scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning.

The identification of differentially expressed genes between different cell groups is a crucial step in analyzing single-cell RNA-sequencing (scRNA-seq) data. Even though various differential expression analysis methods for scRNA-seq data have been proposed based on different model assumptions and strategies recently, the differentially expressed genes identified by them are quite different from each other, and the performances of them depend on the underlying data structures. In this paper, we propose a new ensemble learning-based differential expression analysis method, scDEA, to produce a more stable and accurate result. scDEA integrates the P-values obtained from 12 individual differential expression analysis methods for each gene using a P-value combination method. Comprehensive experiments show that scDEA outperforms the state-of-the-art individual methods with different experimental settings and evaluation metrics. We expect that scDEA will serve a wide range of users, including biologists, bioinformaticians and data scientists, who need to detect differentially expressed genes in scRNA-seq data.

EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning.

MOTIVATION: Spatially resolved gene expression profiles are the key to exploring the cell type spatial distributions and understanding the architecture of tissues. Many spatially resolved transcriptomics (SRT) techniques do not provide single-cell resolutions, but they measure gene expression profiles on captured locations (spots) instead, which are mixtures of potentially heterogeneous cell types. Currently, several cell-type deconvolution methods have been proposed to deconvolute SRT data. Due to the different model strategies of these methods, their deconvolution results also vary. RESULTS: Leveraging the strengths of multiple deconvolution methods, we introduce a new weighted ensemble learning deconvolution method, EnDecon, to predict cell-type compositions on SRT data in this work. EnDecon integrates multiple base deconvolution results using a weighted optimization model to generate a more accurate result. Simulation studies demonstrate that EnDecon outperforms the competing methods and the learned weights assigned to base deconvolution methods have high positive correlations with the performances of these base methods. Applied to real datasets from different spatial techniques, EnDecon identifies multiple cell types on spots, localizes these cell types to specific spatial regions and distinguishes distinct spatial colocalization and enrichment patterns, providing valuable insights into spatial heterogeneity and regionalization of tissues. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/Zhangxf-ccnu/EnDecon. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Exosome-mediated long noncoding RNA (lncRNA) PART1 suppresses malignant progression of oral squamous cell carcinoma via miR-17-5p/SOCS6 axis.

BACKGROUND: Exosomes derived from oral squamous cell carcinoma (OSCC) could modulate OSCC development. This study aimed to explore effects of exosome-mediated lncRNA PART1 on OSCC cells. METHODS: This study was performed in Tianjin Medical University Cancer Institute from February 2021 to March 2022. Bioinformatic analysis was performed on the public database GEPIA (http://gepia.cancer-pku.cn/). Exosomes isolated from cell lines squamous cell carcinoma 9 (SCC9) and Centre Antoine Lacassagne-27 (CAL27) were identified by transmission electron microscope and western blot. Exosome-mediated lncRNA PART1, microRNA-17-5p(miR-17-5p) and suppressor of cytokine signaling 6(SOCS6) RNA expressions were assessed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Cell counting kit8(CCK-8), caspase-3 activity, and flow cytometry were applied to evaluate OSCC cell viabilities and apoptosis. Meanwhile, OSCC cell migratory ability and invasiveness were evaluated using transwell assay. Bindings between miR-17-5p and lncRNA PART1 or SOCS6 were validated using the luciferase reporter test. Western blot was used for detecting the protein levels of SOCS6, phosphorylated signal transducer and activator of transcription 3 (STAT3) and STAT3. RESULTS: : According to GEPIA, lncRNA PART1 was downregulated in OSCC tissue samples and cells, and it had a positive correlation with the good prognosis of Head and neck squamous cell cancer (HNSCC) patients. After the exosomes from OSCC cells were isolated and verified, PART1 was then confirmed to be secreted by exosomes. Further, overexpression of exosome-mediated lncRNA PART1 inhibited OSCC cell viabilities, migration, and invasiveness but facilitated OSCC cell apoptosis. PART1 upregulated SOCS6 through sponging miR-17-5p. Moreover, exosome-mediated lncRNA PART1 suppressed the phosphorylation of STAT3. DISCUSSION: Exosome-mediated lncRNA PART1 could mediate the OSCC progression via miR-17-5p/SOCS6 axis in vitro, suggesting that lncRNA PART1 might be a target for treating OSCC.

