and neck squamous cell carcinoma (HNSCC) based on single-cell RNA-sequencing (scRNA-seq). RESULTS AND CONCLUSION: We defined the association patterns between these functional states and found the patterns were correlated with the state activity. Particularly, immune response and EMT were negatively, positively, or non-significantly correlated in samples with the highest immune response activity, the lowest activity of the two states, or with the highest EMT activity, respectively. Combining scRNA-seq data of immune cells and four independent HNSCC cohorts, we found the negative relationship between EMT and immune response was correlated with an activated immune microenvironment and a longer survival, while the non-significant relationship was correlated with an immunosuppressed microenvironment and a poor prognosis. Collectively, our results provide insight into the association patterns between functional states in HNSCC, and may facilitate the elucidation of the interactions between cancer cells and immune system during cancer progression.

Tailoring Sensors and Solvents for Optimal Analysis of Complex Mixtures Via Discriminative 19F NMR Chemosensing.

Separation-free analytic techniques capable of providing precise and real-time component information are in high demand. 19F NMR-based chemosensing, where the reversible binding between analytes and a 19F-labeled sensor produces chromatogram-like output, has emerged as a valuable tool for the rapid analysis of complex mixtures. However, the potential overlap of the 19F NMR signals still limits the number of analytes that can be effectively differentiated. In this study, we systematically investigated the influence of the sensor structure and NMR solvents on the resolution of structurally similar analytes. The substituents adjacent and distal to the 19F labels are both important to the resolving ability of the 19F-labeled sensors. More pronounced separation between 19F NMR peaks was observed in nonpolar and aromatic solvents. By using a proper sensor and solvent combination, more than 20 biologically relevant analytes can be simultaneously identified.

Identification of Dysregulated Competitive Endogenous RNA Networks Driven by Copy Number Variations in Malignant Gliomas.

Gliomas represent 80% of malignant brain tumors. Because of the high heterogeneity, the oncogenic mechanisms in gliomas are still unclear. In this study, we developed a new approach to identify dysregulated competitive endogenous RNA (ceRNA) interactions driven by copy number variation (CNV) in both lower-grade glioma (LGG) and glioblastoma multiforme (GBM). By analyzing genome and transcriptome data from The Cancer Genome Atlas (TCGA), we first found out the protein coding genes and long non-coding RNAs (lncRNAs) significantly affected by CNVs and further determined CNV-driven dysregulated ceRNA interactions by a customized pipeline. We obtained 13,776 CNV-driven dysregulated ceRNA pairs (including 3,954 mRNAs and 306 lncRNAs) in LGG and 262 pairs (including 221 mRNAs and 11 lncRNAs) in GBM, respectively. Our results showed that most of the ceRNA interactions were weakened by CNVs in both LGG and GBM, and many CNV-driven genes shared the same ceRNAs in the dysregulated ceRNA networks. Functional analysis indicated that the CNV-driven ceRNA network involved in some important mechanisms of tumorigenesis, such as cell cycle, p53 signaling pathway and TGF-beta signaling pathway. Further investigation of the ceRNA pairs in the communities from the dysregulated ceRNA network revealed more detailed biological functions related to the oncogenesis of malignant gliomas. Moreover, by exploring the association of CNV-driven ceRNAs with prognosis and histological subtype, we found that the copy number status of MTAP, KLHL9, and ELAVL2 related to the overall survival in LGG and showed high correlation with histological subtype. In conclusion, this study provided new insight into the molecular mechanisms and clinical biomarkers in gliomas.