In recent years, RNA interference (RNAi) therapeutics, most notably with lipid nanoparticle-based delivery systems, have advanced into human clinical trials. The results from these early clinical trials suggest that lipid nanoparticles (LNPs), and the novel ionizable lipids that comprise them, will be important materials in this emerging field of medicine. A persistent theme in the use of materials for biomedical applications has been the incorporation of biodegradability as a means to improve biocompatibility and/or to facilitate elimination. Therefore, the aim of this work was to further advance the LNP platform through the development of novel, next-generation lipids that combine the excellent potency of the most advanced lipids currently available with biodegradable functionality. As a representative example of this novel class of biodegradable lipids, the lipid evaluated in this work displays rapid elimination from plasma and tissues, substantially improved tolerability in preclinical studies, while maintaining in vivo potency on par with that of the most advanced lipids currently available.

: Systematically tracking the tumor immunophenotype is required to understand the mechanisms of cancer immunity and improve clinical benefit of cancer immunotherapy. However, progress in current research is hindered by the lack of comprehensive immune activity resources and easy-to-use tools for biologists, clinicians, and researchers to conveniently evaluate immune activity during the "cancer-immunity cycle." We developed a user-friendly one-stop shop web tool called TIP to comprehensively resolve tumor immunophenotype. TIP has the capability to rapidly analyze and intuitively visualize the activity of anticancer immunity and the extent of tumor-infiltrating immune cells across the seven-step cancer-immunity cycle. Also, we precalculated the pan-cancer immunophenotype for 11,373 samples from 33 The Cancer Genome Atlas human cancers that allow users to obtain and compare immunophenotype of pan-cancer samples. We expect TIP to be useful in a large number of emerging cancer immunity studies and development of effective immunotherapy biomarkers. TIP is freely available for use at http://biocc.hrbmu.edu.cn/TIP/. SIGNIFICANCE: TIP is a one-stop shop platform that can help biologists, clinicians, and researchers conveniently evaluate anticancer immune activity with their own gene expression data..

No abstract

Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relational database, ORChID (OH Radical Cleavage Intensity Database), that contains extensive hydroxyl radical cleavage data produced from two DNA libraries. We have used the ORChID database to develop a set of algorithms that are capable of predicting the hydroxyl radical cleavage pattern of a DNA sequence of essentially any length, to high accuracy. We have used the prediction algorithm to produce a structural map of the 30 Mb of the ENCODE regions of the human genome.[Supplemental material is available online at www.genome.org.]While the linear sequence of nucleotides is the level at which most interpretations of a genome are made, a new appreciation of the effect of local DNA structure on genome function is emerging. Much effort has gone into the derivation of general rules regarding the effect of the sequence of DNA on its structure. High-resolution X-ray and NMR structures have clearly revealed the variability of DNA structure (Dickerson and Drew 1981;Calladine 1982;Calladine and Drew 1986;Yanagi et al. 1991;Dickerson 1992Dickerson , 1997Grzeskowiak 1996;Olson et al. 1998;Ng and Dickerson 2001;Barbic et al. 2003;Hays et al. 2005), and have shown that the conformation of a nucleotide residue is dependent at least on its nearest neighbors, and possibly more (Dickerson and Drew 1981;Dickerson 1983;Calladine and Drew 1986;Nelson et al. 1987;Bhattacharyya and Bansal 1990;DiGabriele and Steitz 1993;El Hassan and Calladine 1997;Johansson et al. 2000; Packer et al. 2000a,b;Gardiner et al. 2003). Although much knowledge has been gained from the study of DNA crystal structures, high-resolution structure determinations are resourceintensive and are applicable only to moderate-sized DNA molecules. In order to comprehensively sample the structure of all possible DNA sequences in an unbiased manner, alternative methods are necessary.We report here the construction of a library of hydroxyl radical cleavage patterns of DNA, as a means of compiling structural information for a wide variety of DNA sequences. Although the hydroxyl radical cleavage pattern (Price and Tullius 1992) does not yield a high-resolution three-dimensional structure of a DNA molecule, it is a reflection of an important structural parameter, the solvent-accessible surface area of the DNA backbone (Balasubramanian et al. 1998). The cleavage pattern thus provides an image of the shape of the DNA backbone and how it varies with respect to nucleotide sequence. We describe the use of a fluorescence-based sequencer to obtain cleavage patterns, and introduce methods for normalization and quantitation of cleavage data. We present the design considerations of a relational database, ORChID (OH Radical Cleavage Intensity Database), to hold hydroxyl radical...