Astaxanthin Synergizes with Ionizing Radiation (IR) in Oral Squamous Cell Carcinoma (OSCC).

Astaxanthin (ATX) is known for its antioxidant and anti-inflammation functions yet its role in cancers requires more research. This study is aimed to reveal the potential synergetic effect of ATX with ionizing radiation (IR) in OSCC. Cell survival was measured after human OSCC cells including CAL27 and SCC9, and normal human oral keratinocytes (NHOKs) were treated with different concentrations of ATX for 24 h. Colony formation assays were performed after OSCC cells were treated with IR, ATX (20 µ M), or combined and survival fraction was analyzed. Malondialdehyde (MDA), glutathione (GSH), and intercellular iron levels were measured. Western blot method was used to measure the ferroptosis-related proteins, GPX4, SLC7A11, and ACSL4. In xenograft mice model, we evaluated the tumor volumes, tumor growth, and examined the GPX4/ACSL4 proteins in tumor tissues using Immunohistochemistry (IHC). ATX inhibited viability of OSCC cells but not NHOK. In OSCC cells, ATX further enhanced the cell death induced by IR. In addition, ATX promoted the MDA content, Iron levels but inhibited the GSH regulated by IR in cells. ATX could synergize with IR, further inhibiting GPX4, SLC7A11 and promoting ACSL4 in OSCC cells. In vivo, ATX and IR treatment inhibited OSCC tumor growth and the group with combined treatment showed the most inhibitory effect. GPX4 was inhibited by IR and further inhibited in the combined group while ACSL4 was promoted by IR and enhanced more significantly in the combined group. ATX might synergize with IR treatment in OSCC partly via ferroptosis.

CD73/NT5E is a Potential Biomarker for Cancer Prognosis and Immunotherapy for Multiple Types of Cancers.

Cluster of Differentiations 73 (CD73)/ecto-5'-nucleotidase (NT5E) is a novel type of immune molecular marker expressed on many tumor cells and involved in regulating the essential immune functions and affecting the prognosis of cancer patients. However, it is not clear how the NT5E is linked to the infiltration levels of the immune cells in pan-cancer patients and their final prognosis. This study explores the role of NT5E in 33 tumor types using GEPIA, TIMER, Oncomine, BioGPS databases, and several bioinformatic tools. The findings reveal that the NT5E is abnormally expressed in a majority of the types of cancers and can be used for determining the prognosis prediction ability of different cancers. Moreover, NT5E is significantly related to the infiltration status of numerous immune cells, immune-activated pathways, and immunoregulator expressions. Last, specific inhibitor molecules, like NORNICOTINE, AS-703026, and FOSTAMATINIB, which inhibit the expression of NT5E in various types of cancers, are screened with the CMap. Thus, it is proposed that NT5E can be utilized as a potential biomarker for predicting the prognosis of cancer patients and determining the infiltration of various immune cells in different types of cancers.

2,2'-(3,3'-Dihexyl-2,2'-bithio-phene-5,5'-di-yl)bis-(4,4,5,5-tetra-methyl-1,3,2-dioxaborolane).

In the title mol-ecule, C(32)H(52)B(2)O(4)S(2), the two thio-phene rings are twisted by 67.34 (2)°. In the crystal, weak C-H⋯O hydrogen bonds link mol-ecules related by translation along the a axis into chains.

Diethyl [4-(1,3-benzothia-zol-2-yl)benz-yl]phospho-nate.

In the title mol-ecule, C(18)H(20)NO(3)PS, the benzene ring and the benzothia-zole mean plane are almost coplanar, forming a dihedral angle of 2.29 (2)°. The two ethyl groups are each disordered over two conformations in ratios that refined to 0.59 (1):0.41 (1) and 0.56 (1):0.44 (1). In the crystal, weak inter-molecular C-H⋯O hydrogen bonds link the mol-ecules into layers parallel to the bc plane.

To explore the risk factors and preventive measures affecting the treatment of retrosternal goiter: An observational study.