Background The prognosis for diffuse gliomas is very poor and the mechanism underlying their malignant progression remains unclear. Here, we aimed to elucidate the role and mechanism of the RNA N6,2′-O-dimethyladenosine (m6A) reader, YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), in regulating the malignant progression of gliomas. Methods YTHDF2 mRNA levels and functions were assessed using several independent datasets. Western blotting, quantitative polymerase chain reaction, and immunohistochemistry were used to evaluate the expression levels of YTHDF2 and other molecules in human and mouse tumor tissues and cells. Knockdown and overexpression were used to evaluate the effects of YTHDF2, methyltransferase-like 3 (METTL3), and UBX domain protein 1 (UBXN1) on glioma malignancy in cell and orthotopic xenograft models. RNA immunoprecipitation (RIP), methylated RIP, and RNA stability experiments were performed to study the mechanisms underlying the oncogenic role of YTHDF2. Results YTHDF2 expression was positively associated with a higher malignant grade and molecular subtype of glioma and poorer prognosis. YTHDF2 promoted the malignant progression of gliomas in both in vitro and in vivo models. Mechanistically, YTHDF2 accelerated UBXN1 mRNA degradation via METTL3-mediated m6A, which, in turn, promoted NF-κB activation. We further revealed that UBXN1 overexpression attenuated the oncogenic effect of YTHDF2 overexpression and was associated with better survival in patients with elevated YTHDF2 expression. Conclusions Our findings confirmed that YTHDF2 promotes the malignant progression of gliomas and revealed important insight into the upstream regulatory mechanism of NF-κB activation via UBXN1 with a primary focus on m6A modification.

Due to the rare incidence of spinal cord astrocytomas, their molecular features remain unclear. Here, we characterized the landscapes of mutations in H3 K27M, isocitrate dehydrogenase 1 (IDH1) R132H, BRAF V600E, and the TERT promoter in 83 diffuse spinal cord astrocytic tumors. Among these samples, thirty-five patients had the H3 K27M mutation; this mutant could be observed in histological grade II (40%), III (40%), and IV (20%) astrocytomas. IDH1 mutations were absent in 58 of 58 cases tested. The BRAF V600E mutation (7/57) was only observed in H3-wildtype astrocytomas, and was associated with a better prognosis in all histological grade II/III astrocytomas. TERT promoter mutations were observed in both H3 K27M-mutant (4/25) and-wildtype (9/33) astrocytomas, and were associated with a poor prognosis in H3-wildtype histological grade II/III astrocytomas. In the 2016 WHO classification of CNS tumors, H3 K27M-mutant diffuse midline gliomas, including spinal cord astrocytomas, are categorized as WHO grade IV. Here, we noticed that the median overall survival of histological grade II/III H3 K27M-mutant cases (n = 28) was significantly longer than that of either the total histological grade IV cases (n = 12) or the H3 K27M-mutant histological grade IV cases (n = 7). We also directly compared H3 K27M-mutant astrocytomas to H3-wildtype astrocytomas of the same histological grade. In histological grade II astrocytomas, compared to H3-wildtype cases (n = 37), H3 K27M-mutant patients (n = 14) had showed a significantly higher Ki-67-positive rate and poorer survival rate. However, no significant differences in these parameters were observed in histological grade III and IV astrocytoma patients. In conclusion, these findings indicate that spinal cord astrocytomas are considerably different from hemispheric and brainstem astrocytomas in terms of their molecular profiles, and that the histological grade cannot be ignored when assessing the prognosis of H3 K27M-mutant spinal cord astrocytomas.

Investigate the role of regulator of chromosome condensation 2 () on lung adenocarcinoma (LUAD) metastasis. Clinical specimens were used to assess the impact of RCC2 on LUAD metastasis. Mouse models, cytobiology, and molecular biology assays were performed to elucidate the function and underlying mechanisms of RCC2 in LUAD. RCC2 expression was frequently increased in LUADs (88/122, 72.13%). It was confirmed by analysis of a larger cohort of TCGA RNA-seq data containing 488 LUADs and 58 normal lung tissues ( < 0.001). Importantly, increased level of RCC2 was significantly associated with T status of tumor ( = 0.002), lymph node metastasis ( = 0.004), and advanced clinical stage ( = 0.001). Patients with LUAD with higher expression of RCC2 had shorter overall survival. Cox regression analysis demonstrated that RCC2 was an independent poorer prognostic factor for patients with LUAD. Moreover, forced expression of RCC2 promoted intrapulmonary metastasis and significantly enhanced LUAD cell migration, invasion, and proliferation Further study found that RCC2 induced epithelial-mesenchymal transition (EMT) and also stimulated the expression of MMP-2 and MMP-9. In addition, RCC2 was able to activate JNK, while inhibition of JNK suppressed the effect of RCC2 on LUAD cell migration, invasion, EMT, and the expression of MMP-2 and MMP-9. RCC2 plays a pivotal role in LUAD metastasis by inducing EMT via activation of MAPK-JNK signaling. .

Highlights d High expression of HPK1 is correlated with increased T cell exhaustion d An HPK1-Blimp1 axis facilitates tumor-infiltrating T cell exhaustion d MAP4K1 KO CAR-T cells have enhanced antitumor effects compared with PDCD1 KO CAR-T cells d Both kinase inhibitor and PROTACs for HPK1 exhibited enhanced antitumor immunity