The definition of substernal goiter (SG) is based on variable criteria, leading to considerable variations in the reported incidence (from 0.2% to 45%). The peri- and postoperative complications are higher in total thyroidectomy (TT) for SG than that for cervical goiter. This study aimed to evaluate the preoperative risk factors associated with postoperative complications.From 2002 to 2014, 142 (8.5%; 98 women and 44 men) of the 1690 patients who underwent TT had a SG. We retrospectively evaluated the following parameters: sex, age, histology, pre- and retro-vascular position, recurrence, and extension beyond the carina. These parameters were then related to the postoperative complications: seroma/hematoma, transient and permanent hypocalcemia, transient and permanent laryngeal nerve palsy, and the length of surgery. The results were further compared with a control group of 120 patients operated on in the same period with TT for cervical goiter (CG).Statistical analysis (Student t test and Fisher exact test) indicated an association between recurrence and extension beyond the carina with all postoperative complications. The group that underwent TT of SG showed a statistically significant higher risk for transient hypocalcemia (relative risk = 1.767 with 95% confidence interval: 1.131-2.7605, P = .0124, and need to treat = 7.1) and a trend toward significance for transient recurrent laryngeal nerve palsy (relative risk = 6.7806 with 95% confidence interval: 0.8577-53.2898, P = .0696, and need to treat = 20.8) compared with the group that underwent TT of cervical goiter. The major risk factors associated with postoperative complications are recurrence and extension beyond the carina.TT is the procedure to perform in SG even if the incidence of complications is higher than cervical goiters. The major risk factors associated with postoperative complications are recurrence and extension beyond the carina.

(m-Phenyl-enedimethyl-ene)diammonium dichloride.

The asymmetric unit of the title compound, C(8)H(14)N(2) (2+)·2Cl(-), contains one and a half of the dications and three chloride anions. The half molecule is completed by crystallographic twofold symmetry with two C atoms lying on the rotation axis. The two ammonium groups in each cation adopt a trans conformation with respect ot the benzene ring. The ammonium groups and chloride anions are involved in the formation of a three-dimensional N-H⋯Cl hydrogen-bonding network, which stabilizes the crystal packing.

1,4-Bis(4-chloro-phen-yl)butane-1,4-dione.

The mol-ecule of title compound, C(16)H(12)Cl(2)O(2), is centrosymmetric. Thus, the asymmetric unit comprises two half-mol-ecules. The two benzene rings are coplanar in each independent molecule (dihedral angles = 0°). The crystal packing exhibits inter-molecular C-H⋯O hydrogen bonds and C-H⋯π inter-actions.

1-(4-Chloro-phen-yl)-3-(2-nitro-phenyl)propane-1,2-dione.

The title compound, C(15)H(10)ClNO(4), belongs to the class of 1,2-diketones, which have important applications in both synthetic organic chemistry and supra-molecular chemistry. A dihedral angle of 9.03 (1)° is found between the mean planes of the two benzene rings. C-H⋯O inter-actions help to stabilize the crystal structure.

Immunological response in H22 transplanted mice undergoing Aconitum coreanum polysaccharide treatment.

In this study, a polysaccharide (ACP-a1), with a molecular weight of 3.2×10(5)Da, was successfully purified and identified from the roots of Aconitum coreanum (Lèvl.) Rapaics. Gas chromatography (GC) analysis indicated that ACP-a1 was mainly composed of ß-d-mannose and ß-d-glucose in a molar ratio of 1.2:3.5. The effects of ACP-a1 on the tumor growth and immune function were assessed in hepatoma H22 bearing mice. Results showed that ACP-a1 significantly inhibited the growth of hepatoma H22 transplanted in mice and prolonged the survival time of H22 tumor-bearing mice. Besides, the body weight, peripheral white blood cells (WBC), thymus index and spleen index of H22 tumor-bearing were also improved after ACP-a1 treatment. Furthermore, ACP-a1 could promote the secretion of serum cytokines in H22 tumor-bearing mice, such as IL-2, TNF-α and IFN-γ. Taken together, our results indicate that ACP-a1 inhibits tumor growth in vivo at least partly via improving immune responses of host organism, and seems to be safe and effective as a novel agent with immunomodulatory activity for the use of anti-tumor therapy.